Analysis and Visualization of Complex 3D Structures - JorgeMarquez

Analysis and Visualization of Complex 3D Structures:
a discrete boundary-based approach
Analyse et visualisation des structures complexes en 3D :

une approche par frontières discrètes.
par
Jorge Alberto Márquez Flores

Rapport de soutenance de thèse - PhD. Dissertation
Soutenu le 6 avril 1999 devante le jury composé de :

Isabelle Magnin Rapporteur
Christine Graffigne Rapporteur
Jean-Marie Rocchisani Examinateur
Gilles Bertrand Président
Francis Schmitt Directeur de thèse
Département du Traitement du Signal et des Images

Ecole Nationale Supérieure des Télécommunications
c JORGE A. MÁRQUEZ PARIS , F RANCE , LE 6 AVRIL 1999

Abstract
Keywords: 3D-image processing, morphometry, discrete boundaries, voxels, structural complexity,
Visible Human Project, amorphous deposition, scientific visualization.
The aim of this work was the segmentation, morphometry and visualization of three-dimensional
complex structures, in particular porous micro-structures and blood vessels with complex branches.
We studied the different problems arising in the analysis of this kind of volumic data, from complex-
features definitions, as described in Chapter 1, to discrete boundary representations (Chapter 2) and
specific applications (Chapters 3, 4 and 5).
As a first step, we identified and characterized morphological features of complex structures
related to specific problems, e.g.: coherency, tubular structures, ramifications, fractal dimension,
interfaces, porosity, roughness and others. Then, we choose a discrete geometry approach for surface
extraction, processing and visualization of volume data. In this approach, described in Chapter 2,
external surfaces or boundaries of detected objects are represented by lists of facets (voxel faces).
An important amount of 3D image processing consists in analyzing and modifying these lists and
their associated data structures by examining neighboring facets and voxels, in order to perform
the desired operation or measurement. Boundaries are then extracted by traversal of the directed
graph associated with the surface of each object. We then introduce several entities and tools for
analysis; in particular: facet, voxel and boundary neighborhoods, geodesic neighborhoods, geometric
interior traversal and boundary-based filters for mathematical morphology operations. Some of these
operators (or subsets) are activated (or extracted) during graph traversal; we describe, for example,
how the local facet configuration allows estimations of local normal and local surface area.
Concerning the application domains, we have worked on two 3D-image datasets, correspond-
ing to different issues in Biomedicine and Physics. The generality and versatility of the boundary
representation model allowed to use the same software tools for both subjects.
The first application, described in Chapter 3, was developed with a biomedical dataset from the
Visible Human Project (VHP) of the National Library of Medicine, comprising both lungs. Anatom-
ical cryo-sections of the VHP posed special problems of segmentation and visualization of internal
structures, hence, we developed an innovative technique for correcting regional radiometric inhomo-
geneities. We also extracted the vascular pulmonary tree, as described in Chapter 4, and obtained
realistic visualizations after different stages of segmentation and 3D image processing, using the
same boundary representation introduced earlier.
The second application (Chapter 5) comes from a collaboration with the Surface Physics labo-
ratory of the Centre Nationale d’Etudes en Télécommunications (CNET), at Bagneux. The problem
consisted in measuring properties of porosity, roughness, connectivity and distribution of morpho-
logical parameters extracted from computer simulations of amorphous photo-deposition of Nitride-
Silicium. Our work included the 3D reconstruction of volume data, connected component analysis
and morphometrical parameter extraction. Visualization and quantification of these data allowed re-
searchers of the CNET to assess: the size and form of pores and deposition clusters, the porosity
distribution in function of temperature and the inter-penetration quality of several atom species. 3D
renderings enable to notice critical transitions of the cluster morphology, clearly organized by color
labels.
Many of the techniques we developed and their application took advantage of the tools of our
boundary-based approach as well as of several concepts and features of complex structures presented
in the first part.
Résumé
Mots clé : Traitement d’image 3D, morphométrie, frontières discrètes, complexité structurale, Visible Human
Project, dépôts amorphes, visualisation scientifique.
L’objectif de ce travail est la segmentation, la morphométrie et la visualisation de structures com-

plexes tridimensionnelles, en particulier des microstructures poreuses et des vaisseaux sanguins qui
présentent des ramifications compliquées. Nous avons étudié ainsi les différents problèmes posés
par l’analyse de ce type de données volumiques, comprenant les définitions des attributs de com-
plexité examinées dans le chapitre 1, les représentations par frontières discrètes (chapitre 2) et des
applications spécifiques (chapitre 3, 4 et 5).
L’étude de tels problèmes nous a amenés d’abord à identifier et à caractériser les attributs mor-
phologiques des structures complexes, tels que : cohérence, structures tubulaires, ramifications, di-
mension fractale, interfaces, porosité, rugosité et d’autres. Ensuite, nous avons choisi une approche
en géométrie discrète pour l’extraction des surfaces, le traitement et la visualisation des données
volumiques. Dans cette approche (chapitre 2), les surfaces extérieures ou frontières des objets dé-
tectés sont représentées par des listes de facettes. Une partie importante des traitements consiste à
analyser et modifier ces listes et les structures de données associées, en examinant les facettes et les
voxels voisins pour effectuer les opérations ou mesures nécessaires. L’extraction de telles frontières
se fonde sur une méthode de parcours du graphe dirigé associé à la surface de chaque objet. Divers
outils sont alors introduits, tels que les voisinages des facettes et des frontières, les voisinages géo-
désiques, le parcours de l’intérieur géométrique et des filtres de morphologie mathématique fondés
sur la représentation par frontière.
En ce qui concerne les domaines d’applications, nous avons travaillé sur deux ensembles de don-
nées volumiques correspondant à deux problématiques différentes respectivement en biomédecine et
en physique. La généralité et la souplesse du modèle de représentation par frontières nous a permis
d’utiliser les mêmes outils informatiques pour les deux problématiques.
La première application a été développée sur des données biomédicales correspondant aux pou-
mons et provenant du Visible Human Project (VHP) de la National Library of Medicine. Les coupes
anatomiques du VHP posent des problèmes particuliers pour la segmentation et la visualisation
des structures internes et nous avons ainsi développé une technique novatrice pour la correction
d’hétérogénéités radiométriques régionales. Nous avons obtenu des visualisations réalistes de l’arbre
vasculaire pulmonaire obtenu à la suite des différentes étapes de la segmentation et du traitement 3D,
toujours en utilisant la représentation par frontières.
La deuxième application a pu être abordée dans le cadre d’une collaboration avec le laboratoire
de Physique des Surfaces du Centre Nationale d’Etudes en Télécommunications, à Bagneux. Le
problème a consisté à mesurer les propriétés de porosité, rugosité, connexité et distribution des pa-
ramètres morphométriques extraits des résultats obtenus par simulation numérique d’un photo-dépôt
amorphe de Nitride-Silicium. Nous avons effectué des reconstructions 3D, l’identification des com-
posantes connexes et l’extraction des paramètres morphométriques. Les visualisations et les mesures
obtenues ont permis aux chercheurs du CNET de connaı̂tre : la taille et la forme des pores, la taille
et la forme des amas du dépôt, la distribution de la porosité par rapport à la température, ainsi que
la qualité d’interpénétration de plusieurs espèces d’atomes. En outre, les rendus 3D permettront de
repérer des transitions critiques de la morphologie des amas, identifiés clairement par des étiquettes
en couleur.
Au total, plusieurs des techniques développées et les résultats présentés profitent des outils de
notre approche par frontières, ainsi que des concepts et attributs des structures complexes étudiés.
Acknowledgements - Remerciements - Agradecimientos.
This page mentions people at the roots, branches, and fruits of my PhD research. I include those
friends or acquitances who, even without knowing, have contributed in no obvious manners to this
work, ranging from academic interactions to personal relationships. My apologizes to those I may
have forgotten.
First of all, I am in great debt with Francis Schmitt, my thesis advisor and Isabelle Bloch, who
co-directed this work. They were always patient, critic and available for any discussion on all topics,
and encouraged me at all times. Henry Maı̂tre was also a constant presence. Thanks to him, as
well as Pierre Duhamel for their hospitality in the former Image Department and the present TSI
Department.
Thanks to the jury members for their criticism and advice: Isabelle Magnin, Christine Graf-
figne, Gilles Bertrand and Jean-Marie Rocchisani.
Thanks
✦ To Sandrine Pata and Jean Flicstein (CNET-Bagneux) both of whom encouraged a fruitful
collaboration and created the deposition simulation software described in Chapter 5.1. I also
aknowledge Marc Sigelle for continuous discussion on various subjects on mathematics, ran-
dom fields, deposition and textures.
✦ For fruitful discussions, comments and insights since 1994, to: Michel Roux, Lars Aurdal,
Yon Harderberg, Bert Verdonck, wonderful Florence Tupin, Hilmi Rifai, Raouf Benjemaa,
Emanuel Trouve, Stephane Chauvin, Olivier Coulon, Sudha Kunduri, Alex Winter, Miguel
Moctezuma, Ma.Elena Algorri, Geneviève Dardier, Sophie Paquerault, Anne Robert, Hans
Brettel, Jean-Pierre Veran, Mehdy Eyvazkhani, Aymeric Perchant, Wirawan, Yucel Yemez,
Jean-Pierre Crettez, all from the ENST, and Seth Hutchinson (University of Illinois). Thanks
also to the wizards of the ”Tivoli” software team: Thierry Géraud, Yan Cointepa and Dmitri
Papanopoulus (plus some already mentioned). I spent a wonderful time at the Image Depart-
ment!
✦ For their technical support, to: Alain Clainchard, Patrick Horain, Dominique Asselineau, ”le
centre de calcul de l’ENST” and the best secretary of the ENST: Patrica Friedrick.
✦ To Michel Ackerman and Richard Banvard (from The National Library of Medicine), who
provided access to the Visible Human Project (VHP) dataset, remarks and advice for the special
work on the VHP.
✦ For technical advice and discusion on discrete topology, voxels and visualization, to: Pe-
tra Wiederhold (UAM-CINVESTAV), Klauss Voss (GMD-SCAI), Paolo Clementi (Silicon
Graphics), Bernhard Pflesser (U. Hamburg) and Rafael Lacambra (LabVis-UNAM).
✦ From the Universidad Nacional Autónoma de Mexico, to: Andrés Buzo, Francisco Ugalde
(signal and image processing professors), Cristina Piña (DEPFI/1982-1992), Francisco Cer-
vantes (CI/1990-1993, ITAM, my former master thesis advisor in Mexico), and Jaime Pi-
mentel (Centro de Instrumentos, UNAM -Cibertrol), all of them criticized, inspired or encour-
aged some ideas that now constitute my line-work. In the same vein, thanks also to: Erick Petit,
Laurent Cohen, J.L. Moretti and Jean-Marie Rochissani from the ”DEA en Génie Biologique
et Médical” at Paris XIII.
✦ To friends and colleagues in Mexico, who have influenced, supported or inspired my work
these years in France in one way or another (approximated chronological order): Javier Sierra,
Armando Solar and Manuel Estevez, Laura Sánchez and Diana Servı́n (who also became
very close friends), Carlos Yañez, José Saniger, Kent Brailovsky and Gabriel Corkidi (who
contacted me with Etienne Hirsch in 1992 and signed as ’asesor nacional’), Marı́a Garza, Patri-
cia Ostrovski and Ricardo Toledo -the five of us started our close encounters with applications
of image processing, back in 1988, and coauthored many works, forming also a great team.
Grant formalities and other support are debt to: Comité de Becas del CIUNAM, Gerardo Ruiz
(academic secretary), Claudio Firmani and Felipe Lara (directors of the CI), Maria Elena Hernández
and Patricia Vidal (DGAPA), Mauricette Teti, Stephane Bonenfant (ENST), and Patrick England
(France Ambassy in Mexico).
Other friends who don’t appear above did contributed with other kind of support, and I shared
with them 6+ years in Paris: Philippe Anglade and Etienne Hirsch (DEA advisors, from the Hôpi-
tal de la Salpêtrière); Michel Gouéry, Michel Salsmann, Michaéle Schatt, ”Tara” and Cécile Theisen
(from the Ecole de Beaux Arts), and finally, from the ENST or elsewhere: Asli and Emanuel, Miung,
Claudia, Fabien, Ingeborg, Selim, Gérard, Cuahutemoc, Olga Odgers, Olga Sodolova, Céline, Car-
men, Gabriel, Lorence, Florent, Muriel, Luc, Mariel, Marc, Mr. and Madame Tupin, Madame Dart,
Benoit and Aline, Alicia, Plotr, Alfredo, Linda, Lety, Laura V., Pablo, and Göran.
This work is specially dedicated to my sister Carmen and my best friends (alphabetically): Cé-
cile, Chantal, Diana, Florence, Laura and Paty.
A la memoria de mi Madre,
A mi Padre y mis hermanos,
Table of Contents
Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Résumé . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Notation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1 Characterization of sets with complex structures in R3 21

1.1 Preliminar Notions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
1.1.1 Neighborhoods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
1.1.2 Boundaries and Interfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
1.1.3 Connected Sets and Objects . . . . . . . . . . . . . . . . . . . . . . . . . . 26
1.2 Intrinsic Properties of Solid Shapes . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
1.2.1 The Approximating Ellipsoid, Isotropy and Deformed Shapes . . . . . . . . 28
1.2.2 Shape Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
1.2.3 Shape Decompositions and Local Descriptions . . . . . . . . . . . . . . . . 34
1.2.4 Convexity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
1.2.5 Coherence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
1.2.6 Scales of Representation and Characteristic Lengths . . . . . . . . . . . . . 42
1.3 Extrinsic Properties of Solid Shapes . . . . . . . . . . . . . . . . . . . . . . . . . . 45
1.3.1 Complex Relations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
1.3.2 Many Bodies and Clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
1.3.3 Complex Objects in Feature Space . . . . . . . . . . . . . . . . . . . . . . . 47
1.3.4 Complex Representations . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
1.4 Fractal Dimensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
1.4.1 Dimension Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
1.4.2 Morphological Features of Fractals . . . . . . . . . . . . . . . . . . . . . . 54
1.4.3 An Example: Particle Aggregates . . . . . . . . . . . . . . . . . . . . . . . 56
1.5 Notions and Measures of Complexity . . . . . . . . . . . . . . . . . . . . . . . . . 56
1.5.1 *Kolmogorov Complexity . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
1.5.2 Information Theory, Algorithmic Entropy and Scientific Observations . . . . 60
1.6 Shape Taxonomies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
1.6.1 Tubular Structures (I) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
1.6.2 Ramified Thin Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
1.6.3 Surfaces, Boundaries and Interfaces . . . . . . . . . . . . . . . . . . . . . . 68
1.6.4 Description of Other Shape Features . . . . . . . . . . . . . . . . . . . . . . 69
1.7 Other Properties of Complex Information . . . . . . . . . . . . . . . . . . . . . . . 70
1.7.1 From Structure to Texture . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
1.7.2 Noise, Blurring, Distorsion and Inhomogeneities . . . . . . . . . . . . . . . 71
1.8 Discussion and Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
2 From Raw Data to Models in N3: A Boundary-Based Approach 77

2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
2.2 Discrete Volume Representations and Boundaries . . . . . . . . . . . . . . . . . . . 80
2.2.1 Boundary Representations . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
2.2.2 Relevance and Potential Uses of Discrete Boundary Representations . . . . . 82
2.3 A Facet-Based Model for Discrete Surface Representation . . . . . . . . . . . . . . 84
2.3.1 Discrete Elements: Scenes and Voxels . . . . . . . . . . . . . . . . . . . . . 84
2.3.2 Discrete Elements: Faces and Labels . . . . . . . . . . . . . . . . . . . . . 87
2.3.3 Discrete Elements: Facets and Boundaries . . . . . . . . . . . . . . . . . . . 89
2.3.4 Discrete Adjacency and Connectivity . . . . . . . . . . . . . . . . . . . . . 96
2.3.5 Voxel (Euclidean) Neighborhoods . . . . . . . . . . . . . . . . . . . . . . . 102
2.3.6 Facet (Geodesic) Neighborhoods . . . . . . . . . . . . . . . . . . . . . . . . 104
2.3.7 Voxel Geodesic Neighborhoods . . . . . . . . . . . . . . . . . . . . . . . . 106
2.3.8 Discrete Boundary Neighborhoods . . . . . . . . . . . . . . . . . . . . . . . 108
2.4 Surface Tracking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
2.4.1 Surface Tracking Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . 114
2.4.2 Facet Traversal by Lateral Circuits . . . . . . . . . . . . . . . . . . . . . . . 117
2.4.3 Interior Traversal and Object Labeling . . . . . . . . . . . . . . . . . . . . . 119
2.4.4 Run-Length Interpretation of Interior Traversal . . . . . . . . . . . . . . . . 124
2.5 Boundary-Based Processing and Analysis of 3D Objects . . . . . . . . . . . . . . . 126
2.5.1 An Example of Boundary-Based Morphometry: Euclidean Area Estimation . 128
2.5.2 Boundary-Based and Volume Processing (Examples) . . . . . . . . . . . . . 129
2.6 Visualization of Complex Structures . . . . . . . . . . . . . . . . . . . . . . . . . . 135
2.6.1 Surface Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
2.6.1.1 Hidden Surface Removal and Surface Shading . . . . . . . . . . . 135
2.6.1.2 Discrete Normal Estimations . . . . . . . . . . . . . . . . . . . . 135
2.6.2 Three-Dimensional Data Structures. . . . . . . . . . . . . . . . . . . . . . . 137
2.7 Summary and Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
3 Radiometric Homogenization of the Color Cryosection Images from the VHP Lungs for
3-D Segmentation of Blood Vessels 143
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
3.2 Problem Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
3.2.1 Gamma Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
3.2.2 Visualization of radiometric inhomogeneities . . . . . . . . . . . . . . . . . 146
3.3 Local Adaptive Homogenization . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
3.3.1 Inhomogeneity Characterization by an Auto-regressive Model . . . . . . . . 150
3.3.2 Local Coherence Hypothesis . . . . . . . . . . . . . . . . . . . . . . . . . . 152
3.3.3 Correction Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
3.4 Discussion and Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
4 Extraction of Bronchial Blood-Vessels from Color Cryosections of the VHP 161

4.1 Anatomy of the Branching Structures in the Lungs . . . . . . . . . . . . . . . . . . 161
4.1.1 Tree Structure of the Pulmonary Artery . . . . . . . . . . . . . . . . . . . . 164
4.1.2 The Lungs of the Visible Human Male . . . . . . . . . . . . . . . . . . . . . 166
4.2 Blood-Vessel Extraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
4.2.1 Other Imaging Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
4.2.2 Detection Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
4.2.3 Fusion of Cross-Sectional Segmentation . . . . . . . . . . . . . . . . . . . . 176
4.2.4 Local Thresholding with Hysteresis . . . . . . . . . . . . . . . . . . . . . . 179
4.2.5 Region Growing Segmentation . . . . . . . . . . . . . . . . . . . . . . . . . 185
4.3 Conclusions and Perspectives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
5 Analysis and Visualization of Computer Simulations of Amorphous Photo-Deposition 191

5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
5.2 Objectives of the Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
5.3 Monte-Carlo Simulation of Amorphous Deposition . . . . . . . . . . . . . . . . . . 194
5.3.1 Model and Simulation Parameters . . . . . . . . . . . . . . . . . . . . . . . 195
5.3.2 Morphological and Topological Dynamics . . . . . . . . . . . . . . . . . . . 196
5.4 Characterization of Deposition Morphology . . . . . . . . . . . . . . . . . . . . . . 197
5.4.1 Surface Features and Bulk Features . . . . . . . . . . . . . . . . . . . . . . 197
5.4.2 Complex Internal Features . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
5.5 3D Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
5.6 Analysis methods and feature extraction . . . . . . . . . . . . . . . . . . . . . . . . 203
5.6.1 Other Possible Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
5.6.2 Visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
5.7 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
5.7.1 Porosity, Roughness, Connectivity, and Anisotropy . . . . . . . . . . . . . . 213
5.7.2 Surface Density, Interfaces Surface . . . . . . . . . . . . . . . . . . . . . . 213
5.7.3 Interpenetration Quality and Segregation of a Three-Species Deposit . . . . . 215
5.7.4 Experimental Validation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
5.8 Conclusion and Perspectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
Conclusions and Perspectives 225
APPENDICES 228
A Further Definitions of Object Subsets and Boundary-Related Subsets 229
B Tubular Extraction Methods and Branching Analysis 239
C Synthesis of 3-D Phantoms of Complex Porous Structures by Diffusion-Limited Aggre-

gation with Relaxation 249
Résumé long 252
Bibliography 259
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Notation 11
Notation
The following list refers mainly to notation used in the theoretical foundations of discrete spaces,
our boundary-based approach and the specific applications in the present work. Some literals may
I
have a local meaning; for example, is used to represent the tensor of inertia in Chapter 1, and d
refers to distances or fractal dimensions, depending on context.
Symbol Description First used in page #
X = ”expression” ”X ” is defined as ”expression”. 24

a iff b, a () b ”a if and only if b”. 25
∅ φ The empty set fg, the Greek literals ”phi”, ”Phi”, and diameter. 25
a b] ]a b The closed and the open intervals from a to b, with a b 2 R. If
a b 2 N, a < b then a b] = fa a + 1 : : : bg.
26
(a b) An ordered pair (or vector) of entities a b. 26

fangNn=M Finite sequence (set) of (N ; M + 1) elements
faM aM +1 : : : aN ;1 aN g, with N M 2 N and M N .
85
~a = (a1 : : : an) An ordered set (n-tuple or vector) of n entities fa k gn

k=1. 29
<x> Expected value (average) of x 2 X , with X Rn. 27
int(x) Greatest integer int(x) x, with x 2 R. 103
Fractional part of x 2 R, i.e., frac(x) = x ; int(x).
frac(x) 103
card(A) Cardinality of set A (number of members). 27
A n B A ; B The set difference between sets A and B . 25

Ac a The complement of set A; the 1-complement of boolean a. 23
_ ^ XOR Boolean logic operators: OR, AND and exclusive OR, where 24
a XOR b = (a b) (a b)._ ^ ^
A B A
B A B A B Mathematical-morphology operators (dilation, erosion, opening, 51
closing) of set A by structuring element B .
A n B n-Iterated dilations of set A by structuring element B . 133
O P Q U V W Sets in Rn (objects, regions, scenes). Also, discrete sets in N3 23
V W Scene domains in R3. 86

V Cubic grid (scene domain in N3). 86
∂ Partial differential operator (e.g., f (∂xy
∂
x ).
) 50
@V V V V
N3, @ is the discrete face-based
V
The boundary of the set . If 24
boundary of .
@^ V Continuous point boundary of a voxelized set . V 92
V The voxel-based boundary (or solid boundary) of V N3. 93
K V V
The voxel-based boundary of , under K -connectivity. 93
12 Notation
@j V The j th connected component of the (face-based) boundary of . V 231

jK V The j th K -connected component of the voxel-based boundary of , V 112
under K -connectivity.
Vj+ = interior(@j V ) @j V V
Positive and negative solid interior of @ j . 229
Vj+ ] V ] V V
Filled interior of j+ , (cavities are blocked out). 235
AbB
Boundary A is nested within boundary B ; A interior(B). 231
Nfacets = Nbf (V ) = card(@ V ) Number of boundary faces of @ V .

92
Nvox = Nvb (V ) = card( V ) Number of boundary voxels of V . 93
N@ (V ) = card(f@jK Vg) Number of K -connected components of the face boundary @K V =
S N@ @ V : When V N3 , then K 2 f6 18 26g.
231,101
j =1 jK
NV (V ) Vol (V ) = card(V ) Discrete volume (voxel cardinality) of V N3. 101
pq pq1 pq1 Line segment between points p q 2 R3 and its two half-line ex- 27
tensions excluding pq, with: pq 1 = pq1 n fp qg (i.e.,

excludes p q).
d(p q) = kp ; qk Euclidean distance between points p q 2 R3. 24
d@ (p q) Geodesic distance between points p q 2 @V V R3. 26
dK Discrete distance under K -connectivity between grid points p q 2

98
V N3, and K = 6 18 26.
X Y Z (x y z) Orthogonal axis (right-hand trihedron) in R 3 or N3; point coordinates 85
and vectors.
u+ u;
2f g
Refers to oriented faces in positive and negative directions of axis 85
u x y z .
F6 = fx; x+ y; y+ z; z+ g V f g
Partition of @ into sets of six face orientations f k 5k=0 in the or- 91
thogonal grid N 3. Each subset forms a facet wall.
U = (;ê1 e^1 ;ê2 ê2 ;ê3 ê3 ) Ordered set of unit vectors grouped by opposite pairs of orthonormal 85
orientations: ê 1 = (1 0 0) ê2 = (0 1 0) ê3 = (0 0 1).
U = fu^ kg5k=0
F
Refers sequencially to each of the six orientation vectors assigned to 85
oriented boundary faces 6 .
v(x y z) v m Voxels at points (x y z) and boundary voxel elements vm 2 V
2
, 86
with m 1 Nvb ].
fk Oriented face, f k 2F 2
6 , with k 0 5]. 87
fn = (vm f k ) Discrete facet or boundary-face element fn 2 V @ , with n 2
2 2 V
89
1 Nbf ] k 0 5], v . Index n depends on m k and the
V
shape of @ . Unit vector u 2^k U is assigned to f k .
v0 v1 V c V
0-voxel in (void or background label ”0”) and 1-voxel in (object 89
or foreground label ”1”).
f = f(x y z k) Short notation for a facet at boundary voxel v 1 (x y z), and oriented
2 2
91
face (f k u^ k) k 0 5] ûk U . Isomorphic to a particular
ordered pair (v1 v0).
opface(f) Opposite face operator. Given a boundary pair (v 1 v0 ) and f = 91
(v 1 f i ), orientation is reversed by opface(f) = (v0 f j ), with
;
j = i + ( 1)i .
opface(@ V ) = @ V
! ! 2F
Opposite operator on an oriented facet boundary. Swaps all facet ori- 92
entations u+ u;, and u; u+ (with u 6), in a discrete
facet boundary @ V with a choice of facet orientation vectors U .
Notation 13
@ V ; = opface(@ V ) Negative boundary, the reverse-oriented version of @ . V 92
v((x y z) u
v =
^ k) main front voxel and main back voxel of v1 (x y z) at a given facet
2
109
f(x y z k) k 0 5].
f = f((x y z) u^ k ) main-front facet and main-back facet of facet f(x y z k). 109
@;V The back-face boundary of .V 110

@+V The front-face boundary of V . 110
;V The back-voxel boundary (or endo-boundary) of .V 110
+V The front-voxel boundary (or exo-boundary) of V . 110
++ V The next-front-voxel boundary of V . 110
@ @ Any of the two facet-based boundaries, @+ or @ ; . 110
Any of the four voxel-based boundaries, , + , ; or ++ . 110
facettovox(@ V ) = V Facet-to-voxel operator to build V from @V . 110
voxtofacet( V ) = @ V Voxel-to-facet operator to build @ V from V . 94
O = O n @O Geometric interior of continuous set O. 25
V = V n V Discrete Geometric interior of voxelized set V . 93
interiorx (@ V ) V
Discrete solid interior of a face-based boundary @ by x-runs of 96
V
voxels.
G V Fat-boundary neighborhoods of @ , defined by union-set combina- 112, 102
V
tions of voxel boundaries . For example, G+ = (
V V V
+ )
is the immediate neighborhood of @ .V
B n (r p) Euclidean sphere or spherical neighborhood in Rn of radius r
2
24
around p Rn; also (closed) n-ball, or n-disk.
A nB
If B is an euclidean sphere B n , then A nB A n B . 133
NK (p) Discrete neighborhood around p, including p, under a specific K - 102
connectivity.
EK = NK (p) Same as above, used as structuring element for Mathematical Mor- 102
phology operations, with K = 6 18 26.
N (p) Neighborhood around p, excluding p. 24
Nbf (p N ) = card( @ V \ N) Number of boundary faces in a neighborhood N (p). 208
N@ (r p) B@ (r p) Geodesic neighborhood of radius r around a point p 2 @V : 104

N = card(N@ (r p))
geo Number of points of N@ (r p). 104
@ VA\B Interface between regions VA and VB (for example, the face-based 25
@ Vj Boundary @ V restricted to ”condition”.

inter-species boundary).
condition 236
@ Vj The outmost boundary components of @ V (all sub-boundaries with- 235
out parents). The filled interior of V is defined as: V ]
out
=
interior(@ Vj ).
@ Vjz=0
out
Boundary patch corresponding to initial conditions (sustratum geom- 203
etry) before deposition along axis Z .
14 Notation
@ Vjz Boundary patch corresponding to the last deposited layer (axis Z ). 206
@ Vjz=+1 = +1.
last
Projected boundary (top surface) as seen from z 207

I(x y) f(x y)
Vj
Intensity 2D images; each one refers to a projected boundary 207
@ z=+1 interpreted either as a rough surface f(x y) or an intensity
image I(x y).
Vz]y]x] Marginal index array representation of a scene V (specific to soft- 137
f g 2
ware implementation).
umax umin Maximum and minimum values of a set ui N i=0 , with ui R. 154
argmax
v
(f(v)) Argument value (or vector) v which maximizes a scalar function
f(v).
argmin(f(v)) Argument value (or vector) v which minimizes a scalar func- 33
v
tion f(v). In discrete sets, the index iarg = argmax ui N i=0
i
f g
uiarg = umax = maxf g
ui Ni=0 (similarly for
min() argmin() ).
is such that
ROI, VOI Region Of Interest (usually in 2D) in a given image and Volume Of 62
Interest in a 3D scene.
fIng Volume as a set of n stacked color images after gamma correction. 144
H n(u) = Histo (I n ) Histogram (function) and histogram operator of a color image I n (or
2f g
147
ROI) with u R G B , the intensity per channel.
mode () The mode of a distribution curve in some defined domain. 41
XY Y Z ZX Orthogonal planes in R3 or N3. 102
IXY Axial set: a scene or ROI organized (resampled) as a set of slices 176
(images I n (x y)) orthogonal to the Z -axis.
IY Z Coronal set: ... (as above)... orthogonal to X -axis. 176
IZX Saggital set: ... (as above)... orthogonal to Y -axis. 176
Sunder(V ) Sover (V ) Under-segmentation and over-segmentation output volume. 178
JXY Conjunctive combination of segmentation results. 178
J\XY Disjunctive combination of segmentation results. 178
J\ XY Associative combination of segmentation results. 178
~n ~t? ~tk Normal, binormal and tangent vectors to a curve of a surface @ V

68, 239
R3. Usually, ~t? = ~tk ~ n).
k ? Characteristic feature lengths (e.g., peak or valley width and height, 45
respectively) tangent (any direction in plane XY ) and perpendicular
(axis Z ) to a surface z = f(x y).
2
hRMS RMS roughness of a 2.5D surface z = f(x y) defined as the Root 198
Mean Squared deviation from mean height < h >).
Notes about text notes, captions and figure symbols:

✦ The meaning of acronyms is first introduced in italics. For example: Mathematical Morphol-
I ogy (MM), and indicated at the external margin with a triangle, as reminder.
Notation 15
✦ Bibliographic references are listed in square bracket format: [LastNamesYY,...].
✦ Caption labels are set in parenthesis: (a). Outside the figure, they may be found in a 22
array to the right of the legend, representing subfigure components.
✦ The symbol “ ” is used to tag an object in the figure, a reference vertex or point.
✦ Bolded arrows with a white tip represent special vectors in 3D. Some directions (orthogonal
axes, for example) appear represented by black tip arrows.
16 Notation
17
Preface
The first “complex” objects to be throughly analyzed by Science were fairly simple. Very high num-
ber of components or features, dimensionality, and the length of descriptions demanded computer
tools and special mathematical treatment (e.g., many dimensions, fractals, measures of complexity,
etc.), which have been developed only this century.
On the other hand, biological, natural and medical objects have been studied in rather qualitative
fashion, with poor mathematical treatement until recent years in which non-linear phenomena and
several advances permitted more formal approaches to study and synthesize irregular shapes. Digital
Spaces, Discrete Topology problems (also called Digital Topology) and their applications are one
example of the topics increasingly present in current literature, converging with computer and theo-
retical advances, but also fostered by the increasing interest in formal approaches to difficult subjects.
One explanation of the late appearence of such topics, besides technological achievements for the last
twenty years, is their location at the boundary between Computer Engineering and Discrete Mathe-
matics, the first being specially pragmatic and the second highly formal. If interdisciplinary activities
could be modeled as any dynamic system, it might be seriously argued (and not just as metaphor) that
“unmiscible domains tend to develop complex interfaces” even in scientific and engineering fields.
To know the context of the present work, some personal informations may help. My coming to
France and my research subject have their background in the National Autonomous University of
Mexico (UNAM), where I worked as an engineer in the Image Laboratory1 of the Centro de Instru-
mentos of the UNAM2 . By 1993 we were doing very simple signal- and image-processing applica-
tions in Biomedicine, and worked close-together with biologists and physicians. Yet the problems
were interesting and results very fruitful. A particular project with the Electron Microscopy Labo-
ratory of the School of Sciences of the UNAM motivated the design and development of tools of
analysis of three-dimensional (3D) chromatine bodies in animal cell nuclei. Shapes were very com-
plex, numeric measures on slices and contours did not show clear patterns and no commercial tools
were available for this analysis. During development of methods for discrete-surface extraction, I
came to France for a similar application, in the study of the Parkinson Desease, at the U-INSERM
238, where the main concern was the geometric distorsions of images and the lengthy microtome ses-
sions. A grant from the UNAM allowed me to obtain a DEA in Génie Biologique et Médical and start
this thesis work in the Département Images of the Ecole Nationale Supérieure des Télécommunica-
tions (ENST) by end 1994. (Details about people and laboratories appear in the Acknowledgements).
1
http://www.cinstrum.unam.mx:8001/pub/ima imagenes.html
2
http://serpiente.dgsca.unam.mx/rectoria/htm/demo2.html
18
Problem Definition, Applications, (and what came of it:)

Thesis Organization.
A personal aim for my DEA and PhD was to start and develop a line of research about complex-
shaped objects from natural Sciences and Physics, and their analysis in 3D with image-processing
methods3. This is a too general goal for a single thesis: how to delimit the subject while studying
the topics I was interested in? At present, this also had the inconvenient of limiting interdisciplinary
work and quantitative results, becoming more concerned with the state of the art, methodology,
developpment, theory and visual results.
Since we did not have in mind a very specific problem, nor wanted to focus in a unique, single
application, we state here what the initial aims looked-like, knowing that the present work only
achieved some of them, and even partially. We also summarize how the problems and their treatment
constitute the chapters of this manuscript.
A first objective was to do an extensive bibliographic research, in order to identify and have
preliminar knowledge of how complex shapes are defined, their feature descriptors, key-concepts
of what is “shape complexity”, and “complex”, in general. From this survey, a number of specific
characterization problems with 3D data was expected to arise. We illustrated some of the subjects
with our own past experiences, in the UNAM and during the DEA. Continuous and discrete repre-
sentations and their morphological parameters were studied, with emphasis in the latter.
A broad idea was to use discrete boundary representations (3D borders or frontiers) as the main
paradigm, since, excluding force fields and internal sources, most objects and phenomena (natural,
or generated by man or computer) have important interactions at their boundaries and it is our first
(or only) approach to them in several cases. Thus, one of the initial objectives was to present a large
sample of shape features described and analyzed through discrete representations and processing
to organize data and extract morphometric characteristics. Together with the first objective, this
produced the material for the Chapter 1 and Chapter 2.
Chapter 2 also includes a description of the model of boundary representations in digital spaces
(Z3), some aspects of algorithm implementation and analytic methods based on boundary traversal.
Having obtained access to the Visible Human Project (VHP) database, we had the opportunity
to analyse complex objects, such as the lungs and the brain, from several imaging modalities, in
particular anatomical color photographs. Degraded radiometric information of high resolution posed
enough problems to occupy a significant part of our time, and Chapter 3 is devoted to the solution
of this problem.
The second part of the previous work on the VHP consisted in the extraction of the blood-vessel
tree of the VHP lungs. This lead us to consider methods of segmentation of these structures, and to
propose specific tubular detection methods. Chapter 4 presents our progress in these directions.
While developing the extraction methods of the blood vessels, a second application in Surface
Physics attired our attention due to its multiple aspects in shape-complexity problems from a col-
laboration with the laboratories of CNET-Bagneux. It is the three-dimensional structures produced
by computer simulation of amorphous deposition. Such data and the aims of the CNET laboratories
are representative and illustrative of the kind of problems we were trying to study, with the aim of
accessing bulk and roughness information about porous structures, in function of simulation param-
eters. The collaboration also may give us later the opportunity to test and validate results against
experimental data, which were not warranted to be produced during the thesis work. The problem,
methods and preliminar results of this work are described in Chapter 5.
3
http://www.tsi.enst.fr/ ˜marquez/
19
Time limitations did not allow us to present here other results and related applications; but most
of them are roughly described and referenced, specially in Chapter 1.
A symbolic notation list is given in page 11. All chapters have a short abstract and an overview at
the end of each introduction describes the sections, goals and development of the exposition. There
are sections in small font which can be skipped in a first lecture. A section of conclusions and some
perspectives are also found at each Chapter.
Jorge Márquez, ENST, Paris, February 1999.

20
Chapter 1
Characterization of sets with complex

structures in R 3
Abstract
In this chapter we make a survey on complexity in continuous space (R 3), from the point of view of
shape and morphological features of physical, computer generated or digitized objects from differ-
ent application domains. These features comprise simplified representations, form factors, convexity,
coherence, decomposition into simpler elements, scale invariance properties (fractal dimensions),
and other notions useful to describe and measure complex objects or sets, and complex relationships
between them. An emphasis is given to concepts related to boundary representations, in view of the
analytical methods presented in Chapter 2, and the applications described in the other chapters.
1.1 Preliminar Notions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

1.1.1 Neighborhoods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
1.1.2 Boundaries and Interfaces . . . . . . . . . . . . . . . . . . . . . . . . . 24
1.1.3 Connected Sets and Objects . . . . . . . . . . . . . . . . . . . . . . . . 26
1.2 Intrinsic Properties of Solid Shapes . . . . . . . . . . . . . . . . . . . . . . . 28
1.2.1 The Approximating Ellipsoid, Isotropy and Deformed Shapes . . . . . . 28
1.2.2 Shape Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
1.2.3 Shape Decompositions and Local Descriptions . . . . . . . . . . . . . . 34
1.2.4 Convexity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
1.2.5 Coherence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
1.2.6 Scales of Representation and Characteristic Lengths . . . . . . . . . . . 42
1.3 Extrinsic Properties of Solid Shapes . . . . . . . . . . . . . . . . . . . . . . . 45
1.3.1 Complex Relations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
1.3.2 Many Bodies and Clusters . . . . . . . . . . . . . . . . . . . . . . . . . 46
1.3.3 Complex Objects in Feature Space . . . . . . . . . . . . . . . . . . . . . 47
1.3.4 Complex Representations . . . . . . . . . . . . . . . . . . . . . . . . . 47
1.4 Fractal Dimensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
1.4.1 Dimension Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
22 Characterization of sets with complex structures in R3
1.4.2 Morphological Features of Fractals . . . . . . . . . . . . . . . . . . . . 54

1.4.3 An Example: Particle Aggregates . . . . . . . . . . . . . . . . . . . . . 56
1.5 Notions and Measures of Complexity . . . . . . . . . . . . . . . . . . . . . . 56
1.5.1 *Kolmogorov Complexity . . . . . . . . . . . . . . . . . . . . . . . . . 58
1.5.2 Information Theory, Algorithmic Entropy and Scientific Observations . . 60
1.6 Shape Taxonomies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
1.6.1 Tubular Structures (I) . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
1.6.2 Ramified Thin Structures . . . . . . . . . . . . . . . . . . . . . . . . . . 64
1.6.3 Surfaces, Boundaries and Interfaces . . . . . . . . . . . . . . . . . . . . 68
1.6.4 Description of Other Shape Features . . . . . . . . . . . . . . . . . . . . 69
1.7 Other Properties of Complex Information . . . . . . . . . . . . . . . . . . . . 70
1.7.1 From Structure to Texture . . . . . . . . . . . . . . . . . . . . . . . . . 70
1.7.2 Noise, Blurring, Distorsion and Inhomogeneities . . . . . . . . . . . . . 71
1.8 Discussion and Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Introduction
We review in this chapter some concepts closely related to complex objects in three dimensions.
Since the subject of Complexity is too large for any single work, we have selected those concepts
defining complex shapes that can be studied in a framework of biomedical and physics applications,
with medium-level computer resources. At the same time, we study those morphological features
related to the quantitative analysis and visualization approaches presented in Chapter 2, and the spe-
cific applications of Part II. Our choice is based on what we believe is relevant and common to many
applications, hence, theoretical details and related topics are to be examinated in the bibliography.
Some of our own experiences are also cited.
Complexity, in the context of our work, will mean static complexity, as defined in Section 1.5,
but also we restrict the subject to morphological or shape complexity, in object space. However, we
review in this chapter some other related meanings (non-convex shapes, ramified structures, fractals
and Kolmogorov Complexity, mainly), how they may be useful in shape description, and how to
formulate some of them with the discrete boundary-based approach we present in Chapter 2. We
further restrict ourselves to the class of rigid, non-deformable, non-fuzzy and constant-density ob-
jects, considering mainly their geometrical shape and spatial configuration. The terms ”structure”
or ”structural” are employed often. The intended meaning is not only intrincacy but also shape
organization, that is, how an object is constructed, described or how its parts are arranged.
It is worth noticing that in many cases morphological descriptions follow general rules that relate
shape and structure in the physical world to morphogenic process. The latter includes, for example,
water and wind erosion in geosciences, growth and homeostasis in Biology, or a set of user-specified
probabilities and parameters in the computer simulation of some model. The construction rules
may be non-deterministic, i.e., subject to stochastic process and noise. They may however determine
statistical properties of the shape of a physical object, from branching structures (trees, blood-vessels)
to porous media (particles, deposits), to shapes and configurations called laminar, granular, tubular,
convoluted, etc.
Consider also the fact that other aspects of the shape remain unpredictable, such as the exact
location of each pore, fold or protuberance, number and length of branches, etc. This fact may
be irrelevant, but a general characterization should provide estimations of averages and RMS (Root
1.1 Preliminar Notions 23
Mean Square), values of specific features. Physical pressure and temperature are typical examples of
macroscopic and statistical properties of many-particle systems. In a similar way, the final morphol-
ogy or configuration of many dynamic systems is usually the result of underlying non-deterministic
process, impossible to fully track along several spatial scales, and requiring statistical models to
predict macroscopic properties, as well as morphological features. Image processing examples of
macroscopic features are texture, roughness, entropy and fractal dimensions. The quest for under-
standing most dynamic process and the validation of their mathematical models strongly relies on
description and understanding of their associated morphology. It is in this spirit that this work was
conceived.
Sections in this chapter are organized as follows:
✦ In Section 1.1 we define some concepts that will be used often in the present report. These
include boundaries, neighborhoods, and interfaces. Appendix A, in page 229 further presents
interiors, cavities, nested boundaries and other notions.
✦ In Section 1.2 and Section 1.3 we describe a set of features that have always posed some
kind of problem to shape understanding, manipulation, and modeling, and make a general
characterization of what is commonly described as ”complex three-dimensional objects”. We
have divided them into intrinsic properties and extrinsic properties of solid shapes.
✦ Scale invariance, auto-similarity, self-affinity, and several fractal dimension definitions are
reviewed in Section 1.4. Morphological features of fractals are also discussed.
✦ In Section 1.5 we review some notions and measures of complexity and their relations with
shape. These consist mainly of Kolmogorov Complexity, Algorithmic Complexity and En-
tropy.
✦ In Section 1.6 Classifications of different shapes are analyzed in terms of local or global fea-
tures characterizing a specific class of shapes. We suggest some ways to describe and quantify
those features, by analyzing relations between internal, external and boundary points of the
object.
✦ In Section 1.7.1 and Section 1.7.2 we mention some problems (subsampling, deformation) and
parasitic information (noise) that contribute to ”the complexity” of an object studied through a
set of data observations.
✦ In Section 1.8 we summarize all reviewed notions and high-level characteristics common to
features describing complex shapes.
1.1 Preliminar Notions

O
We introduce in this section some basic definitions specially applied to solid shapes. Let be in gen-
eral an object, a scene (set of objects) or a set of points p in R3 (continuous) or in N 3 (discrete). Any
O
subset (region or points) of is often considered as the ”foreground” with respect to some predicate
about points p 2O , or some operation on p (e.g., edge extraction). In this case, the complement c O
O O
is called ”the background of ”. Note that if there are other objects in c , the background depends
on definitions of what was called foreground. These definitions are predicates and operations on p
to determine if p 2O O O
. Both and c may be composed of one or more connected components
(several objects, cavities, etc.). We introduce discrete connectivities in Chapter 2, Section 2.3.4,
and restrict here most definitions to the continuous case. Since we often use the concept of ”neigh-
O
borhood”, ”boundary” and ”interior of ”, definitions of these and related concepts are given here
and in Appendix A. As general references we cite [Weisstein98, Kiyosi96a, Kiyosi96b, Iyanaga68,
Koenderink90, Coster89, Barnsley88, Herman98, Klette98]. Symbolic notation is summarized in
page 11.
1.1.1 Neighborhoods
D EFINITION 1.1 (Continuous Spherical Neighborhood in Rn )
Let p 2
Rn (with n 2
N) and let kk
denote the Euclidean distance in R n. Let B n (r p) =
f 2 j k ; k g
q Rn p q r . We call B n (r p) the closed n-ball of p, closed n-disk, closed spherical
neighborhood or closed Euclidean sphere of radius r.
An open n-ball or disk is defined by n (r p) = q B

f jk ; k
p q < r . If nothing else is g
indicated, ”ball”, ”disk” and ”sphere” will mean by default ”closed ball”, etc. We sometimes use also
B 2
r (p) to denote a discrete neighborhood of p N 3 and radius r. In general, a neighborhood (p) N
N
or K (p) around p may have a shape other than the spheric (e.g., cubic or rhombicuboctahedral
N
if K (p)
N3 ). Subindex K is a parameter characterizing connectivity, scale, shape or other
properties (see also below, geodesic neighborhood). We set r = " to indicate that r > 0 is ”small”.
It is also referred in mathematical literature as an epsilon-neighborhood. We notice that some authors
call ”neighborhood of p” the set (p) = N

N ;f g
(p) p . This is also a special case of an open annular
neighborhood, defined as follows:
D EFINITION 1.2 (Open Annular Neighborhood in Rn )

2
Let p Rn, with r1 r2 R. Let 2
B n (r1 r2 p) = fq 2 Rn j
r1 < kp ; qk < r2 0 < r1 < r2g
We call B n (r p) the open n-ring or open n-annular neighborhood of radii r1 r2.
Note that the special case r1 = 0 corresponds to an open n-ball without p. We use discrete annu-
lar neighborhoods as 2D sliding windows or roller memory buffers for local analysis in Section 3.3.3,
and for 3D tubular detection in Section B. Tubular and boundary neighborhoods are defined and dis-
cussed in Section B and Section 2.3.8.
1.1.2 Boundaries and Interfaces

D EFINITION 1.3 (Continuous Boundary in Rn )
Let O
Rn and let
@ O = fp 2 O j (8 " > 0) (9 q1 q2 2 B n (" p) such that (q1 2 O) ^ (q2 2 Oc ))g

where ”^” denotes the logical ”and”. The set @ O is called the boundary of O.1
Remark 1. Some authors set q 1 = p, which defines a boundary as a subset of the object.
O
Boundaries are also called ”frontiers”. The set @ of a single object may be composed of several
connected components which make up the external and internal surfaces (cavities) of (see Def- O
inition A.6 below). Such properties are examinated later. The discrete version of @ poses some O
1 ^
We use the symbol ∂ for partial derivatives and @ @ and for various boundary definitions.
O
problems in relation with membership of a point (pixel, voxel) to . Membership and neighboring
relations depend on connectivity definition in N n . We deal with the latter in Section 2.3.4, page 96.
Figure 1.1a-d illustrates the definitions of continuous and discrete boundaries.
D EFINITION 1.4 (Open/Closed sets, Closure.)

O O
Let a set and @ its boundary. Then
✦ O is a closed set iff @ O O. 2
✦ O is an open set iff (8 p 2 @ O) p 2= O.

✦ The set O = @ O O is called the closure of O.

Let the set difference ”n” (or ”;”) between sets A and B be defined by:
A n B = A ; B = fa j (a 2 A) ^ (a 2= B)g:
D EFINITION 1.5 (Geometric Interior)
The set

= O On O
@ is called the geometric interior of O.
Some authors use the definition of interior to denote geometric interior (or strict interior). In the
following definitions we deal only with closed sets, that is OO 2 O
. Thus, any point p @ belongs
O
also to . We also make some remarks on the discrete case but leave the equivalent definitions for
Chapter 2.
D EFINITION 1.6 (Interior and Exterior Points, Boundary Points)

Given a set O
Rn and a point p Rn: 2
p is an interior point of O iff p 2 O, and
p is an exterior point of O iff p 2 Oc .
p is a boundary point of O iff p 2 @ O.
O may belong to the boundary or to the geometric interior of O. It may
Thus, interior points of
happen in Nn that a set O does not have geometric-interior points, i.e., O= ∅. Some authors use

the notation int(O) and ext(O) referring to the geometric interior or exterior of O (the exterior is
actually its complement).
The notion of boundary separating foreground (O) from background (Oc ) can be extended to
that of interface, as the set of points in common between two closed regions O A OB of different
nature (e.g., different labels A B , material or color). More precisely (see Figure 1.1e):
D EFINITION 1.7 (Continuous Interface in Rn )

O O O O \ OB 6= ∅, and define:
Let A B be closed sets such that A\B = A
@ OA B = fp 2 OA OB j 8 " > 0 (9 q q 2 B n (" p) such that (q 2 OA ) ^ (q 2 OB ))g

\ 1 2 1 2
If (OA B n @ OA B ) = ∅, then @ OA B is called the interface between regions OA and OB (or

also, common boundary), and sometimes denoted @ (OA OB ).
\ \ \
The definition of a discrete interface depends again on connectivity relations and boundary rep-
resentations and is given in Chapter 2.
2
”iff” = ”if and only if”, we also use the symbol “ () ”
(b) (d) (e)

pb N(pb )
Oc
OA OB
pc O
(a)
pa (c)
O N(pa )
U U O
4O
U
8O OA U
B
Figure 1.1: Boundary @ O0 of an object O R2. (a)0 Point pa is a boundary

N (pa), there are points pc q 2 N (pa) such that p 2 O and q 2 Oc. (b) An external point pb has a
point iff for any neighborhood
neighborhood N (pb ) O , and (c) an internal pc point has a neighborhood N (p c ) O. (d) In the discrete
case (O N2), the boundary definition and neighborhoods N K (p) depend on connectivity relationships,
(”K -connectivity”, with K 2 f4 8g). (e) Interface @ OA\B between two regions OA and OB .
D EFINITION 1.8 (Geodesic Neighborhood)

2 O
Let p @ . Then the set:
N@ (r p) = fq j q 2 @ O ^ kp ; qk rg
is called a geodesic neighborhood of p, with radius r.
Remarks. Strictly speaking, the Euclidean distance kk

should be replaced by a geodesic metric,
with paths between boundary points strictly following geodesic lines of @ (which are minimum- O
length paths, using the geodesic metric), instead of taking the intersection with a n-ball. For small
neighborhoods and very smooth surfaces we consider the approximation as acceptable 3. The more
Q
general definition uses then a geodesic distance d Q ( ) defined on a set :
N (r p) = f q 2 Q j d (p q) r g:
geo Q
In a boundary-based representation, Q may in turn be the boundary set @ O, and the geodesic distance
between points p q 2 @ Q is denoted by d @ (p q ).
1.1.3 Connected Sets and Objects

We introduce further definitions concerning boundary components, interior and their organization.
In these definitions we deal only with closed sets in R 3 and their boundaries as closed surfaces. We
need again some basic notions first:
N OTATION 1.1 (Closed and Open intervals)

Let a b 2
R, with a
b, then a b] denotes the closed interval fx 2 R j a x bg, and
f 2 j
]a b denotes the open interval x R a < x < b . If a b g 2 N, a b] is the set of integers
f ; g
a a + 1 a + 2 : : : b 1 b .
Notation (A B) is reserved for ordered pairs of entities A B (numbers, sets, vectors, etc.).
A connected set is classically defined as a set that can not be expressed as the union of disjoint,
open sets. We give an alternative definition in terms of connected paths between points in a set.
3
Such approximation is inadequate for example in describing neighborhoods on convoluted surfaces, (e.g., cortex sulci).
D EFINITION 1.9 (Connected and Disconnected Set) An open set A 2 R is called disconnected
3
2
if there are two open, non-empty sets U V R3 such that:
U \V =∅ and U V =A (1.1)
A set A 2R 3 which is not necessarily open is also called disconnected if there are two open
U V 2 R3 such that:
(U \ A) 6= ∅ ^ (V \ A) 6= ∅ (1.2)
(U \ A) \ (V \ A) = ∅ (1.3)
(U \ A) (V \ A) = A: (1.4)
Finnaly, if A is not disconnected, it is called connected.
It is generally easier to show that a set is disconnected than showing connectedness: if there is a point
62
x A, then that point can often be used to ’disconnect’ A into two new open sets with the above
properties.
We will rather use a connected path definition for discrete sets in N 3 in Chapter 2. Many non-
connected sets may be expressed as the union of N connected sets, which we name the connected

components of A, and card A = card(A) = N is its cardinality.
D EFINITION 1.10 (Object)

Let O O an object, iff
R3 be a set of points. We call
9 N 2 N 9 fOk R j Ok is a connected set

k = 1 : : : N g
+ 3
N
such that O = Ok
k=1
Remarks. If we let Nk O
1 for each set k k = 1 : : : N we verify that they are themselves
O O O
objects, which we call connected components of . Note that @ @ k are also objects under this
definitions.
D EFINITION 1.11 (Body, Solid object)

An object O is called a body, solid or solid object iff O 6= ∅
that is, if it has geometric interior.

We also refer all p 2 O as the foreground and p 2 Oc as the background. Note that a single-
0
component object may have several boundary components. We give bellow an definition of con-
nected components as ”fragments” of O in terms of its boundary components.
Finnally, < x > will denote the average or expected value of a population of samples x 2 Rn,
and pq will represent a line segment joining any p q 2 R ; i.e., pq = fs j s = p + t(q ; p) (8 t 2
3
R 0 t 1)g.
These definitions and some presented in Appendix A (which may be skiped on a first lecture)
are extensively used in the following sections and other chapters. We propose in particular some
equivalent concepts in discrete spaces, in Chapter 2. None of the traditional description methods
from Fourier analysis or from differential geometry was included, nor used, having in mind a “more”
discrete approach, and now proceed to present the intrinsic properties and features of solid shapes.
1.2 Intrinsic Properties of Solid Shapes

Single objects may present several shape characteristics that make description and analysis lengthy
or difficult. Traditional classifications and names for shapes such as ovoid, flat, potato-like, spongy,
trabecular, denticulated, fasciculated, etc., depict proportions, repetitive patterns, part arrangements,
and salient characteristics by intuitive similarities with real-life objects and geometrical abstractions.
A repetitivity study alone would deserve an exposition on frequency-domain techniques of analysis,
together with concepts such as spatial correlation. Shape diversity and complexity has turned popular
terminology imprecise and ambiguous, and formal, useful descriptions are still arising. We mention
in this section some of the most elementary features of global and local descriptions of isolated
objects: principal axes (or diameters), decomposition into simpler parts, convexity properties, and
ways to proceed from coarse to fine descriptions with these features. We have called them intrinsic
properties, because they do not depend on external attributes, such as position and relationships of
the objet with its context and other objects.
1.2.1 The Approximating Ellipsoid, Isotropy and Deformed Shapes

A simple but powerful global feature of an object refers to the axes of the triaxial ellipsoid that
best fits (or approximates) the object, whatever its shape. One of the roughest assumptions about a
bounded shape is that it can be always approximated by an ellipsoid. This extreme simplification ad-
dresses the question of proportions between length, breadth and width (or height and depth). Fitness
can be expressed as some optimal criterion, as Least-Square differences, but a mechanical approach
is already available from Physics4: When a physical solid has an homogeneous density of matter
(for the sake of morphological description), there exists a virtual ellipsoid representing the object (its
solid contents and its shape), denominated the ellipsoid of inertia. It is suitable in Classical Mechan-
ics to describe universal dynamic properties of all solids, no matter how intricate they are. Solids
O
or sets of solids are first reduced to a dimensionless point that corresponds to the center of mass
”CM” I O
CM( ))= (xCM yCM zCM) or geometric centroid (if density is uniform), and then represented by an
ellipsoid with angular momentum and other attributes which depend on shape and mass distribution.
To simplify further, we assume uniform mass density equal to unity, to concentrate description only
in morphology.
O O
Let be an object in R3 and @ its boundary, as already defined. Without loss of generality, we
O
locate the origin of the coordinate system at the centroid of , thus (x CM yCM zCM ) (0 0 0). Let
2f g
u v w x y z be three coordinate axes, in permutated order (right-handed system). We define:
R R R u dx dydz
uCM u = R R RO dx dy dz
= (1.5)
R R R uvO
dx dy dz
uv = R ROR dx dy dz u 6= v (1.6)
R R R (v2 + w2)dx dy dz
O
uu = OR R R dx dy dz v w 2 (fx y zg; fug): (1.7)

O
The integrals uv are the uv products of inertia (sometimes refered as ”moments about plane w”),
and integrals uu are the moments of inertia about the u axis. Note the normalization with respect
O
to the total mass of (volume element times mass density, which we assumed here to be 1). For
4
In 2D, the best-fit ellipse is defined equivalently as the ellipse whose second-order moments equal those of the object
[Jain89].
1.2 Intrinsic Properties of Solid Shapes 29
varying mass density %(x y z ), the centroid refers to the geometric center (as when % is constant),
and the center of mass integral has a weighting term %(x y z ), as well as integrals uv and uu .
For a set of N identical point masses located at positions ~x i i = 1 : : : N , the centroid is given by
P
~xCM = 1=N Ni=1 ~xi. The matrix or tensor of inertia in Classical Mechanics is defined by:
0 1
xx xy xz
I = @ yx yy yz A (1.8)
zx zy zz
I
Since is square and symmetric, it is possible to find a coordinate transformation to express I in a
A
diagonal form. Let the matrix formed by the three column eigenvectors of ; then: I
0 0 0
1
a
ID = A;1IA = @ 0 b 0 A (1.9)
0 0 c
I f g I
where D is a diagonal matrix whose entries are the eigenvalues a b c of , and the column
vectors of A correspond to the three principal axes of the ellipsoid (also called principal moments
of inertia). The equivalent concept in Statistics is the scatter matrix or covariance matrix, and its
diagonalization is called the Principal Component Analysis (PCA) of the object, conceived as a J ”PCA
(random) distribution of points in R 3. The mass density is then substituted by the probability density.
To obtain in practice the product moments, the integrals uv are numerically calculated just over
O
finite subsets of . A uniform, isotropic and orthogonal discretization of space provides a set of N
samples pn N3, with pn 2O n = 1 : : : N (see Figure 1.2 for the special case of the center
O
of mass, CM( )). Samples pn are voxels with unitary volume and unitary density. Then uv is
replaced by the discrete moments uv , with u v 2f g 2
x y z and x y z N, and normalization is
done over the N samples. We do not demonstrate the latter in this document, but only give an intuitive
argument: given a partition of O O
= Nn=1 n , linearity permits to rearrange the integral terms of
O
uv , in order to calculate partial centers of mass for each n n = 1 : : : N (see Figure 1.2b). In
a dense sampling, the error between these partial centers and the nearest sample from a set of N
random samples is small and cancel itself on the average.
O
As a special case, the tensor of inertia of the discrete boundary @ may be an acceptable ap-
O
proximation of the tensor of inertia of , (except for a proportional term). Figure 1.2e illustrates this
approximation in 2D. In general, a ”filled” object and its boundary alone present different physical
moments of inertia with respect to most axes. When morphological considerations are the only con-
cerned, the boundary approximation allows to compare different shapes, using only their boundary-
moment representation. To distinguish moments and tensor of inertia calculated either over or over O
O I
@ , we add a superindex @ to indicate ’boundary’: @uv and @ . We recall that under some conditions,
volumetric integrals uv may actually be precisely calculated from the boundary information, using
the Gauss Theorem as described in Section 2.5.1.
Isotropy There are simple measures obtained from the principal axes (principal components or
eigenvalues) that describe eccentricity and global isotropy of a shape. While eccentricity is described
in two dimensions by one single parameter (usually the ratio " = a=b of semi-major-axis/semi-minor-
axis), three-dimensional eccentricity requires a three-component feature vector for a complete de-
f g
scription. Let a b c denote the eigenvalues of the ellipsoid of inertia associated with an object,
O
set or region . These are the principal axes, equal to twice the semiaxes a b c. Without loss of

generality, we assume 0 < c b a. At least three independent isotropy indexes I 1 I2 I3 can
(a) (b)
*
* * * *
* * *
*
* ... *
** *
{O } {p }
n n
N
O O = U { On }
n=1
CM( O ) = CM ( { CM( On )} ), n=1,...,N
(c) (d) (e)
* *
p ∋ ∋
n O, n=1,...,N { (xn , yn )} pn O, n=1,...,N
Lim CM( { p } ) ~ CM( O ) CM( O) ~ CM( O)

N n
8
Figure 1.2: Center of mass (CM) approximation by finite samples (uniform mass distribution). (a) CM( ): O
O
R 2 can be averaged to obtain
O O O
the centers of mass of the elements of a partition (b) of a continuous object
its CM( ). (c) The CM can be approximated by random samples of , or (e) from its boundary @ . (d)
Discrete samples in N2 are a particular case between (b) and (c).
be defined:
I1 = 2+a
b c
I2 = 1=2 + b
a
c
I3 = 1 ; a ; b ) 3(+(2+a ;2+c ) +2 ) (b ; c )
( 2 2 2
a b c
These indexes are best descriptive when the following combinations of conditions apply:
✦ if c a and b a, then I1 measures an elongated, prolate uniaxial anisotropy. Equiv-

alently, it measures 2D isotropy of mass distribution along the plane orthogonal to axis a, as
in the case of planar ecentricity ". The ratio I1 is high if one direction predomines.
✦ if
c b and c a, then I2 measures a ”flat”, discoidal or oblate uniaxial anisotropy.
Equivalently, it measures 2D isotropy of mass distribution in the plane orthogonal to axis c
(note differences and similitudes with I 1 ). I2 is high if two directions predomine at the same
time.
(b) (c)
(a)
Figure 1.3: Ganglion neuron 3D reconstruction from confocal microscopy imaging. Approximate contour of
the global ellipsoid of inertia (a) (re-scaled); local ellipsoid of inertia for one dendrite (b). The dotted profile
(c) represents the 3D convex hull (see Subsection 1.2.4), whose ellipsoid of inertia do not match with that of
the neuron. 3D data is public domain.
✦ I3 is the relative intervariance eccentricity; if it is high (case a

b c), isotropy is
omnidirectional; if it is low, anisotropy occurs between axes directions taken two at a time.
In all cases, a perfect isotropic shape (not necessarily a sphere!) satisfies I1 = I2 = I3 = 1.

An application example is presented in Section 5.7.1, page 213 for measuring pore distribution in
a deposit. The interest in isotropy measures is that they can be obtained locally, allowing to know
isotropy and orientation of shape features, and textural characteristics at several scales.
In a cross-sectional and bidimensional approach to 3D problems, we could have also defined a
vectorial eccentricity ~ 6
" = 1=3(a=b b=c a=c), with at least b c = 0. The normalization factor 1=3
is introduced to have ~"k k 1 for a sphere.
Finally we note that when 2D features depend on scalar properties on two axis (e.g., the moment
uv , or the eccentricity ratio a=b), it is often the case that in 3D the equivalent are vectors or tensors
to include diverse pairwise combinations of properties along coordinates u v w 2f g
x y z . Second
order combinations include uv , u2 and u2 + v 2 terms, for example. In approaches for studying a 3D
object with 2D morphometry on cross-sections, the analysis may end up with too many parameters
that are only meaningful in the plane of definition XY Y Z , or ZX . Quantitative Stereology is a
particular way to do something similar: to obtain estimates of 3D measures from 2D samples, using
statistics, integral and stochastic geometry.
Features that Result from Shape Deformation Several shape anisotropies and morphological
features in general can be understood in terms of deformed simpler features. When the shape charac-
teristics can be described as deformed patterns, several deformation modes exist: torsion (rotational
deformation), shear in one or more directions, inhomogeneous shrinking and expansion, bilinear
warp (that which maps parallelepids into trapezoids), and higher order warps. Most of these de-
formations may be modeled or approximated by a series of linear transformations T1 T2 : : : Tn
on each point ~xi 2O , as: ~yi> = T1T2 Tn~x>i . This is an example of how certain shape features
can be represented in terms of other, simpler features, as the result of a geometrical transforma-
tion. Biological descriptions and models of shape morphology and morphogenesis often proceed in
terms of adaptive change (deformations) of basic structures, or entire systems. Bookstein describes
a quantitative approach to biological shape change in [Bookstein78] and Murray examines pattern
formation, development and morphogenetic rules in chapters XVII and XVIII of [Murray93]. We
describe morphological deformations in dopaminergic cell neurons due to pathological stress and
neural death-compensation phenomena (”Apoptosis”) in [Anglade93, Anglade95, Anglade97].
If a 3D object is digitally represented as stacked slices z k , rigid and non-rigid transformations
may be applied in 2D, slice-by-slice, with parameters varying with z k , in order to model several
deformation combinations. Many common reconstruction and shape restoration problems constitute
the opposite process: a set of deformed individual slices have to be aligned and/or unwarped to
recover the original shape, which may in addition present intrinsic deformations. A severe problem
is the lack of information about the set of transformations T i, or whether their inverses exist and are
well-defined (insensitive to noise). We discuss further this subject in Subsection 1.7.2.
1.2.2 Shape Factors

Compacity A first measure of shape, quantifying some degree of complexity (”irregularity”), is
compactness. It describes how efficiently the shape is embedded in space. ”Roundness” measures
are discussed later.
Conventional compacity is defined by shape area/perimeter ratios in 2D, and by volume/surface
ratios in 3D. However, the inverse ratios are widely used under the name of shape factors. Let P , A
C
denote the perimeter and area of a 2D shape (a closed contour) ; a normalized shape factor is then
defined by:
ff 2D = P 2 =(4A) (1.10)
The smallest value, ff 2D = 1, corresponds to a circle, and higher values to more irregular (less
compact) shapes. For this behaviour, some authors call compacity, the inverse of ff 2D , and a non-

compact object is defined as having ff 2D 0 .
O
In 3D, Let S , V be the (external) surface area and volume of an object . A normalized shape
factor is defined by:
p
ff 3D = S 3=2=(3 4V ) (1.11)
In this definition the surface and volume of any sphere constitute the lowest bound f f 3D = 1,
and ff 3D increases with irregularities (e.g., bumps, protuberances, crevices). However, there exist
objects with the same shape factors and enormous differences in morphology. For fractal shapes,
the surface, as well as the perimeter in 2D depend on the measuring scale and tend to infinity with
increasing resolution. The common practice is to introduce some smoothing, which fixes a bounding
scale of measurement. Compacity and sphericity (circularity in 2D) are often treated as different
notions, the latter being defined by morphological operators with a structuring element which size
plays the role of a resolution bound [Serra82], pp. 336.
A second measure of shape complexity is given by the difference between an object and its ap-
proximating ellipsoid. Measures of goodness of fit, dissimilarity or distance to any specific primitive
or other shapes can be obtained in several ways. For example, Bribiesca proposes in [Bribiesca96]
to estimate the ”work done” while transforming one shape into another, after spatial registration and
scale normalization (both shapes must have the same volume). Similarity measures between two
objects or with respect to a selected model of its shape provide thus a relative-complexity measure.
For example, a relative form factor fI with respect to the ellipsoid of inertia is readily calculated: let
O O I I O
S ( ), V ( ), S ( ), V ( ) be the surface area and volume of the object and its ellipsoid of inertia,
I
represented by . We first normalize the ellipsoid principal semi-axes a b c to have the same volume
I O
as the object; thus V ( ) = 4=3abc = kV ( ), with k the normalization constant. Let S ( 0) be the I
surface of the normalized ellipsoid. The ratio
S (I0)=S (O)
fI = (1.12)

satisfies 0 fI 1, and is close to 0 for irregular shapes. To distinguish f I from shape factor ff 3D ,
we call fI the Ellipsoid-of-inertia Form Factor.
Other methods to estimate goodness of fit are part of a spatial registration or matching process,
and are based on mathematical-morphology (MM). These methods use various distance measures and J ”MM”
distance fields, or other ”potential” fields. Malandain et al. and Mangin, review and evaluate several
distance transforms for 3D shape matching (city block, chess board, octagonal and Chamfer distance,
which all give reasonable approximations of the Euclidean distance) [Borgefors84, Malandain93a,
Mangin95].
Shape factors based on measurements over distance fields have been proposed. They are closely
related to goodness of fit, since shape factors are normalized with respect to a common primitive
(e.g., circles and spheres). Danielsson proposed in 2D a ”G-factor” measuring the average distance
between an interior picture point and the nearest boundary point [Danielsson78]. An average distance
d can be calculated from the first-order moment (or center of mass) of the object, normalized to its
area A:
Z Z
d=
O
k~p ; ~q k dx dy /A (1.13)
where ~
p = (x y) 2 O and
~q = arg0 min k~p ; ~q 0 k
~q 2 @ O
is the closest boundary point to ~
p (see Figure 1.4). The G-factor is defined in such a way that G = 1
for the circle, and G > 1 for other figures:
G= A 2 (1.14)
9 (d)
In comparison with the common 2D shape factor ff 2D , the G-factor is insensitive to small intrution
or protrution variations, and describes better large features. Its robustness allows for quick estima-
tions, using only a fraction of all p 2O
in a similar way to second moments approximations. Equa-
O
tion 1.13 shows that the average distance d to @ can be obtained from integration of the internal
O
distance map on all , defined by:
( )
d(O) = (~p k~p ; ~q k) j (~p 2 O) ^ (~q = arg0 min k~p ; ~q 0k ) :
~q 2@ O
The generalization to Nn is straighforward, once discrete distances have been defined. Note that sets
of all equidistant points at a given distance define level sets, such as isocontours in 2D an isosurfaces
in 3D.
∋
p O
∋
dA q O
dA = dx dy
Figure 1.4: Computation of G-shape factor of an object O, by measuring the average of the distance of all
points p~ 2 O to the closest point in the boundary (~q 2 @O). Note the area element dA = dx dy.
The interest in our work of factor G or similar shape descriptors, is their definition in terms of
interior and boundary points, which we are able to extract, traverse or sample in efficient ways, as
described in Chapter 2. To our knowledge, no application of G has been reported in current literature.
Besides shape factors, there exist particular characteristic lengths (e.g., the caliper and Frênet
diameters). Some may be obtained from measures on the equivalent parallelepid enclosing the el-
lipsoid of inertia, or from the convex hull or from other fitting primitives as the maximal included
O
ellipsoid and the minimal ellipsoid containing . We will come back later with the ellipsoid-of-
inertia concept and the object’s principal axes, as we examine its potentialities in our work.
1.2.3 Shape Decompositions and Local Descriptions

A first step in refining the ellipsoid approximation is to break the object into two or more compo-
nents, usually more convex than the original (convexity is examined in the next subsection). In turn,
these may be approximated by elemental geometric shapes. This ”divide and conquer” or construc-
tive approach can be further refined by recursion, as suggested by Cordella and Sanniti di Baja with
CAD primitives [Baja84a], by Ranjan and Fournier, and Rourke and Badler who analyze unions of
spheres [RourkeDS79, RanjanUOS95], and by Phillips et al. and Chaudhuri et al., who use ellipsoids
[Phillips86, Chaudhuri91]. Complexity of the description is defined by the structure of a decomposi-
tion into elliptic elements, its number and their spatial relations. This description can be based only
on connectivity or proximity relationships (see Figure 1.5-right); or hierarchical, through ellipsoid
approximations at different scales (see Figure 1.5-left). In each case, the decomposition may be
coded in a connectivity tree structure or a hierarchical tree structure and further detailed by mul-
tiresolution or scale-space representations of the object. Topology notions are naturally introduced,
beginning with the simple counting of components and subcomponents, including holes and cavities,
and how they relate with their neighboring elements, as well as their organization in nested sets (see
in Appendix A the Definition A.2 and compare with the containment tree structure of Figure A.3 in
pages 231 and 234).
In consequence, if the shape parameters of single primitives constitute the first order elements
to describe complex sets, then the relational elements such as trees, graphs, adjacency matrices and
other discrete mathematical entities become the second-order elements that describe complex sets.
The decomposition or partitioning may be subject to levels of detail or to the number of desired
primitives to approximate a shape. In this case, the problem has similar characteristics to cluster
analysis when the number of classes is unknown. The problem has been studied the other way
h
d i
c
a b f
a
c d e j g
e f
h i
b
g
j
Figure 1.5: Elliptic decomposition of a 2D shape (left) and connectivity tree representation (right). Labels
identify each fitting ellipse and the corresponding clumps are separated by narrow necks. Concavities of the
shape (or, equivalently, background convex components) can be represented by ”negative” ellipses (one
is indicated by the arrow at left). Note that other kind of decompositions are possible (e.g., by proximity,
perceptual groupings, and hierarchical approximations). The criterion for considering ”connectivity” between
components is the intersection of the fitting ellipses.
around: clusters of scattered points (”clouds” of points, usually in feature space) are grouped and
represented as closed regions, whose shape is analyzed (see for example [Edelsbrunner83, Radke88,
Preparata77, Diday70, Diday76]).
It is clear that complexity, understood as ”high number of elements”, has also a Newton-mechanics

counterpart: systems of many bodies (N 3) are difficult to treat by deterministic analysis because
it ends up with high-order and non-linear differential equations with no analytic solutions, and too-
sensitive numerical solutions (i.e., not useful for precise predictions). Thus, image processing or
quantification strategies to treat many-interacting component problems in a mechanistic-like frame-
work may step into a similar many-body problem. Such frameworks may arise in deformable models,
for example.
The decomposition of an object into simpler parts is itself an important topic closely related
to segmentation, multiresolution and MM. If the object cannot be decomposed by discriminating
different densities or colors, an hypothesis or assumption must be made on the grounds of shape
composition. These assumptions may have a functional or physical basis, or consist of the degree of
connectivity or narrowness between clumps, and the size of the separation ”necks” to be identified
(the zones between labels in Figure 1.5-left). Literature repports how superposed discs generate an
arbitrary shape in 2D, and how watershed segmentation or clump splitting through concavity analysis
achieve separation into convex components [Russ90, YeoCLUMP94]. We have ourselves used this
technique for astronomical image analysis [MarquezNGC91, Santiago92]. Held and Abe propose
a decomposition scheme for binary shapes by maximal approximated convex subparts, which may
overlap [Held92]. They also extend the idea of decomposition into meaningful parts [Held94].
Similar techniques exist in 3D (see [Bloch90b, Mangin95] for watershed segmentation exam-
ples). When some degree of non-convexity is allowed, we ourselves have used a partial watershed

3D segmentation by simple morphological iterated erosion (N -times, with N = 3 1) and then
conditional dilation, as described by Márquez et al. and López et al. in [Marquez93b, Marquez94b,
Lopez95, Marquez96a]. Further discussion and a 3D-implementation of this procedure is explained
in Section 2.5.2.
A complementary approach in shape composition analysis is the study of the local tensor of
inertia behavior. We intentionally change the denomination of ”ellipsoid of inertia” to (local) ”tensor
I
of inertia” to stress that the corresponding matrix and moments uv are no more measured over the
O
whole object , but over “small”, “medium” or “large” neighborhoods of each sample point, with
scale categories defined in terms of the size of the smallest and greatest features of interest, (or at
least resolvable). Each point in space then has a local tensor associated with it and its neighborhood.
O I
If is embedded in a heterogeneous region, with other objects, can be measured even in points
O
external to .
1.2.4 Convexity
If the ellipsoid of inertia or scatter matrix may well represent an object in some situations (Classical
Mechanics), it is far from describing further details. The next step to study local and global properties
of a shape is examinating its global and local deviations from the approximating shapes, such as the
ellipsoid of inertia, tangential planes, or from another simplified object that approximates the object
under some criterion.
Before entering into a brief discussion about local convexities, we recall the following definition
of ”convex” in R3 generalizing the one given by Stoyan in [Stoyan94], pp. 353, for R2:
D EFINITION 1.12 (Convex) A set O R is said to be convex when for each two points x x 2
3
O O
1 2
, the line segment x1x2 lies in , i.e.
fx 1 + (1 ; )x2g 2 O with 2 0 1]: (1.15)
At the surface level, details at a point p are constituted by variations in local surface curvature
K (p), at direction , that may be accentuated, diminished or sign-inverted. Such variations are sim-
ply known as ”convexities” or protruding regions, when curvature is positive for all (all directions)
and ”concavities” when they are all negative.
Anisotropic curvatures occur when K (p) changes sign in function of . In this case ”convexity”
and ”concavity” are no more the adequate concepts. The largest and smallest curvatures 1 2 are
used to describe local curvature and always occur in mutually orthogonal directions. Their sign de-
termine three types of local surface curvature (see Figure 1.6):
convex: 1 > 0
2 > 0
concave: 1 < 0
2 < 0
saddle: 1 > 0
2 < 0 (or 1 < 0
2 > 0)
There is still a fourth type of local surface curvature called a ”monkey saddle” with principal curva-
tures having an inflection point, i.e., 1 = 2 = 0 at some point p. A typical example of the presence
of ”monkey saddles” are the networks of tubular structures (e.g., capillar vessels and mouths of
alveoli in the lungs [Weibel79b], pp.89). Examples of the application of these notions are given in
Section B.
Differential Geometry offers a set of concepts for a proper analytical description in terms of local
j j
principal curvatures; the features that can be so described include discontinuities when 1 or/and
j j
2 are infinite or very large. The combinations of all possible cases (e.g., 1 2 > 0) are known
as ridges, valleys, cusps, humps, dimples and corners in surface patches [Koenderink90, Clarysse97].
Differential Geometry becomes a ”heavy” tool for the simplest of cases, and cumbersome to use at
discontinuities and very rough surfaces, but its analytic power is best exploited in models of physical
phenomena on surface boundaries.
(a)
(b)
(c)
Figure 1.6: Surface curvatures in function of local positive and/or negative radii of curvature. (a) Convex,
(b) concave), (c) saddle (extracted from [Weibel79b]).
The size and distribution of concavities and convexities on a surface can be subject to harmonic
analysis. There are many physical phenomena that give rise to repetitive patterns, but also to har-
monic deformations of an object, in accordance to natural oscillation frequencies for example, or
elastic coefficients. Fourier-descriptors in 2D allow to characterize frequency distribution of har-
monic components in a closed or open contour [Zahn72]. Its extension to 3D has not been easy,
because the field of complex numbers extends rather to 4D quaternions.
The harmonic analysis also exemplifies another approach to shape description, treating a shape
as a deformated version of a reference norm or template. In Medicine and Biology, the basis for
anatomical atlases is the construction of a representative specimen or prototype for identification of
major structures and interpretation of the differences, which may be intra-individual (the same subject
at different times or conditions), inter-individual, inter-race, or abnormal. This kind of reference
models are built regardless of other differences, based in specific deformations. The latter may
be natural (from morphogenics, development, environment adaptation or evolution), pathological,
congenital or just statistical. An ambitious goal is then to model and identify the nature of shape
variations themselves.
Convex Hulls and Alpha-shapes. Non-convexity is the most familiar feature of an object irreg-
ularity and can be expressed in several ways. Let O O
be a solid with volume V ( ) and surface
O
boundary @ (cf. Definition 1.3). The importance of concavities and regions with saddle points can
be characterized by the volume differences between the object and its convex hull, defined as follows
[EfronP65, Edelsbrunner85, Santalo76, Chassery83a]:
D EFINITION 1.13 (Convex Hull.)

Let OR3 be an object or a set of points (either connected to form a single object, or with no
structure at all). Let C i be any convex set such that O
Ci, with i = 1 : : : . Then, the set1
\
1
co(O) = Ci
i=1
is called the convex hull of O.
O
A particular case is to consider for Ci the set of half-spaces5 containing . Another way to state
O
Definition 1.13 is that: for each non-convex set there exists a smallest convex set, the convex hull
O
co( ), such that O O
co( ).
A concept that generalizes convex hulls is that of an -shape, or -complex [Edelsbrunner94].
It can be defined as a simplicial complex, that is, a polytope 6, which is not necessarily convex nor
connected, and can be derived from the weighted Delaunay triangulation of a point set. The param-
eter controls the level of detail. An -shape can be defined for a single solid object or for a set of
unstructured points, or small objects.
D EFINITION 1.14 (Alpha-shape)

O2
Let S O
R3 an object. Consider the surfaces ( ) defined by a MM rolling-ball closing operation
O 2
on by a set of spheres R , with 0 1] a real parameter, and R ranging from data resolution
S O
to infinity. ( ) is called -shape, with the convex hull the special case of R = . The surface 1
S O
( ) R3 is defined by [Chassery83b]:
8 2 0 1] 8 p q 2 S(O) : (p + (1 ; )q) 2 S(O) (1.16a)
In the context of shape decomposition into smaller shapes, this definition illustrates an ap-
proach consisting in measuring concavities or other features in function of MM notions [Vincent90,
PitaVene90a, Heijmans94b]. This is interesting in applications where MM operations can be imple-
mented in efficient ways (parallelization or boundary-based).
We note the importance of a surface or boundary representation of the solids of interest. It is
common to define ;1 1
+ , and R as 1=. In this case, an -shape ( ) is defined as S O
follows [Edelsbrunner94]:
D EFINITION 1.15 (Alpha-shape bis)
B
Let (R p) a closed ball of radius R = 1=, centered at p 2 O, and B c (R p) its complement, then,
if > 0 S(O) = Tp 2O B(1= p) such that O B(1= p)
if = 0 S(O) = co(O) (the convex hull)
if < 0 S(O) = Tp Bc(1= p) such that O 6 B(1= p)
2O
A method to generate discrete approximations to convex-hulls and -shapes from boundary rep-
resentations is suggested in Chapter 2. Unfortunally, we were unable to test a program implementa-
tion of this algorithm due to time limitations.
The same as with the fitting ellipsoid, shape features can be extracted from the comparison of
convex hull or the alpha shape of an object and the object itself. This can be done in a global or
in a local fashion. We present in the following paragraph just an example, together with a practical
estimation of the convex hull in 3D.
5
Any plane divides the space 3 in two half-spaces.
R
6
A polytope is defined as the intersection of a finite set of half-spaces.
Convexity-based Shape Factors In 3D, Phillips et al. proposed a simple approximation of the
O
convex hull of an object , called the convex enclosure [Phillips86]. The object is projected into
orthogonal planes, and the 2D convex hull of the projections are used to construct, by boolean inter-
eO
section, a 3D convex shape, the convex enclosure co( ) of the object (see Figure 1.7). They further
O
propose a shape factor that measures the ”convexity deficiency” of , defined by the ratio:
e O)) ; V (O)
Cdef(O) = V (co( V (O)
O
Two important remarks: ramified thin objects and networks have a very high C def ( ), as in the
example of Figure 1.3, where V (co( )) eO O
V ( ). The second observation is that the construction
eO O
of co( ) and the ratio Cdef ( ) strongly depend on orientation of a coordinate system, since they are
based on features from projections on the orthogonal planes X Y and Z . A way to compensate for
this bias is to align the coordinate system with the principal axes.
(a) (b)
111111111100
000000000011
111
000
000
111
000
111
000
111
0000
1111
11111
00000
000
111
000000
111111
0000
1111
00000
11111
000000
111111
00000
11111
1111
00000
11111
000000
111111 0000
1111
000000
111111
0000
0000
1111
0000
1111
00000
11111
00000
11111
000000
111111 0000
1111
000000
111111
0000
1111
0000
1111
0000
1111
0000
1111
00000
11111
00000
11111
000
111
0000
11110000
1111
000000
1111110000
1111
0000
1111
0000
1111
00000
11111
0000
1111
000
111
000000
111111
01 1111
0000
000
111
00000
11111
0000
1111
00
11
000
111
00000
11111
0000
1111
(c) 00
11
Figure 1.7: The convex enclosure. (a) A 3D particle and (b) its orthogonal plane projections. The convex
enclosure is the intersection of the three orthogonal prisms defined by displacing the 2D convex hull (c) of
each of the projections.
In the case of global features, form or shape factors as those presented in Section 1.2.1, can be
better analyzed in the case of convex shapes. The surface area A and the volume V of a bounded con-

vex set Sn in Euclidean n-space Rn are connected by the isoperimetric inequality, A n nn UV n;1
where U is the volume of the n-sphere. If the set Sn is itself the n-sphere, then this becomes an
equality.7
The relations between different-dimensional measures, such as compactness (sphericity or shape
factors) are a special case of the problems on isoperimetric inequalities, which link measures on
boundaries and their contents in multiple-dimensions (thus, they are rather isovolumetric). In re-
cent decades this concept has been extended to include inequalities connecting geometric or physical
quantities that depend on size, shape and configuration of a set [Kiyosi96b], pp. 857. It even includes
inequalities on eigenvalues of partial differential equations under given boundary conditions. For ex-
ample, vibrating membranes possess characteristic modes satisfying different eigenvalue inequalities
7
that shape factors f f 2D ff 3D correspond to cases n = 2 3.
in function of the shape and area of the membrane, and its proportions (as with the length of vibrating
strings)[Polya51].
In a local approach, surface features can be approximated by polynomials, splines, superquadrics,
or other surface patches. In these approaches a new problem is introduced: the compromise of local
fitting versus continuity across patch boundaries. Complexity is then determined by the number of
coefficients, the number of patches and their assembly under matching constraints. Sophisticated so-
lutions have been proposed, as that by Keren et al. who construct a shape model with superquadrics
on an orthonormal wavelet basis, allowing the representation of surface singularities (e.g., cusps,
umbilics, abrupt ridges and other differential discontinuities) [KerenDCO92].
It is clear that these problems and a local differential-geometry approach lead to the concepts of
continuity and coherence; we treat only the latter in the following subsection, in the context of shape
complexity.
1.2.5 Coherence
Differential geometry of curves and surfaces treats mostly smooth, continuous shapes in a rather
local, differential way. Surface discontinuities or singularities are topics of active research, requiring
a special treatment. As the present work deals with discrete representations, we only mention in
this section the relevant issues concerning coherent structures. Most of the other sections in this
chapter deal with some lack of continuity and irregular boundaries that are not ”smooth” at some
particular scale of analysis (or at all scales, in the case of mathematical fractals). Koenderink noted
first the importance of ”scale of analysis” of a shape through the concept of blurred derivatives
[Koenderink90] and scale-space filtering [XinLimHong95]. In fact, most methods dealing with ill-
posed problems involve smoothing and regularization techniques to avoid singularities. Many of
these methods exploit a principle of coherence.
The term coherence in general is defined as ”natural or due agreement of parts”. It denotes the
presence of repetitive patterns, and is the measure in which two or more things stick together, or
maintain a constant relationship or harmony. In optics, coherence refers to certain phase, orientation
or wavelength relationships of electromagnetic waves, and is often considered for a specific wave-
length range. Coherence can also name the similarities or simple relationships between two or more
feature distributions. Such relationships may consist in constant differences, for example. Thus, we
can deduce two general concepts, following Gröller and Purgathofer [Groller95]:
✦ Spatial Coherence refers to spatial homogeneity, consequence of constant or slow varying

relationships in the spatial arrangement of data features, or of the objects themselves.
✦ Object Coherence refers to known local relationships between objects or parts of an object.
As a contribution of the present work we introduce two complementary principles that hold in com-
mon situations:
✦ the Object-Coherence Principle, which stipulates that local neighborhoods are likely to be
occupied by the same objects, and
✦ the Spatial-Coherence Principle, which refers to local constancy of feature values.
These principles can be formulated as hypotheses to be tested for a particular problem. In terms of
pixel or voxel populations with a gray-value label, this local constancy results for example in local
histograms of intensity values remaining constant or slow-varying from one region to another, or
k ; k
from one slice of an object to the next one. Let p1 p2 be two voxels such that p 1 p2 < ", with
N
" > 0 ”small” (p1 p2 are located in contiguous slices, for example); let (p) denote a neighborhood

around voxel p, and H ( ) a value/label histogram of a specified region; then we postule a Label
Coherence hypothesis for p1 p2:
8 " > 0 9 > 0 such that kmode fH (N (p ))g ; mode fH (N (p ))gk <
1 2
(1.17)
where mode fg

is an operator to extract the principal mode of the histogram H ( ) (the most frequent
value of samples fN g
(p1)) ). After several experiences, we observed that this principle holds even if
the object is very complex and even if undersampling or partial volume effects are significant. 8 We
postpone to Section 3.3.2 a further discussion and an application of the Spatial-Coherence Principle,
using a particular color version of Equation 1.17.
Special cases of the object- and spatial-coherence properties have been widely used in computer
graphics algorithms for incremental update operations, that is, to make calculations only when an
important change occurs. This cases include scan-line coherence [Foley92] and span coherence
[Crocker84], but there are also depth, area, temporal, frame, projective, ray, cluster and volume
coherence [Groller95, Max90, Wilhelms91, Hubschman82, Horvath92].
A formal definition of coherence in signal processing and statistics summarizes some of the
above notions as follows:
D EFINITION 1.16 (Coherence)

X
Let t = (Xt Xt : : : Xt )
(1) (2) (p)
2
C p p N t 2 2
R be a complex-valued stationary process,
(k ) (l)
kl
and let S (! ) be the cross Spectral Density Function (SDF) of X t and Xt at frequency ! , with J ”SDF”
2f g 6
k l 0 : : : p and k = l. Then, the quantity:
kl(!) = S kkjS(!)(S!ll)j(!)
kl 2
(1.18)
is called coherence of Xt at frequency !.

(k)
In this definition, coherence kl(! ) is a measure of the strength of association between X t and

Xt(l) at frequency !. Generally, we have 0 kl(! ) 1. Coherence is not a measure of information
contents, but it is rather a measure of order. Complex signals or process far from thermodynamical
equilibrium may present different levels of organization in which coherent structures appear. Several
properties of time series data and stochastic process are expressed in terms of the SDF, the cross SDF,
correlation, autocorrelation and coherence, and are related to moving averages and autoregressive
models (also known as Auto Regressive Moving Average (ARMA) models). It is worth noting that J ”ARMA”
analysis of complex 3D objects in a discrete grid with coordinates i j k can be done in terms of
signal sequences if one coordinate, say k is treated as ”time”, and the other coordinates are treated
as a sequence of image slices i j . In this way, the general definition of coherence is applicable.
We present in Chapter 3.3.2 a problem where the spatial coherence principle is employed as
a working hypothesis for radiometric inhomogeneity correction of color images, when a complex
structure (the bronchial-vessel tree) is present. An ARMA model is also used for description of the
problem and the correction method.
8
We see in Section 3.3.2 that this holds for " > 0 smaller than shape features whose variations are smaller than
H (N(p))).
Directional Coherence We introduce another definition of coherence, in terms of a ”similar-

orientation” principle. Observing the normal vectors on a smooth surface, or the tangential vectors
along a smooth tubular segment, small variations (or no variations at all) correspond to a coherent
behavior: the same average direction. Other feature vectors can be also coherent if they are ”similar”
enough. This can be stated as a local or a global property as follows (see Figure 1.9):
D EFINITION 1.17 (Local Directional Coherence)

O
Let be an object, p 2O N
N
, and (R p) a ball-neighborhood of radius R. Let N N = card( (R p))
be the number of points q , with q 2N V fg
(R p). Let p = ~vi i = 1 : : : NN a set of vectors in R3
(e.g., normals, tangent or feature vectors), associated with p. Let
X
~v =< ~vi > = 1=NN ~vi
~vi 2N (Rp)
f g k ;k
be the average of ~vi and let v = < ~vi ~v 2 > its standard deviation vector. Then, the set p V
N 9
is locally coherent in (R p) iff " > 0 such that v < ".
D EFINITION 1.18 (Global Directional Coherence)

V
Let p a set of vectors associated with each p 2O
. The pair ( O V p) is globally coherent iff
8 p 2 O Vp is locally coherent in N (R p):
A convenient size R of neighborhood of analysis must be chosen. Note that, as with the notation
”-shape”, a more accurate nomenclature is ”R-local coherence”. The Directional Coherence defi-
nitions allows a characterization of tubular structures (see Appendix B, Section B and Figure B.1).
Note that the average < ~v > may vary at each p, but coherence exists if its standard deviation
v remains small. In the case of normal vectors, the lack of coherence is a measure of rough-
ness. The RMS roughness is in fact the standard deviation from average height, a scalar feature
(see Section 5.6). Figure 1.9 illustrates coherence of the normal vector as describing smooth and
textured, rough surfaces. In the case of surface tangent vectors, coherence measures for example
the irregularities of a 3D filament with respect to a smooth version of it. Bifurcation points of a
filamentary structure are characterized by at least ”two directions”, thus, two coherent measures of
the local tangent vector. It also may happen that coherence exists only in some orientations, hence it
is anisotropic coherence. 3D columnar structures and oriented textures are also examples in which a
coherent direction characterizes distributed ”parallel” components.
Local Directional Coherence can be used as a distinctive characteristic of thin tubular structures
and was applied in this work for the design of a discrete tubular detector of bronchial blood-vessels
(see Appendix B). A differential coherence definition could serve to characterize local variations.
N
In this case, instead of small neighborhoods (R p), we must consider surface elements dS on the
tubular structure.
1.2.6 Scales of Representation and Characteristic Lengths

We conclude this section illustrating the notions of scales of representation (usually it is also the
scale of analysis) and of characteristic lengths with an example. We first introduce the most relevant
levels of description used in literature.
Barret separated shape description into three general aspects that depend on scale [Barret80]. He
used the terms:
(a) (b)
n p
d n V
p
N( R, p)
<r >
order
11
00
00
11
Figure 1.8: Some uses of the normal vector ~n of a surface. (a) Local depth or thickness maps in the normal
direction at surface points p also characterize average branch diameters 2 < ~r > in tubular structures. (b)
N
The normal behavior in geodesic neighborhoods (R p) of surface points p help to characterize roughness
features (see Figure 1.9).
nk nk
σ( n k ) ∼
∼0 σ( n k ) >> ε
Figure 1.9: Coherence of the normal vectors of a surface. A small standard deviation of the normal in a local
N
geodesic neighborhood @ (R p) (or surface element dS ) defines a high local coherence, corresponding to
smooth surfaces (left), (~ N
n)k 0, with k indexing the points inside @ (R p). A high standard deviation
( (~
n)k " for some " > 0) in a local geodesic neighborhood (low normal coherence), characterizes tex-
N
tured or rough surfaces. Note that coherence definitions depend on the scale of analysis, that is, the size of
the neighborhood. To define differential coherence small geodesic neighborhoods @ (R p) become surface
elements dS on the tubular structure.
✦ shape for large-scale variations (the general form of an object);

✦ roundness for the degree of smoothness in vertices and smaller variations (concavities, protu-
berances); and
✦ surface texture for short-range fluctuations superimposed to the latter variations.
In terms of 2D Fourier coefficients, some authors describe “shape” retaining the first 5 Fourier
coefficients [Serra82], while what is called texture starts at some level that depends on application
f g
and resolution limits. If A k k = 0 1 : : : are the Fourier coefficients of a radial function r(x y ),
Beddow et al. suggested the following shape measures of 2D contours [Beddow77]:
✦ global structure: X
n1
Ln1 = A2k
k=1
✦ roughness parameters: X
n3
R n3
n2 = A2k
k=n2
2
where n1 n2 n3 N are chosen in function of the shapes to analyze (typically, Beddow et al.
repport the values of n1 = 5 n2 = 5 n3 = 20, as those coefficients bearing “enough”
information, but no justification has been given).
(k)
(b)
(c) (l)
(a)
(m)
(d) (n)
(e)
(j) (g)
(f)
(o)
(i)
(h)
Figure 1.10: Complex shape characteristics in 2D slices as found in hystological preparations. (a), (b) and
(f) show features described at different scales, with arrows indicating characteristic lengths , tangential and
perpendicular to the ”average” contour. (k) and (o) are shape representations at different scales of analysis.
See the text for a more detailed description.
Figure 1.10 shows an example of these and several other aspects of shape description that do
not fit well in the scale-based description of Barret. This shape is representative of hystological
preparations. Circles in Figure 1.10 depict scale variation corresponding to: (a)-(b) surface texture
or roughness details, (c) smooth areas (roundness features), and (f), (h), and (j) large shape features.
Other features, as (g) have with one dimension belonging to subsampling scale (texture scale) and
other dimensions to larger-scales; these features are difficult to detect and to integrate in a shape
multilevel description (notice a perceptual alignment of some (g) features with cavity in (j)). There
are also features that suffer a topology change (connectivity) at different scales of analysis, as from
(d) to (l), and from (g) to (m). We observe that pores (g) bear similarities to surface texture in (b), be-
longing to a smaller scale of analysis, but they may be in 3D the components of thin tubular sections,
or surface variations in other slices (as in (d)). At coarser resolutions as in (m), they disappear or co-
alesce into single gaps, in function of proximity relations. A 3D object may appear in a cross-section
as composed of several features (i), that are mistaken as part of the 2D shape at lower resolutions (k).
1.3 Extrinsic Properties of Solid Shapes 45
At larger scales of analysis some structures are identified as: (j) concavities, (f) protruding regions,
and (h) cavities, tunnels or transversal sections of cavities appearing as holes. With lower resolutions
all these features may remain or gradually fuse into the global shape (o).
Characteristic lengths are sometimes analyzed in terms of an average shape contour as tangential
or perpendicular to this average contour (see Figure 1.10b). The degree of contour smoothing is
a relative notion. Both lengths are also called, respectively, characteristic width k (if parallel or
tangential) and characteristic height or depth ? (if orthogonal). Note that k in 3D gives rise to two
independent lengths. These concepts for 3D irregular surfaces are introduced and used for roughness
characterization in the application described in Section 5.6. page 5d. In this case, instead of an
average contour used as reference, the mean height of a multiple-valued function zk = fk (x y ) is
used to measure k and ? . We have detailed another application in 2D texture discrimination in
[Corkidi98].
High level characteristics in Figure 1.10 such as the alignment of features (h), (g), (e), or the
fisure in (g) and the cavity (j), are extrinsic properties of shapes, and are briefly described in the
next section. The detection and quantification of such characteristics belong to Pattern Recognition
analysis, a subject not deeply studied in the present work.
Scale-Spaces. We have already broadly justified in another section the (vague) terms “small”,
“medium” and “large” applied to scales of analysis (neighborhoods) as being relative to the size of
the features of interest or available resolution. Multi-resolution is the concept introduced to deal with
several scales of representation and analysis at the same time. It has evolved in the last years into a
very rich and growing field in Computer Vision including concepts from human vision, differential
geometry and dimensional analysis. The core of this theory is the study of the structure of the discon-
tinuities in the scale-space, in such a way that analysis is done considering the structure features in
such scale-space and their differential properties. We cannot enter here into details, but just mention
that relevant literature includes works by Koenderink, Lindberg, Haar Romeny, Alvarez and Morel,
Florac, Kimia, and others [Haar90c, Lindeberg92b, Florack92, Alvarez93, Kimia93, Lindeberg94,
Romeny94, Florack95b, Romeny96].
1.3 Extrinsic Properties of Solid Shapes

We mention in this section some features not belonging to a shape per se, but which depend of its
context or configuration in a larger space. This features can in turn be treated as if they constituted
a physical object, having themselves ”intrinsic” properties similar to those already presented (coher-
ence, convexity, isotropy, characteristic lengths, etc.). Most aspects of extrinsic properties belong
to the fields of Pattern Recognition, Gestalt Perception and high-level descriptions. Since we have
focused our work on the intrinsic properties, this section is only a rough overview, but some points
are discussed in the Section 5.8 of Perspectives.
1.3.1 Complex Relations

Timely problems in industry include those posed by highly engineered synthetic fibers (fatigue con-
trol, optimal textile machining [Subhash94]), ultrathin carbon fiber threads, composite parts, or new
materials which require understanding of microstructure, and even of complex woven and braided
structures. Textured layers of fibers (like fiberglass, paper or ”knitwear” fabrics) pose related prob-
lems [Groller95b]. In these researches, few 3D data are produced in similar ways as medical imaging
techniques, but computer simulations of process and material configurations do produce volumic data
and virtual objects that have to be analyzed and compared with available observations of real proto-
types.
When applying ”divide and conquer” strategies to decompose an object into simpler components,
shape complexity is translated into multiplication of elements, features and relations (e.g., intercon-
nections, assembly). There may be interpretative, functional, or physical justifications of how the
analysis or decomposition has to proceed, identifying the object itself as an aggregate, a composite,
or the result of some manufacturing process. In the latter case, prior blueprints, CAD models and
assembling protocols may exist already (prototyping), describing how constituent parts go together.
Additional complexity problems arise due to assembly protocols, in which not only a specific or-
der is required, but several operations must be performed at the same time, or following intrincate
schedules.
Reverse Engineering (RE) consists in obtaining or completing such blueprints and protocols
from an existing man-made object, and it is considered as a complex discipline, relying heavily on
restoration and the tackling of inverse problems. Even in the absence of documentation, a lot of
prior information exists for similar objects and functionalities. Either inverse or direct, it is clear
that engineering and modern technology require very complex descriptions of products and devices,
and these descriptions are attached to the object itself, not only for its replication but for its use and
maintenance.
Virtual copies of museum pieces pose similar problems, but in this case the goal is a faithful
documentation. Available data from sensors (laser scanners, for example) may consist in unstruc-
tured clouds of points, and optimized matching between multiple views has to be done [Benjemaa98,
LiaoMedioni95]. In this case, several reconstruction, filtering and segmentation techniques are ap-
plied, and complex morphological features pose several problems, such as occluded views, physical
access of the sensor, and camera calibration.
1.3.2 Many Bodies and Clusters

When considering a set or aggregate of several objects, the distribution of morphometric attributes
may present homogeneities and reflect an internal structure, a ”shape”. For example, the presence
of two populations of shapes (big and small, or round and irregular) may reveal two superposed
modes of a physical phenomenon, or two distinct phenomena giving shape to a global population.
In a dynamical system, a state transition may be characterized by abrupt changes in function of
some parameter. Section 5.7.3 presents an example of application in which the quantity and inter-
connectivity of components reflect features of a physical process, in function of temperature.
To reduce complexity in a given description, there are at least two situations: a single complex ob-
ject may be described as the result of the aggregation, assembly or interaction of many simpler and
heterogeneous parts. The converse situation arises equally often: clouds of thousands of particles
may be treated as one single (virtual) object, or an associated shape (their convex hull, a morpholog-
ical closing, or other), or as a cluster of objects. In this approach intrinsic properties (e.g., topology
and compactness) are analyzed on the virtual shape.
Complex features may thus appear as perceptual structures of higher order (comprising many
components), and be characterized by proximity and neighboring relationships, distance distributions
and zones of influences. ”Shape analysis” is then translated into studying the spatial organization or
arrangement of the composing elements. Spatial relationships are coded by adjacency graphs and
matrices, where adjacency is defined in terms of contact, distance or proximity measures. These
representations also comprise the topological features of the set in the form of nodes or vertices,
1.3 Extrinsic Properties of Solid Shapes 47
branches, circuits, cycles, Euler number, connectivity, vertex degree, etc. Topology invariances are
one of the most important properties, because two similar objects or patterns can be matched if
corresponding topological features (bifurcation points, holes, centroids) are correctly paired, even if
one pattern is deformed. Hierarchical approaches allow to relax topological conditions, to account
for small variations or noise in these features.
Mathematical morphology operators are often used to intentionally modify topology: a cluster
of nearby objects is treated and measured as a single ”big shape”. As an example in biomedical
applications, we have intensively used traditional closings and openings to identify mitosis for cell-
proliferation analysis [MarquezMIT90, Garza92, Corkidi98], where a virtual shape, the mitosis, is
detected when a definite number of small characteristic components appear clustered together (data

consists of gray-level images of 20 chromosome particles). If the cluster is too open or too closed,
it is counted apart, and textural features are then considered to discriminate them from artifacts.
1.3.3 Complex Objects in Feature Space

From the above paragraphs, when comparing or characterizing several objects, either similar, distinct
or composing together a single object (real or virtual), it is clear that the morphological features and
attributes themselves give ”shape” to clusters, patterns and objects in feature spaces, and the number
of attributes determines its dimension. A familiar case is color, which has several vector represen-
tations in different 3D color spaces (RGB, HSL, CIE, L*a*b, etc.). When a high number of objects
is present, histograms account for feature populations. Another remarkable example are dynamical
systems, whose behavior is studied in parametric spaces, where stability or equilibrium structures
(attractors) appear and present complex, fractal shapes. An important tool to reduce feature-space
dimension is PCA, as described in Section 1.2.1, where only the axes (equal to attributes) that have
the highest value (i.e., those that concentrate most energy) are retained for further analysis.
A particular phenomenon related to shape description is that of feature dependence on spatial
position. Let be a morphometric parameter, say, mean diameter of a particle distribution. In
some situations = f (x y z ) depends on position in some local coordinate system, and there is
a ”gradient” of sizes and, at constant spatial density of particles, mean mass density varies, even if
each particle has constant density. Color and texture distribution on an object or a set of objects are
other common examples of spatial varying attributes.
1.3.4 Complex Representations

When analyzing several representation models, it is not clear how the tradeoffs, approximations,
and rough assumptions (e.g., linearity, symmetry, scale-invariance, first-order relationships) may in-
troduce complex features attached to the model and not belonging to the object or structure being
represented. However, several examples are at hand in which such features are useful. In Scientific
Visualization and Engineering the trianguled surfaces give rise to many models and approaches that
emphasize a particular aspect of a problem, like efficiency, realistic renderings, or physical proper-
ties, and leave room for introducing a priori information. Their complexity allows to introduce, for
example, analytical formulations. Another reason for introducing some degree of additional com-
plexity is the search of linear representations. For example, 3D rigid transforms and perspective
projections are best expressed by 4D homogeneous vectors and quaternions (a special case of 4x4
matrices, or 2x2 matrices with entries in C ). Complexity is thus present in the ways an object is
represented, and the study of minimal-length description is the subject of Section 1.5.1.
Even if fractal sets ideally possess infinite details, they may in turn constitute a simplification in
shape description, since they have scale-invariance properties, easy to describe. If a fractal model
may imply an infinite number of elements (thus, resulting in a ”very complex” representation from
the point of view of ”number of details”), their interrelations are often described in a very com-
pact way, by iterative process. The same as with Fourier and Wavelet analysis (global periodicities
and spatial-localized periodicities), fractal models constitute a well-adapted representation for many
shape-description problems. To understand this and other aspects of irregularity features, we examine
in the following section the subject of fractal dimensions in relation with shapes and morphological
characterizations.
1.4 Fractal Dimensions

Literature on the subject of fractal sets and applications has often reported fractal dimension measure-
ments that are meaningful, over reasonable scale ranges, for virtually all kinds of irregular objects
and data sets. They are strongly associated with intricacy and infinite details. Even if fractal dimen-
sions (or multifractal dimensions) are not a universal morphological feature, its very absence would
constitute a singular feature of complex objects, at least as important as non-convexity, anisotropy,
asymmetry, incoherence, and other ”negative” properties. As many fractal dimensions rely on op-
erational definitions which end up with a graphical plot, even in extreme non-fractal cases, use-
ful information is obtained in the form of a ”signature” (measure versus scale behavior), when a
logarithmic-regression slope is not meaningful (the slope is the fractal dimension).
This section presents some excerpts from a fractal tutorial [Marquezftuto92], updated after fur-
ther bibliographic examination. Abundant illustrations and examples of all dimension definitions and
fractal features can be found in the basic bibliography [MandelbrotFGN82, Barnsley88, Armin91,
Armin94, Armin96, Takayasu90, Marquezftuto92], and we present only the main definitions and
properties concerning irregular structures and sets.
2
We make first a survey of dimension definitions of a set F Rn, and then discuss properties of
fractals in terms of complex shapes.
1.4.1 Dimension Definitions

Excepting d and dT , all the following dimensions take values in R, between the associated integer
dimensions d and dT . Sometimes D alone is used to represent a generic fractional dimension, but is
also identified with the Hausdorff D H or the capacity, or box-counting D C dimensions [Mattila84].
In the following L denotes a linear length size, and L-box a square or cubic box of side L.
1 Remarks. Literature notation (Dsubscript , or dsubscript ), is not homogeneous. We simply adopted lowcase d for (a
priori) integer dimension definitions, and capital D for (potentially) fractional dimension definitions.
Euclidean dimension d Also known as Embedding Dimension d, (or D, when using d for ”dis-
tance”) refers to the dimension of the Euclidean space Rn in which F is embedded (thus d n).
The symbol DE is sometimes used. For a warped surface in R3, for example, the topological dimen-
sion (see below) is dT = 2 and the Euclidian dimension is d = 3. ”Non-Euclidean fractals” is an
ambiguous term (by definition of fractal dimension, all true fractals ”are not Euclidean”), it should
refer to fractal sets embedded in hyperbolic geometry (or Lobachevsky-Bolyai-Gauss geometry), or
elliptic (Riemannian) geometry, but it is sometimes misused in basic literature. All non-Euclidean
1.4 Fractal Dimensions 49

dimensions D satisfy D d. When D is very close to d, the irregularity and roughness features are
accentuated and the fractal set tend to fill the embedding space.
Topological dimension dT This dimension is defined on local properties for all points in a set

F Rd, and corresponds to the intuitive notion of dimension d T = 0 for points, dT = 1 for lines
and smooth curves, dT = 2 for surfaces, etc., without regard of how F is embedded in a higher
dimensional space (that is, it is invariant under homotopic transformations). Thus, d T varies in
function of the scale of analysis. A recursive definition can be given:
(a) dT = 0 if F is not connected (e.g., points),

(b) dT = k k 1 if any p 2 F has arbitrarily small neighborhoods N r (p) whose boundary
@ Nr (p) has dimension dT = k ; 1,
and the intuitive notion follows, because for k = 1, all neighborhood of points in a smooth curve is
just an interval whose boundary consist of two points with dimension d T = k 1 = 0. A closed ;
curve may be the boundary of a point on a surface, and a closed surface defines a solid, etc. The
topological dimension is preserved when a homeomorphism deforms the object. Though there are
severe difficulties for the notion of dimension which would behave that way [Peitgen92].
Similarity dimension DS This dimension measures invariance of F to scale transformations (di-

lations and shrinkings). It is strictly applied only to sets with exact autosimilarity or self-similarity.
However, a non-deterministic definition (stochastic self-similarity) exists, and self-affinity is a more
general terminology denoting statistical scale-invariance. Autosimilar fractals are built from scaled
(maybe also deformed) copies of the whole, and this process is repeated at smaller scales. In Rd, a
;
power law with exponent d D S measures how characteristic feature lengths vary with scale.
Hausdorff dimension DH Also known as Dimension of Hausdorff-Besicovich, it is defined by

the most efficient covering, that is terms of the Hausdorff measure d ("): Let d " R, and let 2
!
N (") = f (d)"d a set of test functions f : R R, such that N (") is the number of discs, balls,
boxes, or any covering, of diameter (size) " needed to cover F . Then, there exists a critical, unique
real value d = DH , which we call Hausdorff dimension of F , such that:
d < DH ) N (") ! 1 and d > DH ) N (") ! 0

d (") is the measure obtained from the covering formed by all test functions, which can be interpreted
as a value between length and area, area and volume, etc. A square has an infinite number of points
0 , an infinite ”length content”9 1 , it has a finite, non-zero area 2 , constant for any ", and a zero
volume 3 . The Hausdorff dimension is the most useful definition of fractal dimension, but it is
difficult to calculate. So, it is customary to estimate D H using the similarity dimension D S , or the
capacity dimension DC , defined in the next paragraph.
Mandelbrot gave three definitions of fractal. The first comes from the intuitive etimology of his
coined term (fractus: fractured (irregular), fragere: fragment, fraction). The second introduces the
concept of self-similarity: a fractal is a shape made of parts similar to the whole in some way. The
third definition is the technical accepted one, using D H and dT : A fractal is by definition a set for
which dT < DH < d; that is, the Hausdorff Besicovitch dimension of the set strictly exceeds the
topological dimension [MandelbrotFGN82].
9
Defined for example as the perimeter of a Peano curve filling the square, the covering being segments of size ".
Capacity Dimension DC
Also named box counting dimension [Voss86, Falconer90], defined by covering with identical
spheres, cubes or other test elements. DC is usually estimated by counting the number N box of cubic
L-boxes, containing at least a point (or pixel, voxel, etc.) of the set. For example, if Lmax is the size
of a square gray-level image, its capacity dimension DC is defined by:
L DC
Nbox(L) = max
L
Where Nbox is the number of cubes occupied by a pixel value in the 3D space defined by the image
coordinates and the intensity axis. N box is calculated for different sizes L, and a linear regression
on the coordinate plane log(Nbox) log(L)] allows to estimate DC . As an example of application,
Chuang et al. report [Chuang91] the measurement of DC of the brain surface, as a measure of its
convoluted shape. The drawback in their method is to measure discrete surface area as ”number of
voxel faces”, introducing an important error which may explain the mismatch between their result
and other measurements [Majumdar88]. We introduce in Section 2.5.1 a corrected surface estimation
for anisotropic voxels.
Information dimension DI
Probability distributions of samples from F allow to define D I . It applies to stochastic distribu-
tions of points and can be calculated by uniform sampling of space into N cell cells of length L (or
”L-boxes”). Let Pi (L) the probability that one randomly chosen point is in the ith cell. Then the
I
information (L) is defined by [Takayasu90, Taylor91]:
Xcell
N Xcell
N
I ( L) ; Pi (L) log Pi(L) with Pi(L) = 1
i=1 i=1
and the information dimension (or entropic dimension) D I is defined if I (L) follows a logarithmic
law:
I (L) = I (0) ; D I log L
qth-order information dimension Dq This is an extension of D I . Dimensions DC , DI and the

correlation exponents result to be special cases of D q . Several dimension features associated with
fractals can be obtained from the probability P (m L) of having m points (pixels, voxels) inside a
L-box. Mandelbrot [MandelbrotFGN82], Sarkar and Chaudury [Sarkar92] proposed to calculate the
moments M q (L) of the distribution P (m L), for all L:
( PN mq P (m L) if q 6= 0
M q (L) = m=1
1 if q =0
M (L) = M 1(L) is called the mass dimension. The q th-order information dimensions D q are
then defined from the expected value of the logarithmic derivative of the moments, with respect
to L, which is a formal way to express linear regression, that is, the estimation of a fitted line by
least-squares, with slope D q , to a cloud of n point samples (log L i log M q (Li)), with i 1 n]: 2
8 D ∂ log M q (L) E
>< 1=q ∂ log L if q 6= 0
Dq = > ∂(PN log mP (mL)) (1.19)
: 1=q m=1∂ log L if q =0
where < X > is the expected value of the random variable X , and corresponds in practice to
selection of some (few) samples of L, covering the range of scales where the fractal is defined. The
operation
∂ log M q (L)

∂ log L
is the expected value of the slope D q at a particular point (L M q (L)) in log-log scale. To avoid
O
confusion with the boundary of a set, @ , we use symbol ∂ to denote partial derivatives but also
employ rather the discrete notation log M q (L )
i
log Li
2
with i 1 n] to indicate linear least-squares fitting of n samples.
Lyapunov dimension DL
This measure is used to characterize the dimension of the chaotic attractors 10. It is defined in
terms of the first two Lyapunov Characteristic Exponents (LCE) 1 2 as:
DL = 1 ; 1 =2
The LCEs 1 2 give the rate of exponential divergence from perturbed initial conditions of a sys-
U
tem [Chirikov79]. LCEs are defined in terms of the average deviation (t) from the unperturbed
evolution of the system at time t:
i = tlim
!1
log kU(t)k
i 2 f1 2g:
We only mention here the relevance of dynamic systems in the study of complex structures as
a two-way relation: non-linear dynamic process give rise to very complex physical structures (from
atoms to storms, and even organisms, viewed as stable (homeostatic) processes). At the same time,
a geometrical description of the phase space (or state space) of a dynamic system involves complex
shapes or point configurations, often fractal, which constitute the chaotic attractor.
Spectral dimension D ~
It is related to random walk properties on fractal structures. ”Spectral” or fracton dimension is
useful to describe the kind of physical process confined within a fractal network or generating such a
structure (aggregation process). As computer simulation of these systems involve Brownian motion
(the random walk trajectories of interacting particles), understanding of such process is related to
shape of the resulting structures. An example of this relation is given in the Appendix C, where
a Kardar-Parisi-Zheng (KPZ) equation predicts roughness in amorphous deposition. It is to note
that D~ and other dimensions are different of each other because they contain different information
(temporal behavior, probability transitions, harmonic composition, and many others, some not yet
fully identified).
Minkowski or mathematical-morphology dimension DM
A Mathematical-morphology dimension may be formulated in terms of Minkowski addition and

subtraction operators, thus, we give an operational definition. Let X E Li represent the mathematical
morphology dilation of set X by a structural element E Li of characteristic size Li i 1 Nscales]. 2
Here, ELi plays the role of the L-box coverings. Usually E Li are disks of variable radius i =
10
The attractor of a perfect elliptical orbit of an object around a planet, is a single point in phase space (velocity
and position), while systems far from equilibrium possess fractal-shaped (or ”chaotic”) attractors, also called dissipative
structures, because energy is dissipated from the system. In general attractors are the limit set of an iterated map
2
Li , with i 1 Nscales]. Each sampled point on the boundary of an object (@F ), is dilated (the
equivalence of being covered with disks) to create a dilated boundary called the Minkowski sausage
with an area:
A(Li ) = A(@F ELi )
The Minkowski dimension D M , is calculated from the relation:
A(L) / L2;DM
by linear regression on log A(L) vs. log L. Note that D M is a particular case of the box counting
dimension DC , but with emphasize on MM operations. The wide use of discrete MM in Image
Processing and in our discrete boundary approach makes DM an interesting shape feature.
An alternative definition was given by Serra in [Serra82], suggesting a linear regression on
2
log A=(2L) against log L. He uses i as the resolution scales, i 1 Nscales] of a sequence of
images, and Nscales dilations with a single structuring element B , the unitary disk. Using his nota-
tion, we replace Li by i, and ELi by iB . He then calls ”length of the boundary set” the following
A(@F iB)
quantity:
L(@F i) = 2i
which allows further interpretations. In the continuous case, for example, a self-similar fractal con-
!
tour has infinite length (perimeter), at the limit of i 0.
Table 1.1 summarizes the dimensions above discussed and includes some other definitions found
in the literature. Several other dimension definitions are possible but it is clear that many of them
are not conceptually different, and some of them are just different ways to estimate a few important
fractal dimensions: DH DC DS Dq or to measure very particular features, or scale and lengths in
different spaces or different metrics. Just to cite an example, the chemical distance introduces the
graph or chemical dimension, meaningful in the study of percolation clusters.
Table 1.1: Summary of dimension definitions and characteristics. F is the set under analysis
Symbol Nomenclature Description and characteristics

1.4 Fractal Dimensions
D Fractal dimension Generic term often identified with DH or DC

d Euclidean dimension Dimension of the Euclidean space in which F is embedded, d N 2
dT Topological dimension Locally defined, invariant under homeomorphisms, d T N 2
DS Similarity dimension Defined for strictly self-similar objects
DH Hausdorff dimension Defined by the most efficient covering
DC Capacity dimension Defined by covering with spheres, cubes, etc.
Dp(x) Pointwise dimension Defined for a point x in function of its neighborhood
DI Information dimension Calculated from probabilty distributions of samples from F
Dq qth-order information dimension An extension of D I , using the moments of the distribution
DL Lyapunov dimension When F is a chaotic attractor, D L characterizes its dimension
D~ Spectral dimension Related to random walk properties on fractal structures
D^ Spreading dimension It describes fractal connectivity and is not restricted by the embedded space
D(L) Scale-dependent dimension Generalization of a dimension as a function of observation length
Dcor Correlation dimension Defined from the correlation integral and related to attractors
D Scale-space dimension Defined in linear scale-spaces with Gaussian kernel
DM Minkowski dimension Defined by banks of mathematical-morphology operators
53
1.4.2 Morphological Features of Fractals

In addition to formal definitions, several types of fractals have been identified, in function of how
they are embedded in space and to what features refer their fractal dimension. To mention three
examples:
Surface or boundary fractals: Dense objects where only the surface or boundary is scale invariant
[Russ94]. Its fractal dimension characterizes ”roughness” of the surface. A classical example
in 3D is the brain cortex and mountain reliefs.
Mass fractals: Fractals in which both the internal structure (mass distribution) and surface are frac-
tal (Pfeifer, 1989; Gouyet, 1991; Russ, 1994; Zahid and Ganczarczyk, 1994). Its fractal di-
mension characterizes the space-filling ability. Natural examples are the blood-vessel system
of the lungs, botanical trees, and lettuces. An artifical example is found in some communica-
tion networks.
Pore fractals: Dense objects in which hole or pore structure and its distribution are fractal (Gouyet,
1991; Russ, 1994) or the pores and surface have similar scaling properties (Pfeifer, 1989; Zahid
and Ganczarczyk, 1994). Some natural sponges constitute an example.
We finally give in this section a summary of qualitative salient morphological features of fractals.
A. Roughness. Fractals are too irregular to be locally described with conventional Euclidean geom-
etry.
B. Fine structure. Details appear at arbitrary small scales; i.e., the Fourier spectrum of a (mathe-
matical) fractal signal has infinite suport.
C. Fractional associated measures. Not only the spectrum of a fractal signal is infinite (details at
all scales), but the autocorrelation (power spectrum) function of a fractal time series f : R R!
has a particular curve shape: if linear, it may have fractional slope. Similar features can be
observed for 2D or 3D curves and surfaces. In order to describe signal or system properties of
fractal process by integral transforms and differential equations, the need arises to introduce
fractional orders of integration and differentiation. For example, a fractional Brownian motion
”fBm” I (fBm) can be described as a fractional ”integral” of white noise. fBm has been successfully
used to describe natural reliefs, for example.
D. Scaling. Fractals often exhibit ”scaling”, self-similar or autoaffine properties, that is, features are
unchanged by scale transformations, or they can be described as being copies of the same
set at a different scale. This scale-invariance may be exact (periodic fractals), approximative
(deterministic fractals) or statistical (random fractals). Conversely, and for a fractal object or
set of points, its dimension is a scale-invariant feature, describing the ratio of the number of
features at one scale to the number of features at another (larger) scale. A deterministic and
real fractal exhibit a constant ratio, independent of the scale.
E. Recursive construction. Autosimilar fractals admit a recursive description and construction, or
can be defined by component organization rules using conventional geometries, becoming the
limit set of iterative process f k+1 g(fk ). Even non-deterministic fractals may admit an
approximative model through stochastic constructions. An example is the Iterated Function
”IFS” I Systems (IFS), introduced by Barnsley [Barnsley88], and often used in fractal compression.
These systems specify affine transformations and sets of probabilities to make of any shape or
data set the attractor set of an iterative process that approximates the shape.
F. Non-integer dimension. The ”fractal dimension” (as defined operationally or theoretically esti-
mated) is a non-integer number, larger than the topological dimension of the object. There are
sets that exhibit some properties of fractals (self-similarity, infinite detail), while having integer
dimensions (the Peano curve, the Hilbert curve and other space-filling sets, for example).
G. Space-embedding properties. Fractal objects may be considered ”to lay” between points and
segments, segments and planes, planes and solids, but they may tend to fill or occupy space in
many other ways: aggregated clusters and porous media, branching structures, complex sheets
and manifolds. In function of the fractal, its dimension measures roughness features (high or
infinite length/surface or surface/volume ratios) and its space-filling capabilities.
H. Measure of contents. Their content measure depends on the working dimension: it may be ”in-
finite” in the greatest lower integer dimension next to their fractal dimension, or ”zero” in the
least upper dimension, and finite at the fractal dimension of the set. A fractal contour has
”infinite” perimeter, even if its area is bounded. Discrete contours samples (polygonizations)
yield perimeter estimations which depend on the sampling resolution, and increase logarith-
mically with the negative logarithm of the resolution ”yard-stick” (in other words, in a log-log
scale, perimeter is proportional to resolution). The implication is that there exist content mea-
sures between cardinality (number of points) and length, or between length and surface area,
between surface and volume, etc.
For the objectives of our work, we will keep in mind properties G and H , because they relate
fractal properties with boundary morphology, and warn us against dependence of boundary contents
on resolution, when the boundary is fractal. It is interesting to note that early works in Quantitative
Microscopy noted this problem, advising biologists and material scientists to well indicate the res-
olution of their morphometric measurements such as the form factor, which depends on perimeter
[Russ90].
It is interesting to note that fractals and other complex objects are not necessarily described by
”complex” or even long descriptions. Simple formulas for allow to obtain billions of digits of its
infinite decimal representation. Short descriptions are often the case of popular fractal sets, where
procedural descriptions allows a short piece of computer code to recreate with any desired precision
M
otherwise infinitely-describable sets. The classic example is the Mandelbrot set , mathematically
defined by:
M f 2 jn j j 1 2 g
= c C lim fn (z ) < z C
!1
where fn (z ) denotes the iterative process:
fn+1(z) = f (fn (z )) for any n and

f1(z) = z 2 + c with c z 2 C
fn(z ) is also known as the quadratic map, often written as:
zn+1 zn2 + c with zn c 2 C z0 = 0:
A finite region of C is usually explored and zoomed-in, showing unending details. These formula-
tions, and the corresponding computer program to visualize M are not only finite but very short. In
the other hand, non-mathematical descriptions (graphical and verbal) are unable to exhaust the infi-
M
nite details of . The boundary @ M is extremely complex at any resolution, with curled, ”hairly-
like” features, and the ”main theme”, the overal shape M of Figure 1.11a, reappears frequently at
different scales (see for example, at the center of the left inset, Figure 1.11).
In Section 1.5 we describe how complexity measures are based on the minimal length of a de-
scription. In this sense, M should be a ”primitive”, as one could intuitively expect from a simple
2nd-order mapping.
1.4.3 An Example: Particle Aggregates

One of the richest models of irregular fractal structures is the Diffusion Limited Aggregation (DLA)
”DLA” I process [Witten83]. This process considers random walk realizations of particles on a diffusive
medium, under a set of (physical) constraints (e.g., force fields, interactions, viscosity and stickness).
It is simple to describe and has enabled successful Monte Carlo simulation of many physical and bi-
ological process, such as electric discharges, dendritic growth, bacterial colonies, deposition process
as those described in Chapter 5.1. Mathematical models exist to predict some associated macroscopic
quantities: size, fractal dimension and roughness of an aggregate in function of time process.
Figure 1.12 shows a typical simulation of discrete, two-dimensional DLA in a square lattice.
A mass m of about 15000 random-walking particles fall into the central cluster (initially a single
foxed point) forming dentritic branches that restrict movement of incomers. In a ”solid” circular
/
aggregate, mass and radius at time t (in cycles equal to particle life) follow a squared law m t rt2,
for all t. In a DLA cluster, radius increases faster, due to unfilled gaps, following for long t ranges
a fractional-power law mt / rtDC , where DC turns out to be the fractal capacity dimension of the
aggregate. In this example DC was calculated by linear regression of N samples log mk versus
log rk k = 1 : : : N .
1.5 Notions and Measures of Complexity

There are more than 30 measures of complexity proposed in the literature [Gell-Mann95, Gunther94],
but they may be broadly classified into two categories: Static or Dynamic Complexity [Turney90,
Turney90b]. The first addresses the question of how an object, set or system is composed and what
features best describe it. These questions do not depend of the process by which structural informa-
tion is encoded. The second category tackles the question of how much dynamical or computational
effort is needed to describe the information content of an object, set or state of a system. While the
first measures may influence the second (the shape of an object or the configuration of a system deter-
mines its description), both complexities are not equivalent. An object or system may be structurally
simple (i.e. have a low static complexity) but it may have a complex dynamical behavior. As we are
also using the term ”dynamic system”, to avoid confusion we refer to Static or Dynamic Definition
of Complexity.
High cardinality is perhaps the most important property of what is called ”complex”: high num-
ber of elements, inter-connections or features, number of dimensions, size (data volume or high-
resolution representations, in order to preserve fine details), high density of details (related to high
frequencies), and other information in the form of structured relationships and lengthy descriptions.
Simple shapes or configurations may be related to dynamical complex problems (combinatorial com-
plexity): the problem may become intractable because of the huge number of combinations of basis
elements, or bancs of filters for specific data extraction.
Literature on ”Complexity” is highly devoted to computational complexity theory. Besides math-
ematical interest per se, one reason is that complex objects or phenomena are best studied through
systematic descriptions (i.e., computerized), and experimental observations that produce digital data.
Since their study proceeds also through isomorphisms with data structures, computer algorithms pro-
(a)
(c)
1.5 Notions and Measures of Complexity
(b)
Figure 1.11: The Mandelbrot and the Julia sets. (a) The interior of M consists of all points not mapped to 1 after N iterations of the quadratic map
57
zn+1 zn2 + c, with c 2 C , n 2 0 N] and N 0. (b) A Julia set Jc is defined for a particular value of the parameter c as the quadratic map iterated
for all z in a region of C . (c) In the inset at left a magnification 12000 shows the region where c lies (c = ;0:745429 + i0:113008). The shape (b) of this
particular set Jc has no interior points.
(c)
(a)
rc
rb
(b)
Mb α r 2 M c α r 1.27
b c
Figure 1.12: Computer simulation of two dimensional diffusion limited aggregation. A discrete fractal cluster
is generated by aggregation of random-walking particles (a) interacting in a central force field where F /
1=r2. In a non-fractal solid, mass m increases following a squared law with radius (b). Mass in a dendritic
cluster follows a fractional power law of radius (c), with r c rb greater than the discrete grid resolution.
vide testable methods of analysis and description, and give quantifiable means to synthesize and/or
analyze such data.
”CC” I Computational Complexity (CC) is related to the time or memory storage requirements for com-
puting some function, and Algorithmic Information Content (AIC) is the most widely used measure
of CC. Measure AIC is defined as the length of a computer program required to generate the data.

For instance, consider various time series of 1’s, 0’s. The sequence 11 1 has minimum AIC, and a
random sequence has maximum AIC. However, this definition of complexity is unsatisfactory. This
is because a page of randomly generated characters would have higher AIC than a classic-literature
text. It is rather desirable to discover the regularities in the time series data, and be able to compress
these regularities in the form of models. Effective complexity is the AIC of the description of the set
of regularities and their associated probabilities (for a detailed description, see [Gell-Mann95]). In
practice, this is computable only as an upper bound.
1.5.1 *Kolmogorov Complexity

*These two Subsections can be skipped or just browsed in a first reading.
”KC” I Kolmogorov Complexity (KC) is a modern notion of randomness dealing with the quantity of
information in individual finite objects; that is, pointwise randomness rather than statistical random-
ness [LiKolmo93]. Such notion is not possible to define by applying Shannon’s information theory
1.5 Notions and Measures of Complexity 59
because, unlike Kolmogorov measure, information theory is only concerned with the average in-
formation of a random source. The KC measure is known variously as ‘algorithmic information’,
‘algorithmic entropy’, ‘Kolmogorov-Chaitin complexity’, ‘descriptional complexity’, ‘shortest pro-
gram length’, ‘algorithmic randomness’, and others.
We saw in Section 1.2 a common example: geometric primitives are used to approximate shapes,
and data analysis follows often a pattern recognition approach where raw data are organized into ”fa-
miliar” shapes: signals, time-series, images, cluster of points in feature spaces, and so for. Template-
matching is a formal approach in Computer Vision to generate reference data, and evaluate the
matching of a given sample with the template. In more general terms, data from diverse phenom-
ena can often be expressed as a decomposition into unities from a dictionary or basis of primitive
elements, functions or procedures with known properties (templates, Fourier cosinusoids, wavelets,
affine transformations, banks of filters, orthogonal functions, and spline-meshes are common ex-
amples). We suggest that primitives have not to be ”simple” in the classical sense, and ”complex
primitives” can be used as far as their description and realization is compact.
In this analytic approach, once a descriptive basis is selected, comparisons and measures of sim-
plicity or complexity can be sometimes stated in terms of the decomposition spectrum of the object
in a given basis of primitives. For example, IFS fractals are described by a set of geometric trans-
forms (a ”basis”) and a set of probabilities in a Markov-1 sequence, that play the role of (stochastic)
coefficients [Barnsley88]. Fractional Brownian motion is a related example, using Fourier filtering
[MandelbrotFGN82, Mandelbrot68]. A third example is found in botanic trees and blood vessels,
which can be roughly described as being composed of tubular elements of different radii and lengths,
whose relationships are distinctive of the species [West97]. When the basis of primitives is very large
(starting at the hundreds, to say a number, but it may be infinite), its specific distribution can also
take the form of a space of possible states, and then a probabilistic description allows to formulate
;P
the decomposition approach of a set of data in terms of information theory and statistical mechan-
ics, with the Shannon entropy (H = i pi log pi ) in mathematics, or equivalently in physics, the
Boltzmann-Gibbs entropy (S = k log W ), with pi , discrete probabilities, W the number of possible
states with the same energy as the state of the system, and k the Boltzmann constant. In physical sys-
tems, entropy quantifies the amount of randomness or disorder, and the unavailability of a system’s
energy to do work, while the more abstract probabilistic definition is rather linked with information
contents, and efficient codification. As data compression depends on randomness, it results again to
be a measure of the latter: an absolutely random sequence cannot be compressed (reduced).
Randomness or regularity of the basic features chosen to represent an object can be studied and
simulated, and the complexity measure of the computer program to reproduce such an object (or an
instance of its class, given a probabilistic description) can be used to characterize the complexity of
the object itself. The problem of using such description is that if the random law is completely known,
the program may be very simple and the object not “complex”, under this approach. The knowledge
of a random law becomes also closer to a deterministic description; thus the available information,
and how is it coded, is also an element to measure complexity. There are still other definitions of
complexity, randomness and disorder, linked to dynamical systems and thermodynamics, such as the
Kolmogorov-Sinai entropy.
With all these notions in mind, we can state the concept of Kolmogorov Complexity (KC), firstly
in words: KC deals with measures based on the length of minimal description of a set of data.
Given a finite string x of characters (the postscript file of this thesis, for example), its KC measure
is the length of the shortest program in a Turing machine code, in binary bits (or say, in C langage),
which prints string x without any other input. It is assumed that any pattern can be somehow coded
O
(described) into a sequential string x of symbols. In the KC sense, an object is more “complex”
Q O
than an object , if the minimal description x of is longer than the minimal description y of . Q
This intuitive idea can be precisely formulated (see below).
A last remark is that difference of KC with Shannon’s entropy H , as a measure of disorder, can
be stated as follows: H is a quantity for measuring the randomness of random variables, while KC
is a measure of randomness of individual objects based on logic arguments instead of probability
[Kolmo68, Chaitin77]. We now give a more rigorous definition, following Kolmogorov’s one and
our interpretation:
2
D EFINITION 1.19 (Kolmogorov-Chaitin complexity) Let x X y Y , with X Y sets of con- 2
structive objects (as strings of primitives, ordinal numbers, ...), and let A : Y f
1 2 : : : N X g!
and B : Y f 1 2 : : : N g! X be partial recursive functions, and N N Ẇe define: 2
min j 9 2
KA(xjy) = n2N(log2 n A(y n) = x) if ( n N) A(y n) = x
1 otherwise (i.e., no ”n” exists)
(1.20)
The function A is said to be asymptotically optimal iff
(8 function B ) (9 constant C ) (8 x 2 X y 2 Y ) j KA(xjy ) KB (xjy ) + C

(1.21)
j
For an asymptotically optimal A, which is known to exist, K A (x y ) is simply denoted K (x y ), and j
is called the Kolmogorov-Chaitin complexity of x, given y .
The interpretation (or at least one intuitive interpretation) of this definition is similar to that al-
ready given as minimal description length (of the strings of primitives). Constant C is the worst-case
“offset” between two sets of descriptions A B , given a certain knowledge or information (repre-
sented by y Y ). A B are a mapping between interpretations (e.g., descriptions in a human lan-
guage) of objects x and ordinal numbers in order to enumerate them, then compare two indexed
6
strings A(y n) A(y m) n = m, and choose the shortest corresponding to the described object x.
Note that constant C ensures that in a great number of descriptions, two sets A, B give (if A is
j
asymptotically optimal) similar complexity measures K A (x y ) KB(x y ).11 j
1.5.2 Information Theory, Algorithmic Entropy and Scientific Observations
It is worth to note that The Shannon Information Theory doesn’t allow to directly define the entropy
of a single state in a physical system (for example), among a number of them (the ”ensemble”, for
which H has a clear meaning). This difficulty is solved by the notion of algorithmic entropy, in
addition to physical entropy, and for completeness, we just give its definition, using KC [Li92]:
D EFINITION 1.20 (Algorithmic entropy) The algorithmic entropy of a microscopic state of a sys-
tem is the Kolmogorov complexity of that state.
The relation of scientific observations and test of hypotheses with probability theory is natural:
to make a compact description of a set of observations or hypotheses, an observer has an infinite
11
N
The enumeration of strings, propositions, models and theorems (i.e., an isomorphism with ) and the application of
mathematics on such numerical encoding, comes from the diagonal method introduced by Cantor to show that rationals
are infinitely countable. Kurt Gödel used a similar strategy to build his theorem about Incompleteness or Inconsistence
of formal systems. It is thus not surprising that other works on Kolmogorov’s literature deal with metamathematics,
interpretation, model theory, and metalanguages [Li92, Li95, Gunther94].
1.5 Notions and Measures of Complexity 61
X
binary sequence as the outcome of an infinite sequence of possible experiments on some aspect
of Nature (decidability is assumed). Description of X is done through its underlying regularities,
and a ”true random” or ”absolutly random” sequence is its own minimal description, and cannot be
X
compressed [LiKolmo93], pp 46. An investigator tries to formulate a theory governing , which is
consistent with past experiments (observations), and candidate theories or hypotheses are identified
with computer programs that compute binary sequences starting with an observed segment of (the X
N first outcomes). Randomness modeling and simulation continues to be a critical step in hypothesis
testing and prediction [Bosch94], so again, computer programs and Turing-machines enter directly
into descriptions of complex data and structured hypotheses about them (dynamic definition of com-
plexity). The search for regularities is an effort towards simplification, understanding and extraction
of relevant features.
Thus, complex sets of data, even if obtained from static spatial objects, relate with physical
systems through their (minimal length) descriptions. The question of how to code descriptive infor-
mation is addressed by concepts such as entropy and KC, which are associated with computation and
information theory. The association between objects and physical process is particularly verified for
biological objects, which result from growth process and shape formation (morphogenesis), through
long interaction with their environment. This interaction follows ”iterative construction rules”, as
those to generate fractal shapes, and they may appear at different scales. Literature on complex
dynamical systems has been enriched with further examples, the most popular being the Julia sets,
mathematical objects generated by iterative mappings (see Figure 1.11). When a data set is the result
of a natural stochastic process, it becomes natural for a researcher to simulate and try to recreate its
structure and features, through computer models of its originating process.
In this very sense, many features of a complex object are statistically predictable from a complete
description of the process, and it suffices for most practical purposes the study of the generating
process, rather than the detailed morphology of the outcomes.
In the Shannon’s classical Information Theory, a quantity of information is assigned to an en-
semble of possible messages. When all messages are equally probable, this quantity is the number
of bits needed to count all possibilities. To introduce the notion of Kolmogorov Complexity, let’s

take the example of number description with four large numbers: 2 1015, ”one followed by fifteen
sevens”, 1983772192133487 and ”the surface of Jupiter, in m2 ”. These four numbers are of similar
order of magnitude but their description is of different length and spelled in words the first and the
third have a different complexity, which comes from some kind of regularity. Note that the second
description does not provide exactly the same information. Such regularity can be made relative to
a system of reference given by a numerical basis or a language. Taking for example ”the surface of
Jupiter” value as the unity, and the other numbers as the surface value of other masses, all numeric
expressions change, and the first can be as long as the third.
In the approach of Shannon, the meaning of a message is ignored, as we are only concerned with
the communication between sender and receiver. Algorithmic Complexity was then introduced by
Kolmogorov as a measure for the information content of individual objects (messages) [LiKolmo93].
Other important measures of complexity closely related to KC and to shape complexity are: Com-
putational Complexity (CC), Logical Depth, Instance Complexity and Long distance correlation
[SerraR88, LiKolmo93].
KC and related measures have shred light into several vague notions that have been used in infor-
mal fashions, and made clear their relationships with randomness and order. For example, complexity
measures have aided to formulate precise definitions of ”simplicity”, relating this concept with the
empirical principle of economy (or ”Occam’s razor”) used to choose, from several hypotheses, the
”simplest”. It has been demonstrated [Bosch94] that ”simple” not necessarily corresponds just to
”minimal-length descriptions”. Another practical notion is that of ”complicated”, which qualifies the
fact of using a long description, when there exists a much shorter.
Relevance of Kolmogorov Complexity in Shape Analysis It has been argued by Edmonds [Edmonds95]
that KC is a weak definition of complexity in Biology, because it describes the difficulty of compres-
sion of a representation, as limited by storage and algorithmic difficulties in computational biology
and morphogenetic description methods. He argues that this difficulty has little direct connection
with the practical aspects of a functioning organism, and that is presumably used because it is a well-
understood formalism. Literature presents few quantitative applications of KC, since it is difficult
to extract minimal-length descriptions. KC is also a relative measure which depends on available
knowledge and of sets of symbols (in fact of languages and grammars that code the measured de-
scription), all which have prompted rigorous formulations and several levels of abstraction, difficult
to conciliate with natural-Science and real-world applications.
Besides better ways to measure KC, and to be a useful parameter in shape analysis (e.g., tex-
ture discrimination), KC and other complexity measures demand an effort to design minimal-length
descriptions, thus, optimal computer algorithms. In practice the concern of speed and memory cost
tends to produce additional length, since data analysis and modeling are inherent to description. This
overhead appears in the form of theoretical considerations to justify ad-hoc algorithms. To exploit
KC theory results, it also demands higher level descriptions, abstraction and codification into existing
mathematical structures.
In a first approach, we propose to measure the length of the discrete-boundary representation
of a scene. A way to do it is directly linked with a standard compression method, the run-length
coding of binary objects in 3D. In some applications, octrees are more efficient, but it suffies to
translate an object by one voxel to have a very different octree representation. We describe three-
dimensional run-length coding in Section 2.4.4 and how we relate this compression method with
boundary representations, enabling to obtain a complexity measure based on a description length.
Fractal Sets in Computational Complexity (CC) When considering the CC size of an algorithm,
an estimation of the order of the number of operations O(L), is made, with L the number of elements.
”ROI” I In 3D, L may be the number of voxels of a Region Of Interest (ROI) , or the resolution L = N X

NY NZ . For simplicity, assume N = NX = NY = NZ , thus L = N 3, and an algorithm
which depends linearly on volume size is said to be of CC equal to O(N 3). Independence of the
”complexity of the scene” is claimed as an advantage in the performance of many rendering methods,
for example. When dealing with boundaries, perimeters and surfaces, performance estimations may
strongly depend on the shape and the analysis resolution, in a similar way as the shape factor f f 3D ,
defined by Equation 1.11, in Section 1.2.2. In this case, the fractal dimension of the shape (or more
precisely, the Hausdorff measure of contents) gives a better estimation of the number of operations.
In such a case, combinatorial analysis of a 3D algorithm for processing and information extraction
should use for example L = N D as a measure of the contents of elements to process, with D the
fractal dimension of the dataset, and dT < D < d. In the case of a surface boundary, say a mountain
relief, typical values are dT = 2 D = 2:15 d = 3. An algorithm whose length depends linearly on
the extend of this (discrete) fractal surface has a CC of O(N 2:15) operations.
1.6 Shape Taxonomies 63
1.6 Shape Taxonomies

Reductionist approaches for describing complex shapes have been around for centuries. A pletora of
ad-hoc terms and adjectives exist. As a sample we mention: tubular, laminar, t-shape, denticulated,
rosette-shape, knotted, tangled, intertwined, ruffled, granular, vermiculated, trabecular, spongyform,
etc. It is more precise and useful to translate distinctive features into mathematical descriptions that
take advantage of more abstract characteristics, such as principal-axes, surface/volume ratios and
specific pattern relationships. Thus, the adjectives ovoidal (egg-shaped), prolate, oblate, spheroidal,
lenticular and discal are ”coded” by the eccentricities, i.e., the relative proportions of the three prin-
cipal axes a b c of an object, when its shape is well approximated by an ellipsoid. It is ”spherical”
or ”spheroidal” iff a b c; it is ”ovoidal” (prolate-ellipsoidal, cigar-shaped, etc.) iff a > b
and a > c (an axis length predominates), and ”lenticular” (oblate-ellipsoidal, pill-shaped, etc.) iff

a b b > c (one axis is significantly smaller than the other two).
Similar formulations can be made by examinating local and global properties, the shapes of
concavities, the local and global behavior of the normal vector, and the shape of the very distribution
of different components and features. When a graph representation is available, shape description is
translated into description of graph characteristics.
An interesting approach, using MM operators, is to characterize a shape in function of its “re-
sponse” to filtering with specific structuring elements E k , with k an index indicating either size or
topological characteristics (e.g., connectivity). This is the basis for morphologic granulometry, in
which the filter-response function, (an histogram of connected components after morphological fil-
tering with different structuring elements), produces profiles that may be very distinctive of shape
characteristics to the point of being a “signature” of that object (see [Coster89] pp. 119–160 and
[DougPelz92]).
Another approach is the use of morphological “probes”, in the stereological sense. Quantitative
stereology provides a set of tools and methods for estimation of 3D features by measurements on
sets of 2D or 1D samples. Several geometrical probes (called in general ”test systems” [Weibel79b],
pp.11,116–130) are possible: sets of random points, lines, semi-circles, sweeping tangent planes,
structuring elements, intersecting planes, spheres and particles (also called point or line processs,
etc.). The distribution properties of their (random) intersections with the object (statistics of chord
lengths and angles, for example) provide several means to statistically characterize many of its shape
features, and formulas exist to accurately estimate some morphometric parameters. The study of
test systems and stereological morphometry are also topics from Stochastic or Integral Geometry
and Geometric Probability [Santalo76, StoyanSG87, Stoyan94]. Applications related to the present
subject include complexity estimation of 3D scenes for ray-tracing optimization [Cazals97], analysis
of randomness in geometric features [Pennec96], and our own works on textural feature extraction
by intensity-profile sampling [CorkidiAIP98, Corkidi98, Corkidi98b]. Since the present thesis deals
rather with boundary representations, we did not use stereological tools and we restrict this section
to a boundary-based analysis.
The next subsections do not pretend to be a systematic coding of terminology into mathematical
descriptions. We only chose some representative concepts and some ways they can be described or
identified in a discrete representation of a structure, in view of our approach. We start by formulating
a way to explore an object, given some pre-segmented subset (the whole scene, a region of interest,
or the object or set of objects themselves), and then we propose methods to study typical structure
and shape notions.
Let P
f ! Og
= pk : N @ the set of all discrete mappings pk (sequences of point samples) on
the surface boundary of a connected object O2 2
N3, with a parameter k N. If points pk pk+1 are
connected, then at “instant” k = t, pt is a point walking the surface boundary of a connected object
O , and in general it may constitute a 3D traversal of any subset of the boundary: a patch (or a set
of disjoint patches), a circuit (idem), a random walk, or a discontinuous jump or sub-sampling of , O
when no sequential connectivity is defined. Such subsets, also called submanifolds when N n, O
;
have topological dimension D T n 1 (see Section 1.4). In the case of surface patches (DT = 2),
it is natural to introduce two parameters i j and mappings s ij : N2 ! O
@ , but for the sake of
simplicity, we examine here a linear set of points pk 2P O
k = 0 : : : N , on @ (a path). Besides,
O
there is no unique, analytic parametrization of , but we show in Section 2.4.2, how to find a number
of them, using a Hamiltonian traversal of the directed graph associated to . O
Let pk ql 2P 2
k l N, which constitute two different sets of point samples of @ . We give O
now some examples of how features and statistical properties of p k describe topological and morpho-
O
logical characteristics of . More complex combinations and features could be found with several
P
test sets like and more parameters.
1.6.1 Tubular Structures (I)

When considering boundary points, tubular structures or generalized cylinders, such as blood vessels,
are characterized by the profusion of (small, circular) closed loops around the object. Other loops
may be much longer and irregular, thus their mean diameter satisfies
maxm m , with form f g
factor ff 2D
1. From this intuitive approach, we see that there exist ’circuits’ p k , such that f g
2
pk = pk+m for all k and some m N m < N . Such m (the length of a path) can be identified
with a generalized local perimeter in discrete point units 12 . ’Thin’ filamentary structures may be
defined by m < N , with = 0:05, for example. Let a set 4 C O
, be constituted by M circuits
f g C
pkh h = 1 2 3 : : : M . If m1 < m2 < < mM , then 4 is a conic structure (it may
not necessarily be a cone, because we have just chosen some circuit samples p kh ). Principal axes
f g
characteristics of sample sets pk allow to determine if tubular features are more or less round, or
flatenned (eccentricity).
Tortuous tubular structures may be then defined as those structures where a sequence of contour
perimeters mh form an irregular shaped profile (sometimes called ”generalized cylinder”), when mh
is plotted against h. Tortuosity parameters exist for continuous contour representations of blood
vessels [BaskinAA96], and may be characterized through star-polygon contours, as described in
[Verdonck96], pp. 65.
Further discussion on tubular structures with a regional-based approach is found in Appendix B.
page 240.
1.6.2 Ramified Thin Structures

Fine ramifications, in the form of ”spongy” networks are statistically characterized by high inter-
connectivities, and very high surface/volume ratios. Taking a sequence of points p k in the boundary
of such an object, its geodesic and spatial neighborhoods (as defined in Section 1.1) should show
a high density of points p 0k (surface density by volume unit). We study and apply our methods of
analysis to a concrete example in Section 5.7.1.
Several approaches are possible for medium and large branching structures, where a more ac-
curated representation is needed. When considering a set of random planes P i , i = 1 : : : N in-
T
tersecting one or several objects , branching structures are globally characterized by an elliptical
12
O
until now we have not defined how p k lies on @ . A possibility is to place pk along geodesic paths.
cross section in some orientations, and splitting into two or more of these sections, when following
the axis of the branches. If Pi is a sequence of planes along an axis, then a continuous tracking
of each tubular component can be done, except where branches are parallel to some plane Pi (see
Figure 1.13-right).
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Figure 1.13: Intersections of orthogonal planes with a set of ramified objects.
In a local characterization, ramifications are highly non-convex. Ideally, there are at least one
saddle point in the boundary of the bifurcations, since a junction presents at least one zone where
principal curvatures change of sign (see Figure 1.14b,d). Saddle points also exist in tubular bent sec-
tions (see points p 4 p5 in Figure 1.14c). Considering N internal points p j 2T
, with j = 0 : : : N
B
there is a systematic way to univocally identify bifurcations, by studying ball-neighborhoods (r p)
O B \ T
and their intersections with the object itself . Let N \k = card(@ (r p) @ ) be the number of
connected objects (usually contours) of the boundary intersections at radius r k k = 1 : : : M . If
there is some k, such that (N\k = 2) AND (N\k+1 = 3), then the point p j is at a bifurcation region
(see Figure 1.14a). Since small bumps at the surface may be taken as ”branches”, other selection
criteria must be added, as examining larger neighborhoods. It may be possible to have N \k > 3 at
multiple branching points.
Optimal detection of individual branching points, and extraction of a skeletal graph have been
difficult subjects in 3D. Approaches using the Medial Axis Transform (MAT) give often poor re-
sults since they are too sensitive to boundary noise [Ogniewicz94, Schmitt94, OgniewiczTR95,
KresMala94]. More robust representations use Central Axis detection for pulmonary tree extrac-
tion by region growing plus heuristic localization of bifurcations [Niblack90, Wood95, Pisupati95],
and scale-space cores (or medialness representations) with ridge detection [McAuliffe96]. None of
these approaches is suitable for boundary scanning or probing which is more adapted to analysis of
compact structures, where branching is not a dominant feature. A successful strategy for bifurca-
(a) (b) (d)
T
p1 p
2
Br (p)
p3
p (c)
p
T 4
T
U
card { Br (p) T}=3 T
Br’(q) p5
q
p
6,7,8...
U
card { Br’(q) T }=2
Figure 1.14: Branching points are characterized in several ways. (a) Their ball-neighborhoods ideally have
a defined number of intersection with the tubular components. The number of connected-component intere-
sections define the branching degree equal to card(intersections)-2, with 0 indicating no branching, and -1
indicating a terminal point. (b,d) Saddle zones also locate branching points.
tion detection is to execute detection from inside (tubular tracking), and when more than one path is
possible, then spawn new tracking detectors for each path.
Lindenmayer Formal Grammars
From the point of view of modeling ramified objects, iterative, constructive schemas have been
successful in accurately reproducing botanical trees and many other natural structures represented
by graphs with complex topology (besides trees, the brain sulci [Mangin95], and certain cellular net-
works [CorkidiMarquez93, CorkidiMarquez94] and lattices [Prusinkiewicz89], for example). The
most popular construction models are the Lindenmayer grammars L-systems or string rewriting sys-
tems, that introduce a formal language (G W P ), with a set of symbols G (constructive blocks), a
starting string or axiom W (a pattern to follow, an initial configuration), and a set of rewriting or
production rules P [Prusinkiewicz89]. The rules indicate how the symbols are arranged on different
iterations, and control the generation process. Since some decisions (e.g., branching, tubular diam-
eter and which primitive to use) can be randomized following empirical or theoretical distributions,
non-deterministic, natural diverse objects can be modeled, and the production rules may be setup to
simulate physical events (e.g., growth, adaptative change, offspring). Oustanding examples of accu-
rate plant models for several botanic specimens are illustrated in [Prusinkiewicz90, Kaandorp94].
We illustrate L-systems with a 2D ”tree” (Figure 1.15) generated by the following set of pseudo-
instructions at iteration n:
function Plot Branch( n, state)
set diameter=f (n)
plot(segment, diameter)
advance y (n)
if rnd()<thresh1(n)
(a) (b) θn (c)
?
n-1
(d)
Figure 1.15: Branching structure generation with a 2D Lindenmayer-system. (a) Starting string or ”axiom”;
(b) symbol to use; (c) production rules to arrange symbols in varying orientations and sizes (only location and
angle is represented) (c); grammatical construction result after n = 250 steps (d).
rotate '(n) degrees

if thresh1 rnd()<thresh2(n)
rotate degrees;
Plot Branch( n-1, state);

if thresh2 rnd()<thresh3(n)
Plot Branch(n-1, state)
else
plot(last segment, diameter);
;
turn degrees;
if(n>0)
Plot Branch( n-1, state)
return (state)
end
A main program defines a branch segment to be ploted (the ”axiom”) and calls the recursive
function Plot Branch() with an initial value n. The present state is passed, modified and returned
to control recursion. If no bifurcations are decided to take place, this function plots full segments
following a single curled branch (see Figure 1.15a,b). Otherwise, given a bifurcation event, two new
branches are started (the old one is reset to 0, at smaller scale). '(n) controls ”curling”, in function
of n, and is the branching angle plus a random bias. Parameters thresh1, thresh2(n), thresh3(n)
are empirical adjusted, the last two being decreasing functions of n, thus probability of branching
decreases until a full branch is completed and another is continued.
In Section 2.4.4 we further describe tubular thin structures as a “dual” of flat manifolds, char-
acterized by high rate of normal vector changes per volume unity, as opposed to interfaces and
convoluted surfaces. A particular case of branching structures in the bronchial tree of the human
lungs is presented in Chapter 4.
With respect to shapes in natural sciences, a whole discipline called morphogenetics studies
growth phenomena and process that give rise to forms in nature. These are considered as adaptive,
evolutive process, since form or structure changes appear in response to environment exchanges.
Thus dynamical systems play again a central role in complex form understanding and modeling.
Cellular automata [Wolfram84b], genetic or evolutionary computation [FogelEC94] and other recent
topics also exploit biological-inspired paradigms, and have served as models of pattern complexity.
1.6.3 Surfaces, Boundaries and Interfaces

Laminar structures. Plaques or laminar manifolds may be characterized by existence of short paths

in one predominant direction (the local average normal ~n ~ , with ~ a standard deviation vector that
may account for roughness features). We again postpone further discussion to Section 2.4.4.
Convoluted surfaces. As laminar structures, these present short paths, distributed in several di-
rections. A discrete line traversing the scene may intersect several times the same object; thus a
fg
characterization may be given in terms of instersections. Let lk be a set of random lines (the
”probes”), k = 1 : : : M , with M to be determined for meaningful statistics. Let the mean thick-
ness of the intersected object subsets with all probes, and " the mean free path between intersections
(empty space). Then, the number of total intersections and the ratio =" provide quantitative in-
formation about convoluted surfaces, and their distribution in space. For example, the brain cortex
surface should possess at many places a high number of intersections with a high intersection ratio
(the sulci being slender and more or less curved). A lettuce would have a high number of intersec-
tions everywhere, with a constant small intersection ratio (the leaves being very thin). Intersections
with probing planes, spheres, etc. would provide other kind of informations, which may statistically
characterize many other complex features. An example of convoluted surface is presented below, in
the paragraph on complex interfaces (Figure 1.16).
When convoluted surfaces are rather smooth, and constitute height fluctuations of a plane surface,
expressed as z = z0 + f (x y ), with f (x y ) a uni-valued function they are called roughness [Wong86,
Briers93]. The simplest measure of this feature is the root mean square value of fluctuations around
the mean height. Most analysis has been traditionally done by spectral techniques, but other textural-
based approaches are feasible. An example is presented in Section 5.7.1, where we show how to
work with real convoluted surfaces, where f (x y ) is multi-valued, giving rise to surface ’meanders’
or ’overhang’.
Interfaces. Boundaries between objects identified as different, under some criterion form them-
selves virtual surfaces or submanifolds shared by two or more bodies. Thus, interfaces are second-
order structures, arising from neighboring and connectivity relationships.
Interfacial sheets or membranes may be described in a similar fashion as laminar manifolds
and convoluted structures, but we need to re-define segmentation and filtering methods in order to
interpret one side of the interface as ”background”, and the other side as ”foreground” (definitions
may be switched during processing). Discrete representation is also extended, it may still consist of
a list of voxels, but also a list of 18-connected facets (voxel faces interconnected at least at one edge
with another facet). K -connectivity is defined in Chapter 2.
(a) (b)
| a| << | b|
DH( a) < D H( b) =>
Flux a << Fluxb
Figure 1.16: Given two physical media (or bodies), their common boundary defines the exchange rate of
information or material flow. (a) A smooth boundary @a with low Hausdorff dimension D H (a) (or any other
fractal dimension) characterizes a low surface-area interface and a low flux of information, energy or material
Fluxa between both media (small arrows). (b) A very rough, convoluted or fractal boundary @b, with a
j j
higher Hausdorff dimension DH (b) has also a much larger surface-area @b , and in consequence, the flux of
information, energy or mass (denoted by Fluxb, across the boundary is much higher (large arrows). Boundary
shapes may take several different morphologies to fill up the embedding space in efficient ways, following
minimal energy configurations, for example.
A particular example of complex interfaces is illustrated in Section 5.7.2. We only mention that
space-filling interfaces are very important in multi-component mixture understanding, interpenetra-
tion, and seggregation and their proper mastering, i.e., a proper morphological quantification and
measurement of mixture quality determine valuable mechanical or other physical properties in ap-
plications from material science, solid state physics and chemical compounds. As present in natural
phenomena, their interpretation provides clues to material, energy or information exchanges across
them, as illustrated in Figure 1.16, and in a real application, with one example from Cell Biology in
Figure 2.21, page 134.
1.6.4 Description of Other Shape Features

Convex structures. The conventional definition of Paragraph 1.2.4 can be directly applied, using
O 2 O
only point samples at the boundary of . Let p k ql @ and
L = frtjrt = pk + t(pk ; ql ) t 2 0 1]g

then O is ”convex” iff 8pk ql 2 @ O, L O, that is, 8t rt 2 O. Degrees of non-convexity may be
established by measuring the percentage of points r t 2
= O, the geometric interior.

f
Surface Texture. Let a population of ’coupled’ pairs pk ql k l g 2 N, with a coupling rule,
and (eventually) value labels k l assigned to each pk ql . The label is not necessarily a gray-level
density, but any local measure. Then we consider the probabilities of co-occurrence of k l. Surface
irregularity characteristics can then be extracted in a similar way to co-occurrence textural parameters
in planar images. Usually, pk ql constitute the endpoints of chords, and distribution of chord lengths
under certain random process is a common 2nd-order analysis in the case of 2D shapes. In a 3D
context, texture refers to variations in many scales, examined statistically. For example, a distribution
jj ; jj
profile of the random variable pk qk may have two different populations in convoluted and
branching objects: the larger population denotes separated ”sheets”, and the shorter, neighboring
jj ; jj
points. A large average < pk qk > and a small second peak in the profile denote both a very
intrincate, filamentary structure (a sponge). Shape interpretations of ’contrast’, ’2nd moment’, etc,
may also be investigated. See Section 5.7.1 for a particular example. A related approach is that of
run-lengths, where the pk ql in 2D shapes of grey-level images are the intersection of sets of random
or horizontal test lines [GallowayRL75, EllisDRL81, Chu90]. Run-length analysis is adapted to
the structural approach to texture, but we did not considered this for the present work. We present
however other considerations relating texture and complex shapes in the following section.
1.7 Other Properties of Complex Information

Until now, we have limited our attention to solid-shape characteristics for modelling and morpho-
metrical purposes. We have set aside multiresolution and scale-space characteristics, topological
problems and Gestalt or Pattern Recognition problems, which also describe complex information,
and we shall tackle outside the present work. Other kind of characteristics are inherent to complex
data, such as noise, sampling limits, partial surface or volume effects, artifacts and distorsion. Since
these features affect segmentation and shape measurements, we mention in the following paragraphs
aspects of two of these problems, in relation to shape information.
1.7.1 From Structure to Texture

Real-world objects are characterized by a number of features or patterns difficult to describe, even if
the human visual system is able to recognize and distinguish different visual patterns that appear in
a close examination of real objects. These features or patterns are called ’textures’ and ’roughness’.
We make in this Section only some observations. The first concern the transition from what we
may call ”deterministic structure” to what we call ”texture”. As we actually employ digital computers
and finite-resolution measuring devices for data analysis and representation, all measurements and
results are discrete samples of what we try to analyze (plus convolution by Point Spread Functions
”PSF” I (PSF) of other resolution uncertainties in the system). In the case of frequency-domain analysis, the
Nyquist-limit is attained when data resolution lies over the smallest details of the object. If the object
is very intrincate at certain scales, it may then appear as ”noise”. When some structure is present,
a texture appears (for example, when even weak spatial frequencies produce anti-aliasing artifacts).
When trying to model the normal surface of a fractal object to be rendered in 3D, there may be no
way to obtain an average distribution of smooth normals, because the averaging is done on a non-
differentiable surface. A solution would consist in modeling light interactions with physical fractals.
An example of light interaction with fine structures is given by butterfly wings, where in addition to
pigments, the microstructure of wing scales refracts and diffracts light, producing iridescent, metallic,
or pearly effects; in most cases, characteristic feature widths correspond to visible wave-lengths.
1.7 Other Properties of Complex Information 71
As texture may be present at different scales of observation, it is pertinent to ask for their scale-
invariance properties, such as fractal dimensions, and we have already showed some examples.
Lacunarity. Fractal dimension Dq is related to first-order statistics of mass distribution, in func-

tion of scale. Second-order statistics provide information about spatial relationships, and discrepancy
between real and expected measures. Several definitions have been devised for quantifying ”gaps”
(or lacunas), and irregularity fluctuations in textures. Lacunarity (L) at scale length L is a tex-
tural feature that quantifies deviation from translational invariance by describing the distribution of
”gaps” within a set at multiple scales. The more lacunar a set, the more heterogeneous the spatial
arrangement of gaps [MandelbrotFGN82].
A way to estimate (L) is by using the moments M q of the q th-order information dimension
Dq, defined in Paragraph 1.4.1, with q = 2 [Peitgen88]:
M 2(L) ; hM (L)i2
(L) =
hM (L)i 2
At fixed scale L, (L) measures the width of distribution P (m L). It is possible for different
fractal surfaces to have the same dimension DH , and present a different lacunarity (L). Keller
et al. report a measure of lacunarity better adapted for small texture patches, and more suited for
segmentation [KellerChenCrownover89]:
C (L) = M (L) ; N (L)

M (L) + N (L)
In this equation, M (L) is the average mass density within a L-box, and N (L) is proportional 13 to the
number of L-boxes needed to cover the fractal set. From fractal dimension definitions, several lacu-
narities can be proposed. Note that the notion of ”gap” was defined in terms of foreground (”filling”
components of the texture) and background (no foreground). Nothing prevents from considering a
relative lacunarity, in the same vein of interfaces with respect to boundary between two regions (two
foreground classes C1 C2, implying background gaps plus C 1-gaps or C2-gaps).
1.7.2 Noise, Blurring, Distorsion and Inhomogeneities

Data produced by measure devices contain many kinds of information that has to be extracted and
which has also suffered some transformation (distorsion) or degradation, in the form of added noise.
The concept of noise includes unmeaningful information from the source data, extraneous signals
due to isolation problems, and information from uncontrolled sources. Besides introducing distor-
sion and imprecision, the less this information is identified, the more it is useless and considered
as noise that has to be filtered. Precision limits play also an important role, specially if observa-
tions are indirect (low or no observability), and the intermediate device or process, modeled as a
communication channel, is non-linear.
As noise is part of the data, and it is often influenced by data features, it can be as complex as
the data itself. Noise may even be unidentified information, thus containing non-random structure,
unsuitable for stochastical models of noise. The general model consists of an input signal x, and the
y observed output from the measurement device, satisfying :
y = ' x +
13
A dimensional constant was omitted for clarity.

where is additive (random) noise, is the convolution operation with ', the Point-Spread-Function
of the system, which blurs the input. More complex distorsions may exist, including multiplicative
noise (also called structured noise, e.g., speckle), and non-linear intensity or geometric deformations
of the input. Most of restoration processing consists in obtaining the best estimator of x from y
and some knowledge of and '. The simplest approximations include Gaussian (white) noise and
Gaussian convolution.
For other kind of data degradation, such as radiometric inhomogeneities (background illumina-
tion variations, physical degradation or other), an a priori knowledge of data x itself, or some reason-
able assumptions besides those already mentioned allows to filter or reduce noise. Such assumptions
include continuity criteria, such a spatial coherence of data, a specific probability distribution, a
characteristic spectrum (in the shape description, or the density of the data), or other characteristic
feature. We present in Chapter 3 an example where the characteristic feature is the coherence of 3D
structures, along the cross-section axis.
In terms of complexity, the relevance of noise understanding relies in discriminating noise from
randomness. Given the available model about the shape of an object, some kinds of noise may
introduce unpredictable variations not included in the model. When properly incorporated into the
model (e.g., a Gaussian noise ( )), it may explain the random fluctuations of some aspect of
the data. Statistical, topological and linear-transform invariances, robust feature parameters, error
analysis and knowledge of the noise sources are to be incorporated within complexity measures, as
in any experimental routine.
Several generalizations of the above problems have been proposed in terms of physical measure-
ment models and estimation theory (see for example [Serra82] chapter 1 and [Mintz1994]). Follow-
ing an experimental approach, given a ’theoretical’ feature, X , any measurement device or algorithm
has access only to a certain set of Nobs observations (estimations, approximations) of X :
Yk = k (X ) k 2 1 Nobs]
where k is a sequence of transformations induced by the observation or measure process. Ideally,
j = k , for all j k, and consists of affine transformations for geometric features, convolution
plus noise for spectral attributes, etc. In general k are spatial and time-varying transformations,
comprising several types of distorsion, noise, etc. The first concern is to select robust features X with
high invariance under k , and then measure Yk , either as a substituting feature, or as an estimation
of X . The latter approach is routinely used in mathematical morphology, where the transformation
of isotropic closing regularizes the contour of certain shapes. The perimeter P of a digitized shape
is an example of a non-robust measure X , in which the sampling resolution is included in ( ),
under the form of a scale transformation, or a sampling function (decimation, round-off), which

provides different measures Yk = k (P ) P . These measures appear for example in the form of
an estimator
P~ =< ~ ;1 (Yk ) > k 2 1 Nobs]
sensitive to shape irregularities, the scale of observation, noise and indeterminacies in the process of
contour detection and machine precision.
We have ourselves experienced two situations where several transformations altered data in-
put. The first is described in [Anglade93, Marquez94b], where ultra-microscopic slices from cell
nuclei were digitized from electron microscope negatives. The goal was to seek pathological-
induced modifications in cell-nuclei morphology. These were mixed with important incertitudes in
slice thickness, anisotropic mechanical and heat-induced deformations, radiometric inhomogeneities
and offset due to contrast-product and irregular thickness, electron-beam control and blur, dust
1.8 Discussion and Conclusions 73
and chromatine artifacts, histochemical blur, photographic developpment incertitudes and artifacts,
rigid mis-registration, camera acquisition calibration, and errors from bilinear-unwarping approx-
imation of geometrical non-linear distorsions. Under these circumstances, only differential (rela-
tive) analysis could be done, with poor statistical validation. The second situation was far more
tractable, comprising color radiometric inhomogeneities and is presented in Chapter 3 and reported
in [Marquez96b, Marquez98].
Thus, even for ”simple” objects, there may exist complex noise, complex measurement proto-
cols and incertitudes (the PSF of a sophisticated observation device), and complex methods of data
filtering and analysis.
1.8 Discussion and Conclusions

Being such a large and rather recent domain, we cannot give a detailed list of the various problems,
approaches and concepts of Scientific Visualization and processing of complex objects and data. We
have given an overall review of some key aspects, in view of a quantitative analysis. Many of these
characteristics can be handled in a medium computer environment, available in average research
laboratories for applications that approach the image processing standards: morphometry, object
manipulation and data visualization.
The following conclusions can be drawn:
✦ The notion of ”complexity” embodies and relates with the following properties:
– Cardinality: high number of elements or components.

– High number of topological features: connections, holes, genus, knots. A particular
feature is space embedding and configuration with respect to other objects..
– Bifurcations (branching), either physical or abstract (graphs, behavior, response).
– Higher order properties: high number of inter-relations, interactions or interconnections,
– Non-linear descriptions.
– Long descriptions. The lengths of the shortest descriptions are important measures, and
the very structure of the description has its own complex features.
– Partial regularities, lack of them, or its presence implies lengthy descriptions.
– Partial scale-invariances, (local) non-convexities and concavities, hierarchies (grouping
and clustering at various levels), repetitive or non-repetitive patterns, textures, fractal
dimensions, degree of order and randomness, etc.
– These characteristics may be present in several ways: information (energy) present at sev-
eral or all frequencies, locallly or randomly. Basis representations need several or infinite
number of coefficients; high-order statistics are needed to describe complex objects, etc.
Whether it is length, information content or cardinality, it is clear that complex objects and
processes give rise to large models. When considering even several descriptive levels, more
than one single model may be required. Additional features of data include their ”natural”
format, i.e. scalar, vectorial, tensorial, multidimensional, etc., and how they are embedded in
space.
✦ Some understanding of complex objects is attained by descriptions involving physical process

(morphogenesis), hierarchization ordering, the amount of randomness, disorder and higher-
degree descriptions (interactions, and the effect of several elements taken as a unit). Noise,
subsampling and other phenomena/artifacts from data acquisition adds for what is ”complex”.
In a second-order analysis, the irregularities of the interconnections, relationships or interac-
tions between the components of an object or system, may also be subject to a similar analysis,
and turn out to be non-linear (not superposable). In fact, in dynamical systems, the objects of
interest lie in multi-dimensional phase-spaces (chaotic attractors).
✦ Many of these notions involve boundaries. They may be the external surface of an object
(frontier between background and foreground) or transition surfaces (interfaces) separating
two media or two components with different attributes. A particular problem (and still another
complex feature) is posed by fuzzy, undefined and ill-defined boundaries.
✦ An arbitrary object can be approximated by simple primitives (e.g., spheres, harmonic or poly-
nomial surfaces), or even by complex known sets (”canonic” fractals, e.g., Iterated Function
Systems, and iterated polynomials as the Mandelbrot’s quadratic map). As complexity has
been also defined at a state of organization between complete, deterministic order and com-
plete disorder (noise) identified with ”chaos”, it may turn out that real complex objects are
even more complex that fractals, in the sense of the Kolmogorov Complexity (KC). This is the
case of self-similar fractals in which a very simple construction rule entirely describes all scale
features. Thus, ”infinite detail” is not necessarily a complexity attribute. The knowledge of an
underlying law or pattern (random laws) seems also to reduce complexity (description length)
in function such knowledge. This simplification is in fact a desired goal in Science.
✦ The utility of complexity measures, such as KC, resides in re-orienting modeling strategies
in the identification and choice of minimal representations, algorithms, languages, etc. If a
pattern is too irregular for Fourier analysis description (spatial periodicities turn out to be
too weak), it may be more natural or economical to use iterative process such as deterministic
fractals, to describe it. If the pattern is poorly scale-invariant, other paradigms must be devised.
✦ To be useful as descriptive tools, complexity measures need to be invariant (stable or robust)

under common transformations and noise. A possible problem is that they tend to quantify
themselves some kind of invariance and repetitive patterns in the observed data, and not their
absence. Still, another practical problem is the difference meaning and use of the terminology
in different disciplines, and the goals in studying complex sets (representational, interpretative,
model-oriented, formal, application-oriented, philosophical, aesthetical, etc).
✦ In a final analysis, must features and concepts around complex or simple shapes and their
description turn to be rather a kind of invariance, continuity, linearity, regularity or any other
simplification more or less present. Real ”complex” attributes begin thus with substantial lack
of some or many of these features.
We can say that many authors have tried several approaches to organize complex information,
but some lack of uniformity and standard definitions can be seen. There are for example ’shape
complexity’ and ’algorithmic complexity’ as two notions sharing some features –the latter is used
to code descriptions of the first. Application contexts strongly determine the language and selection
of morphometrical methods and concepts, but the number of shape features and possibilities make
difficult the choice and interpretation.
1.8 Discussion and Conclusions 75
As a summary, we list in Table 1.2 only the main features of a common data application problem,
according to a difficult qualification of ”low” and ”high”.
76
Table 1.2: Complexity features of data and applications in a scientific visualization problem and coarse approaches. ”STAT” stands for statistical approaches.
Data feature Low difficulty High difficulty Best description or strategy

Data type scalars in N tensors in C n hierarchical data structures
Number of Objects one to ten many (10 10 n )
; data structures, STAT
Number of features few (three) many feature vectors, STAT
Kind of Properties intrinsic-only + extrinsic feature spaces, Gestalt approaches
Independent variables unidimensional multidimensional data structures, STAT
Geometry Euclidean curvilinear, convoluted, fractal Biological inspired approaches
Connectivity & topology genus 0,1 genus n, circuits attributed graphs
Internal features uniform arbitrary (boundary-represent. if uniform)
Branching binary trees multidimensional graphs
Repetitive patterns many none Fourier analysis if many; wavelets, STAT
Scale-invariance none or strong partial (multi)fractal dimensions
Linear behaviour significant non-linear implicit models if non-linear
Time-dependence static phenomena dynamic phenomena phase-space representations
Data size (resolution) < 128 3 > 1283 divide & conquer, STAT
Characterization of sets with complex structures in R3
Chapter 2
From Raw Data to Models in N 3 : A

Boundary-Based Approach
Abstract
In this chapter we discuss discrete boundary representations and present a general technique for
processing, analyzing and visualizing three-dimensional objects with arbitrary shape and topology,
taking into account several considerations of the role of boundaries in many research fields, from
data analysis to modeling in N 3. The technique consists in building first a boundary representation
of objects detected by an implementation of the surface tracking algorithm of Artzy et al. [Artzy81].
This algorithm provides the set of voxel facets for the boundary of each object. As their adjacency
rules are available during surface tracking, we also obtain efficient methods for boundary and vol-
ume traversal, taking into account local information. Hence, boundary representation constitutes the
basis of some of the 3D operations that we perform. These operations comprise three groups: (1) 3D
image processing and object manipulation, (2) measurements (morphometry) and (3) visualization.
Our approach has allowed us to pre-process complex objects in order to reconstruct their 3D shape,
to extract morphological parameters, and to clearly visualize their structure and spatial imbrication.
Applications in the Biomedical and Physics domains are presented in Chapters 3,4 and 5.
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
2.2 Discrete Volume Representations and Boundaries . . . . . . . . . . . . . . . 80
2.2.1 Boundary Representations . . . . . . . . . . . . . . . . . . . . . . . . . 81
2.2.2 Relevance and Potential Uses of Discrete Boundary Representations . . . 82
2.3 A Facet-Based Model for Discrete Surface Representation . . . . . . . . . . . 84
2.3.1 Discrete Elements: Scenes and Voxels . . . . . . . . . . . . . . . . . . . 84
2.3.2 Discrete Elements: Faces and Labels . . . . . . . . . . . . . . . . . . . 87
2.3.3 Discrete Elements: Facets and Boundaries . . . . . . . . . . . . . . . . . 89
2.3.4 Discrete Adjacency and Connectivity . . . . . . . . . . . . . . . . . . . 96
2.3.5 Voxel (Euclidean) Neighborhoods . . . . . . . . . . . . . . . . . . . . . 102
2.3.6 Facet (Geodesic) Neighborhoods . . . . . . . . . . . . . . . . . . . . . . 104
2.3.7 Voxel Geodesic Neighborhoods . . . . . . . . . . . . . . . . . . . . . . 106
78 From Raw Data to Models in N3: A Boundary-Based Approach
2.3.8 Discrete Boundary Neighborhoods . . . . . . . . . . . . . . . . . . . . . 108

2.4 Surface Tracking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
2.4.1 Surface Tracking Algorithm . . . . . . . . . . . . . . . . . . . . . . . . 114
2.4.2 Facet Traversal by Lateral Circuits . . . . . . . . . . . . . . . . . . . . . 117
2.4.3 Interior Traversal and Object Labeling . . . . . . . . . . . . . . . . . . . 119
2.4.4 Run-Length Interpretation of Interior Traversal . . . . . . . . . . . . . . 124
2.5 Boundary-Based Processing and Analysis of 3D Objects . . . . . . . . . . . . 126
2.5.1 An Example of Boundary-Based Morphometry: Euclidean Area Estimation 128
2.5.2 Boundary-Based and Volume Processing (Examples) . . . . . . . . . . . 129
2.6 Visualization of Complex Structures . . . . . . . . . . . . . . . . . . . . . . . 135
2.6.1 Surface Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
2.6.1.1 Hidden Surface Removal and Surface Shading . . . . . . . . . 135
2.6.1.2 Discrete Normal Estimations . . . . . . . . . . . . . . . . . . 135
2.6.2 Three-Dimensional Data Structures. . . . . . . . . . . . . . . . . . . . . 137
2.7 Summary and Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
2.1 Introduction
It has been widely recognized that quantitative analysis and computer processing of 3D images
still lacks the advancement and understanding already acquired for 1D and 2D signal processing
[Pommert93, Wood92, Kaufman94b]. Simple visualization has enabled some basic understanding
of intricate 3D data in similar ways as humans do when they visually examine real objects. Liter-
ature is rich in 3D realistic reconstructions with color, transparence, texture, shadings and specular
reflections, but with limited analysis. More scientific –i.e., objective, quantitative– approaches are
still recent and seldom.
These problems are not only due to increasing data volume, or even higher complexity (either
complexity of the data or of the task to perform), but also to the ways data are represented and ma-
nipulated, taking into account well-defined but punctual objectives. Also, digital computers have
imposed their characteristics and limitations to data analysis, and this has been extended to represen-
tation, modeling and processing, specially in three-dimensional data. Computer Aided Design and
”CAD, CAM” I Manufacturing(CAD, CAM e.g. solid modeling), and engineering have prompted the development
of computer graphics technologies for visualization, modeling and design of geometric and artificial
objects, while Medical Imaging (Tomography, Magnetic Resonance Imaging, Ultrasound Imaging,
etc.), Quantitative Microscopy or Remote Sensing have stimulated the use and developement of tech-
nologies and theoretical advances for Image Processing, Pattern Recognition, volume visualization
and true quantitative analysis.
A CAD approach typically consists of efficient imaging, through fast and simplified repre-
sentations, such as vector rastering, contour extraction and plotting, triangular meshes, polyno-
mial patches, texture-mapping, depth maps and other image buffers, and the corresponding pipeline
and parallel architectures (geometric engines, transputers, etc.). Effective graphic interfaces al-
low humans to grasp visual features of 3D data, and make semi-automated space manipulations
or computer-assisted segmentation and component isolation, while reliable automation of these pro-
cesses is still in development.
2.1 Introduction 79
A discipline called Algorithmic Geometry (or Computational Geometry) has produced efficient
methods for dealing with most of the visualization and modeling problems, specially suited to math-
ematical objects [LeePreparata84, Preparata85]. On the other hand, full quantitative analysis and
processing have been difficult or impossible to incorporate with these approaches, or has shown to
be incompatible with required simplifications, as used for visual realism (e.g., triangulated meshes
and Bezier surface), but difficult to process, in comparison to discrete volume-element representa-
tions which extend the picture-element paradigm.
By “full quantitative analysis and processing”, we mean mainly: Mathematical Morphology
(MM), local and global feature extraction and morphometric measurements, geometry-driven or J ”MM”
morphometry-driven filtering, enhancing or MM-filtering, roughness and fractal analysis, multi-
resolution image processing, and other techniques. We saw in Chapter 1 that particular features
are desirable in the study of complex data: measurements should be robust and present some kind
of invariance (geometrical, topological); they also must permit experimental validation. Even if just
MM is considered, it turns to be a very rich paradigm for analysis of 3D scenes represented as dis-
crete 3D volumes: granulometry, distance fields, medial-axis-transforms, etc., which in turn open
access to various techniques of complex analysis (in the sense of ‘sophisticated’). However, MM is
poorly or inefficiently suited to arbitrary triangular or simplicial meshes and difficult to apply on the
analytical representations used in CAD (e.g., splines, superquadrics, wavelets).
In certain cases, the model characteristics (smooth, analytic surfaces and blended ridges) over-
ride the nature of the original data, hiding or distorting valuable details, or introducing undesirable
features. The surface normal and other differential entities are particularly sensitive to small per-
turbations. Furthermore, after processing and filtering data to extract other pieces of information,
modeling artifacts contaminate the results, requiring ad-hoc and costly correction and validation
[Zelkowitz97, Machiraju96]. A similar argument could be applied to uniform discretization, in which
the staircase artifacts superposes with original data, but very effective techniques exist to clean it up,
using classical Fourier interpolation and decimation or other well-tested methods.
On the other hand, physical-based models and visualization (as for example mechanical and
fluid deformations, fluid dynamics, and even radiosity algorithms), rely on continuous or hybrid
approaches. As such, they have been tackled by analytic and CAD methods, specially those us-
ing finite elements and boundary elements [ThompsonToga96, Gallagher89, Sethian96, Ebert94,
Troutman93]. All these trade-offs have prompted proliferation of methods to pass from continu-
ous to discrete representations and viceversa, in order to suit theoretical advantages to all modern
applications, scientific and industrial.
Discrete images, sets and operators in N3 and Z3 have been developed in the past in accordance
with data structures and computer-science concepts such as voxels, grids, random access locations,
meshes, and their models with discrete mathematics: graphs, n-dimensional incidence structures,
lattices and discrete functions [Voss93, Ritter96]. Besides understanding and representational ad-
vancements, these tools have permitted to alleviate the lack of quantification and processing in the
CAD-based approaches.
In Chapter 1 we have presented and given an overall characterization of geometric and non-
geometric structures from low to high degrees of complexity, as found in the biomedical domains
and physical sciences phenomena. To study such objects and their associated properties, we have
chosen a discrete-geometry approach for surface extraction, volume processing and visualization.
In this chapter we present some theoretical foundations, tools and methods using this approach to
represent and analyze data in scientific applications where fast and realistic visualization is not the
main concern for a depth understanding of their nature.
The sections in this chapter are organized as follows:
✦ In Section 2.2 we discuss the state of the art of discrete volume representation problems and
applications, and their relationships with boundary representations.
✦ In Section 2.3 we present in detail all definitions of elements that constitute a discrete-boundary
representation in N3. They include voxel faces, various boundary sets, connectivity 1 and neigh-
boring relations.
✦ In Section 2.4 we briefly present the boundary-extraction algorithm of Artzy et al. [Artzy81],
using the above definitions and the modifications and enhancements we have incorporated.
✦ In Section 2.5 we discuss how diverse measurements are obtained from boundary representa-
tions and some of our particular contributions.
✦ In Section 2.6 we present some aspects of visualization with boundary representations.
2.2 Discrete Volume Representations and Boundaries

The most successful paradigm of representation, processing and visualization of discrete objects in
two dimensions is the orthogonal grid of picture elements. Hexagonal grids have also become at-
tractive in many applications, because they don’t pose neighborhood-connectivity paradoxes, when
defining foreground and background in the same way. We will examine this issue in 3D in Subsec-
tion 2.3.4.
The direct equivalent of the pixel-based representation of 2D images is the volume-element, or
voxel-based representation, or cuberille model, introduced by Herman and Udupa [Herman83]. In
this representation an orthogonal grid of cuboids or parallelepipeds is used as discretization grid, and
2
mathematically treated as a 3D matrix array of integer coordinates x y z N3 (or indices (i j k))
[Herman83, Chen85]. We introduce our version of this model in Subsections 2.3.1 and 2.3.2.
Most formal and well-tested algorithms and representations in Image Science and Discrete Topol-
ogy use the orthogonal grid representations for digital picture (pixels) and volume data (voxels). A
simple reason is their direct isomorphism with N n . Fourier analysis has provided solid grounds
for conversions from or to Rn, quantization, filter design, interpolation, sampling phenomena, etc.
Equivalent advances for non-uniform tessellations of Rn and arbitrary triangulations are either too
specific, non-robust or often unavailable. These and other requirements strongly favor the discrete-
boundary representations that are compatible with orthogonal grids where volume elements are par-
allelepipeds. There are works on grids other than cubic in 3D, with similar capabilities (e.g., gener-
alizations of the hexagonal grid in 2D [Ponce88, Herman98]).
Data volumes themselves are mainly produced as discrete samples in Nn , or are converted so,
from polar coordinates or interpolations. In many research fields, developments of measurement de-
vices have enabled the obtention of huge matrices of 3D data, with increasing structural complexity

and resolution (starting at 256 256 100 1 byte, for example), in the form of scalar, vector or
tensor quantities, temporal sequences, multiple channels, and higher dimensionality. These features
permit to digitize or scan information in great detail, and represent physical processes and abstract
features at all scales. Large scale simulations also produce increasingly complex data. Thus, 3D
voxel-based graphics has a recent rapid growth, specially in Medical Imaging and Non-linear Dy-
namic Systems. Theory and techniques based on the cuberille model, as applied to such data analysis,
are also called “volumetric imaging”, “volumetric graphics”, or “voxel imagery” [Kaufman94a].
1
Or connectedness.
2.2 Discrete Volume Representations and Boundaries 81
Exceptions to systematic coordinate sampling are laser scanners, and mechanical sensors that
produce very high precision clouds of unstructured coordinates, but in many applications there is a
need to pass through voxel grid representations.
Large amounts of complex data with the mentioned problems are very difficult to analyze, requir-
ing often a pre-processing stage, such as filtering, weak-connectivity component separation, or other
operations in a selective and local fashion [Kaufman94c, Rossignac94, Udupa94b, Lopez93]. To
study such objects and their associated problems, we chose a discrete geometry approach for surface
extraction, volume processing and visualization.
Voxels and octree representations have been extensively reviewed in the literature (see for exam-
ple [Jackins80, Amans85]), and we will rather focus on boundary definitions and regional represen-
tations, in order to introduce our boundary-based paradigm.
2.2.1 Boundary Representations

Boundary-based representations (also known in Computer Graphics as b-reps ) were originated J ”b-rep”
in the CAD-CAM engineering community, to simplify 3D object representation and manipulation
through polygonal facets, patches or primitive boundary elements. Simplification of b-reps is widely
due to the systematic analytic formulation of models, intersections and algebraic operations between
lines, planes, polyhedra, or analytical surfaces (e.g. conics, splines, Bezier curves). Ray-tracing and
radiosity techniques for realistic visualization have successfully exploited this geometric approach to
object representation, even for fairly complex objects.
The same cannot be said about quantitative analysis, specially when signal and image process-
ing techniques have to be employed (e.g., edge-detection operators, mathematical morphology and
scale-space filtering). The geometric primitives introduce irregular biases to measures and require
complicated calculations. Rapid degradation may appear in some b-reps, which have then to be re-
built and verified after processing (to preserve topology, for example). In real imaging applications,
boundaries are not always well defined, textures and noise cannot be separated and the CAD-CAM
approaches poorly represent objects with intricate structures.
More primitive elements have been used to simplify the mathematical treatment without the loss
of a faithful b-rep: triangle meshes and their dual meshes are routinely employed to represent object
surfaces, and constitute a good example of a systematic solution for modeling and visualization
problems of complex objects with numerous features (color, texture, components, contact areas, etc.)
[Boissonnat96, Boissonnat93, Gueziec95]. Nevertheless, many triangulation methods start with a
mesh approximation based on discrete boundaries [Algorri95].
In their 2D continuous version, b-reps for 3D reconstruction from serial slices are based on pla-
nar contours, (continuous) polygons [Boissonnat88], or Delaunay triangulations [Boissonnat84]. In
discrete space, contours have been represented by chain codes in discrete grids [Rosenfeld82], or
coded into topologically consistent representations, such as the cellular complexes that comprise in-
dividual vertices, edges and their inter-connections. The k-chains generalize cellular complexes and
have associated states and an algebraic-topological structure suitable for dynamic systems modeling
[Voss93, Kovalevsky89, Pailloncy97]. Together with other formulations, several b-reps have con-
stitued the basis for important fields of research where data representation is no more the main prob-
lem, but strong links arise with other concerns. This is the case with level-set methods [Sethian96]
and the scale-space primal sketch [Lindeberg92b], where boundaries are organized or interpreted
in higher dimensions. Dynamic boundary representations also appear in the form of solutions or
isosurfaces of differential equations in image processing, and have produced advancements from de-
formable and active contours [Kass88] to curve evolution and the fundamental equations of Image
Processing as an “interpolation” between the heat equation and classical morphological operators
[Alvarez93, Brockett94].
2.2.2 Relevance and Potential Uses of Discrete Boundary Representations

There are at least six important reasons that have motivated our boundary-based approach, and will
reappear frequently along this manuscript, often as arguments for tool design. As our main concern
is the capability to deal with complex structure and data, we review below how a boundary-based
approach can be useful.
Data reduction Visualization, shape understanding and interaction with n–dimensional objects is
;
frequently better achieved through clever (n k)-dimensional simplifications; in particular
O O
boundaries of the object , or through boundaries of subsets of . The adjective “clever” is
not in general true. An example are sequential slices, or even 1D-profilograms, that do provide
some access to data, but poor understanding of three dimensional structure and inter-relations.
When carefully applied, the simplification approach has provided successful results in 2D im-
age processing, where contour extraction and analysis is a common task in many applications.
In gray-level image analysis, the surface-intensity interpretation (with density seen as height
level), and the subsequent decomposition in level sets (isodensity curves), are also examples
of this dimension-reduction approach. It is worth noting that also texture analysis, for ex-
ample, has been represented and treated as roughness of a “2.5-D” surface or range images
[Rosenfeld70], and frequency-domain analysis can be visually plotted with the amplitude as a
third dimension. Finally, higher dimensions are only accessible to human perception through
sets of 3D representations (“level sets”), which imply intensive use of isodensity surfaces.
Fractal boundaries When complex objects are associated with fractals, a particular remark can be
made on the relevance of b-reps: the definition of topology dimension d T of an object O
O
relies on local neighborhoods and relations between , as embedded in an Euclidean space of
O ;
dimension d, and its boundary @ , which has topological dimension d T = d 1. The fractal
O
features of are described by dimension quantities D x whose values satistfy d T
Dx d,
as noted in Section 1.4.
Boundary-based measurements of fractals. From a more general point of view, the notions of
;
complexity and fractal dimensions of irregular sets are highly related to the n k dimensional
O
components (or submanifolds) of an object embedded in a n-dimensional space. Thus, the
;
“material content” of fractal boundaries in n k dimensions (cardinality, length, area, volume,
; ;
etc.) has the property of being “infinite” at some n m dimension (a boundary of a n m + 1
O ;
subset of ) and “zero” at n m + 1. However, it possesses a finite, non-zero fractional value
; ; ;
at n , with m 1 < < m a fraction that codes the (n m + 1)-dimensional space-filling
O
properties of fractal . In this sense, a complexity measure can be obtained to consider the
irregularity and roughness of boundaries only.
Interface phenomena Physical phenomena present particular characteristics precisely at interfaces
and boundaries of objects or sets. This observation directly links structure complexity and
physical interactions. A related remark is that space-filling structures are interfaces (Subsec-
tion 1.6.3). We shall see and illustrate some examples in Chapter 5.1 (Amorphous Photo-
deposition) and 6 (Other Applications: Chromatin and Cellular Nuclei Reconstruction in
Transmision Microscopy). In many physical phenomena, for a given constant volume, the sur-
face extent of an interface augments with increasing rates of exchange of information, or flow
2.2 Discrete Volume Representations and Boundaries 83
of material or energy (e.g. heat dissipation) through convoluted boundaries. Fractal interfaces
tend to develop at active transition regions, and n-dimensional space traversal in a dynamic
system (the blood-vessel networks that have to visit every cell in the organism, for example) is
;
optimized through (n k) dimensional space-filling structures [Wood95, Kalda93]. Moreover,
most differential equations of physics require the knowledge of defined boundary conditions
for their proper solution or analysis, and no numerical method of solution is workable without
such specification, thus boundary-traversal methods, manipulation and feature extraction (or
specification) on discrete boundaries is required in any modeling task.
Boundary-based filtering A set of mathematical relations enable to extract volume characteris-

tics and do morphological operations using b-reps. These include mainly the discrete Gauss
Theorem (Section 2.5.1), and the equivalence bewteen morphological-filtering and boundary-
labeling (Section 2.5). The generality of these relations encourages to further explore ways
to process and extract information of an object or a Region or Volume Of Interest (ROI
or VOI) from its discrete boundaries, and combine it with local, global and internal data
(individual voxel information). Modern theory of image processing has explored relation-
ships between curve-evolution equations, mathematical morphology and scale-space analysis
[Alvarez93, Lindeberg93a]. The resulting mathematical frameworks bear similarities with
boundary-based morphological operations. Besides, it has become natural to extend the curve-
evolution framework on 2D-images to multidimensional manifolds, we only cite some exam-
ples: continuous fronts and level sets [Sethian96], shape description based on incremental
contour deformations [Kimia93], sheet models [Whitten93], estimation of principal curvatures
in cortical surfaces [Joshi95], and manifold mapping of the cortex [Szekely92].
Level-set representations In the framework of level-curve evolution discussed by Cohignac et al.

in [Cohignac92], a 2D image can be either identified with the set of its level curves and then
their evolution is studied, or the image itself can be evolved, using the evolution formulation of
the fundamental equation of image processing, which goes outside the scope of our work, and
we only mention the fact that a similar approach may be devised in three or more dimensions,
giving rise to boundary evolution in n-dimensional images.
A problem related to level sets comes from the fact that volumic data can be rearranged or ac-
cessed in a number of ways, such as stacked cross sections (stereotomies), non-planar internal
surfaces, or scanline samples. These reorganizations allow different modes of volume access,
and different processing and filtering methods: separable operations, dimension-reduction
strategies, data-compression and other specific tasks. Extending this idea, and having in mind
the interpretation of certain 2D-images as sets of level contours, it becomes clear that volume
data can be represented as sets of level boundaries, which may code some kind of homogene-
ity (isolevel or isodensity surfaces, where “density” may comprise more general features, e.g.,
texture measurements).
Layer models Recent works use a similar approach to level sets in the form of discrete fronts or ac-
tive contours [Malladi95, Davatzikos95] and of coupled-surfaces propagation [Zeng98] used
to extract volumetric layers of the cortical gray matter of the brain. This volume representation
is also named “a peeled-onion” model, and allows for some volume processing and under-
standing through sets of discrete “piled” or “peeled” boundaries or layers. A characteristic
drawback is that topology is not well preserved through consecutive layer sets, and homotopic
operations are not always possible, but restrictive principles can be applied, as in the level curve
evolution framework. Homotopy problems can be treated by proper tracking of connected and
unconnected components. An image-processing example of a level-set representation is the
distance field isosurfaces (or isodistance surfaces in this example) of an object O:

Li = fp 2 Oj minq @ (kp ; qk) = zig i = 1 : : : N
2 O
with zi a constant such that 0 z < z < : : : < zN . Level sets Li corresponds to a constant
1 2
distance zi to the nearest boundary points inside an object. This level-set decomposition is
used for example in watershed segmentation of weakly-connected binary objects. In this case,
each distance unit correspond to an order index i of the set of isosurfaces or level sets i L
that constitute the discrete distance field. In a chamfer distance field d(p) N p 2 2
N 3,
two discrete surfaces Sd Sd+1
d(p) which are isodistance subsets separated by one-voxel
unit distance, may share several voxels in function of shape concavities; this property allows
boundary-based characterization and detection of a number of shape features. Another recent
example is 3D thinning by successive nested boundaries 2, generated by simple-point removal
(homotopic thinning) [Marion-Poty94]:
@ 1O b @ 2 O b : : : b @ N O
It is by now evident that discrete boundary representation and manipulation constitute a corner-
stone of numerous techniques of analysis and modeling in all kinds of disciplines. There is still a
lot of work to do for properly relating, integrating and exploiting diverse approaches or frameworks
where b-reps are a timely notion: active (or deformable) models, finite-element and finite-boundary
models, fronts and diffusion equations, discrete differential geometry, integral geometry on geodesic
sets (the boundaries of Euclidean sets), geometry-driven processing, and many other active research
topics. Together with the measurable features of complex shapes reviewed in Chapter 1, we have by
now a broad panorama of analytical methods and potential applications in Scientific Visualization
based on boundary information. We introduce in the following section the elements of a model for
volume and boundary representations.
2.3 A Facet-Based Model for Discrete Surface Representation

The aim of this model is to represent in N 3 a set of solids or regions using their discrete boundaries.
These consist of all the voxels (or voxel faces) that separate objects from background, permitting vol-
ume processing operations and morphometrical calculations. In later sections of this chapter, we use
several definitions which are here presented in a progressive fashion and commented within the con-
text of our work. To this end, in the three following subsections (2.3.1 to 2.3.3) we list the elements
of discrete representations: scenes, voxels, faces, labels, facets and boundaries. In Subsection 2.3.4,
we introduce the adjacency and connectivity relations needed between these elements, and then, in
Subsections 2.3.5 to 2.3.8, the neighborhood relationships that allow to characterize local proper-
ties in voxels (Euclidean neighborhoods), facets (geodesic neighborhoods, along the boundary), and
boundaries themselves.
2.3.1 Discrete Elements: Scenes and Voxels

We review in these paragraphs coordinate systems, scene domains, and voxels. In this and later
subsections some definitions are elementary and can be found in basic literature, such as [Kong89,
2
Recall Definition A.2, and Notation A.1 at page 231: A b B means “A nested within B ”.
2.3 A Facet-Based Model for Discrete Surface Representation 85
Rosenfeld91, Voss93, Udupa93, Udupa94b, Udupa94c, Klette98, Herman98], but we adapt and for-
mulate them to build our model and make more evident their computer implementation. Small-font
remarks may be skipped in a first lecture.
In the following definitions we use real and integer coordinates: points (x y z ) R 3, and 2
2
indices (i j k) N . When (x y z ) are integers, or form a 3D array with fixed distances between
3
points, we say that they form a discrete grid or cubic lattice.
D EFINITION 2.1 (Unit vectors)

The ordered set of unit vectors
U + = (ê1 ê2 ê3) = ( (1 0 0) (0 1 0) (0 0 1) )

is called orthonormal basis or unit system of basis coordinates. The ordered set of axis-
coordinates is denoted by (X Y Z ) and corresponds to basis U + forming a right-handed system U
or trihedron. When any two coordinate axes (or basis vectors) are exchanged or one axis di- êi
rection is reversed, we obtain a left-handed system. The ordered set of negative unit vectors
;ê ;ê ;ê
U ; = ( 1 2 3) is also a left-handed basis.
D EFINITION 2.2 (Grid Orientations)

;ê ê ;ê ê ;ê ê
The ordered set U = ( 1 1 2 2 3 3 ) comprises three orthogonal directions
in the space and six orientations, grouped by opposite pairs. We also define: U =

U . ;
We call U and U vector sets of grid orientations. For convenience, we use also set notation

fu^ g fê g
U = k 5k=0 , U + = i 3i=1, U ; = f;ê g
i 3i=1 , with unit vectors k u^ ê
i , in coordinate u
^k
order as defined for each U U U U .
+ ;
Sets U U are used in the next subsection to associate an orientation and a normal to face elements
of voxels. Other sets and properties will use these sets of vectors, mainly: coordinate offsets, cross
sections, surface tracking and volume-traversal order.
D EFINITION 2.3 (Physical or World Coordinates)

2 f
Let Lx Ly Lz R, scale lengths. The set (x y z ) = (iLx jLy kLz ) j (i j k) 2 N3 g is
called system of physical coordinates or world grid coordinates.
1 Remarks. Non-linear coordinate transformations are usually defined with a mapping W : V ! R3, with
V N3. Then the physical coordinates system is the set x y z W i j k i j k
f( )= ( ) ( ) 2 N 3 g.
D EFINITION 2.4 (Scene Domain or Support)

2 ; ; ;
Let Nx Ny Nz N, and let 0 Nx 1], 0 Ny 1], 0 Nz 1] R be closed intervals. A 3D
scene domain V
R3 (or support) is a 3D array or box of dimensions N x Ny Nz :
V V = 0 Nx ; 1] 0 Ny ; 1] 0 Nz ; 1]
with coordinate indices i j k 2 ;
N, running from 0 to N x 1, 0 to Ny 1 and 0 to Nz 1, ; ;
respectively. We also refer to p 2V as the point coordinates p = (x y z ), where x y z may be
reals or integers. In the latter case, we say that p is a grid point of . V
Remark 1. A n-dimensional image is usually a function from some scene domain to another set (codomain or
range). We will describe later label attributes of a voxel to characterize information of a scene.
Remark 2. It is often convenient to consider a discrete subset of V (or define V in N 3 ) forming a regular grid of
points:
V V = f(xi yj zk ) 2 R3 j (xi yj zk ) = (iLx jLy kLz ) (i jk) 2 N3 g
with Lx Ly Lz 2 R. If Lx = Ly = Lz , then V is called a cubic grid, otherwise it is a rectangular grid or
orthogonal grid. Real matrices with entries fv ijk g is the standard representation of 3D scalar images.
”VOI, ROI” I
Remark 3. A Volume or Region Of Interest (VOI or ROI) of V is often defined as a“box” subset of V as:
VROI = Nx1 Nx2 ] Ny1 Ny2 ] Nz1 Nz2] , such that VROI V. We consider a ROI in general to have any
shape, independent of its contents.
D EFINITION 2.5 (Voxel)

Let V R3 be a scene domain and p = (x y z ) 2 V a grid point. The set
v
v = v(x y z ) = x x + 1] y y + 1] z z + 1]
is called a volume element or voxel at point (x y z ), which is then called reference vertex of v .
Remark 1. Many other grids are possible; they are in general called space tessellations. In many configurations
x y z . For example the points x0 y0 z 0 x y z
62 N ( )=( ) + (1 2 1 2 1 2)
= = = define the voxel centers in a body-
centered-cubic grid. Non-integer coordinates arise also with center-of-mass calculations, sub-voxel precision or
partial volume effect.
Remark 2. When Lx = Ly = Lz , the voxels in world coordinates are called isotropic voxels. Note that
(Lx Ly Lz ) are the physical lengths assigned to the three orthogonal edge dimensions of a voxel, depending on
data interpretation.
Remark 3. A voxel v is a spatial neighborhood of point p = (x y z ), in the body-centered grid, but it is
k k
often treated in literature as p itself. The expressions “ v ”, “v+ (1 0 0)”, etc. refer to coordinate and vector
operations, with k k the Euclidean norm.
Remark 4. In orthogonal grid coordinates v is a cube (and the scene is called a cuberille environment, after
Chen et al. in [Chen85]) with Vol v ( )
1 , in grid units. In world coordinates it is a parallelepiped or prismatic
voxel with 12 side edges, 6 rectangular faces and volume Vol v ( )=
L x Ly Lz . Herman defines a voxel in
general as a Voronoi neighborhood, in other discrete grids (face-centered cubic and body-centered cubic, mainly),
determined by neighborhood configuration. In such cases, voxel shapes are rhombododecahedra or other poly-
hedra, presenting different advantages and properties [Ponce88, Herman98]. We limited our work to rectangular
grids and prismatic voxels. Since we have defined a voxels as closed 3D-intervals, including all 8 vertices and all
6 faces; contiguous voxel intersections (shared faces) are not empty: they overlap (see below).
2.3.2 Discrete Elements: Faces and Labels

It is convenient to fix a systematic enumeration of voxel faces, in order to assign them several proper-
ties as orientation and traversal circuits for b-reps and surface tracking. Our choice was the following:
D EFINITION 2.6 (Voxel Faces)

Let v(x0 y0 z0) 2V
be a voxel. The following subsets of v:
f0 = fx y z j x = x0 y 2 y0 y0 + 1] z 2 z0 z0 + 1]g

f 1
= fx y z j x = x0 + 1 y 2 y0 y0 + 1] z 2 z0 z0 + 1]g
f2 = fx y z j y = y0 x 2 x0 x0 + 1] z 2 z0 z0 + 1]g
f3 = fx y z j y = y0 + 1 x 2 x0 x0 + 1] z 2 z0 z0 + 1]g
f4 = fx y z j z = z0 x 2 x0 x0 + 1] y 2 y0 y0 + 1]g
f5 = fx y z j z = z0 + 1 x 2 x0 x0 + 1] y 2 y0 y0 + 1]g
consitute the 6 faces of v, and denote it by f k 5k=0 . f g fk
Remark 1. Some authors call the voxel faces “3D pixels” [Perroton93], but some confusion arises when con-
sidering voxels as 2D pixels in serial slices. We further introduce orientation properties, thus we retain the term
“voxel face”. Notice that the words “a single voxel” implicitly define v as the foreground against the background
vc (see Definition 1.3).
Remark 2. The order numbering of faces f k f g5k=0 will be associated with the set of grid orientations U (See
Figure 2.1).
Remark 3. Consider two voxels such that v a vb k ; k=1 (thus, “adjacent”, as defined later). Let f ka 5k=0
f g
f g k 5 (
be the faces of v a and f b k=0 the faces of v b. If, for example va v b are voxels at xy z and x ) ( +1 ) y z
respectively, then f 0a is the same set of points that f 1b , and v a vb share the same face (See Figures 2.1d-e). We
make however a distinction of face orientations in order to introduce voxel faces at object boundaries as facets.
Remark 4. Similar enumerations were done for other voxel elements, such as vertices, edges, diagonals and
diagonal planes, when needed in our implementation. Their definitions are straightforward.
It is important to notice that the face centers of a voxel at (x 0 y0 z0) are located at points (x0 y0 z0)+
u^
1=2 k + (1=2 1=2 1=2) .
D EFINITION 2.7 (Oriented Faces)

f g
Let f k 5k=0 be the faces of a voxel v (x0 y0 z0). Let the grid orientations U = k 5k=0 define fu^ g
f u^ g
the six face orientations. Then, the set of pairs (f k k ) 50 is called the oriented faces of voxel
u^
v , and each k is thus a unit normal vector of the oriented face f k .
Remark 1. Let v k 5k=0 be the voxels at x y z

f g ( ) = (x0 y0 z0 ) + u^ k , with u^k 2 U . The set of pairs
f( v \ vk )g^ k also define the oriented faces of v.
u
Oriented faces point outwards of voxel v. For two consecutive voxels v a (x y z ) and v b (x +
1 y z ), the oriented face (f 0a û0) of voxel v a points to the opposite direction than the oriented face
(f 1b û1) of voxel v b (see Figure 2.1). We found convenient to work in certain cases with a comple-
f g
mentary set of inwards-oriented faces, associating f k 5k=0 with U , instead of U . The choice of
one set or another define orientation on a discrete surface composed of voxel faces (described in next
Z
(a)
f1 X
3 f5 Y
f
f0 f2
(b)
(x,y,z)
4 (x,y,z)
f (c)
f 0 or f 1 ^
1111
0000 u 0
0000
1111
0000
1111 f0
0000
1111
0000
1111
0000
1111 (e) (g) foreground
(d) (f) background

Figure 2.1: Voxels and faces. (a) A voxel indicated at point p = (x y z), by a “ ”, chosen as the reference
vertex. Faces f 1 f 3 and f 4 are indicated though not visible at the opposite sides of f 0 f 2 and f 5.
(b) Right-handed trihedron of axis coordinates (X Y Z) used to locate points, voxels and to number their
faces. (c) Other grid and other voxel definitions: face-centered cubic (fcc) and body-centered cubic (bcc), at
(x y z) + (1=2 1=2 1=2). The set of points of face f 0 of voxel (d) is “the same” of the face f 1 of voxel (e),
but an orientation and a unique choice are defined when foreground and background labels are assigned to
voxels (g) and (f) respectively.
subsection). We define the face-based boundary of a single voxel v as:
@ v = ff k gk5
=0

with its orientation ( ) given by the face orientation, either outwards (“+”, choosing U ) or inwards
;
(“ ”, choosing U ).
In order to refer to information in a scene support and identify specific subsets (objects, regions
or points), we define the following attributes of voxels and scenes.
D EFINITION 2.8 (Voxel Labels)

fV g V
Let n N L
n=0 be a set of subsets of a scene domain. We can assign a label to each subset.
f 2 g
Let A = n N n=0 N L and : L V!
A, such that
(8 n 2 0 N ] (v 2 Vn ) ) ) (L(v ) = n ):
L
We say that v has a scalar label n , or that v is a “ n -voxel”.

n-voxel I
A labeled scene or simply scene is the pair ( ) = (

VL V fL(v) j v 2 Vg).
When V is partitioned into NL disjoint subsets, i.e., V NL n , with i = V
j ∅ for V \V =
Remark 1. n=0
6=
i j , with labels A NL= 0 ; 1] N L
, and mapping as above, we call V a scalar field, 3D scalar image or
( )
gray-level volume, and voxel v x y z has assigned a gray-level value v x y z L( ) = L(
N L . ) 2 0 ; 1]
Remark 2. Vector labels of dimension D arise when n 2N D. A common example with D =4 are color labels
denoted by ~ v
L( ) = ( ) 2
R G B describing red, blue, green and transparency intensities for each v V, a color
scene. Real-world data are obtained often as discrete samples of continuous domains, and produce n-dimensional
scalar, vector or even tensor images.
Remark 3. The expression “v xy z( )= ( )

” suggests that voxel v at xy z has assigned a label . But v is
a defined region of points in 3, not a function, and it would be better to use v
R L( ) =
to refer to the label or
( )
“contents” of voxel v at point coordinates x y z .
Remark 4. Six voxel-face labels assigned to the faces f ka 5k=0 of a voxel v a can be rather defined in terms of
f )g
a vector label ~ of dimension 6 assigned to v a , with scalar components
L f ka ka 5k=0 .
f L( ) = g
Remark 5. We call V 2 ( L)
V a set of -voxels or -set. Since it may happen that card(V ) 1 V
> , can
be composed of various connected components. Once defined K -connectivity, we will have K -connected objects,
with connectivity depending on adjacent voxels sharing the same label (see Section 2.3.4, page 96).
N OTATION 2.1 (Binary Labels: 0-voxel, 1-voxel)

LetVV f g
, and let B = 0 1 be a set of binary labels, and the mapping B L : V ! B such that:
LB (v) = 0 () v 2 V c then v is called 0-voxel
LB (v) = 1 () v 2 V then v is called 1-voxel:
LB is called a binary function or labeling, V is the foreground, and V c is the background.
We also call a pair (V L B ) binary scene, with LB as above.
N OTATION 2.2 Let L(v ) 2 f0 1g a binary labeling. We denote its binary-label complement as
L(v) = 1 ; L(v). Moreover, if v is a -voxel at (x y z) 2 f0 1g, we define the -voxel v at
(x,y,z) as the voxel such that L(v) = L(v ) = 1 ; L(v ).
Remark 1. v c is a set complement (“all voxels excepting v”), while v represents a logic 1-complement (the
same voxel with the opposite label of v), defined only for voxels with binary labels.
Selection and classification of points q 2V VL

(or ( )) proceed by stating propositions about q and
L
its attributes, such as (q ) (binary itself, gray levels or other information), and examining if these
propositions are true or false (predicates of the proposition) [Pavlidis74]. A single proposition about
q partitions the scene domain into two sets. This process is the scene (binary) segmentation, which
generalizes Definition 2.1. A 1-object is any W VL
( B ), composed of 1-voxels.
In summary, a binarization process partitions a scene into 1-objects composing the foreground,
and 0-objects constituting the background. The first include all kind of particles, bodies, etc., and
V
the second comprise holes, pores, cavities, etc. Note that the starting scene may have other infor-
mation and binary segmentation came out from a proposition about points in and a segmentation V
procedure to evaluate or estimate the predicate for all the scene.
2.3.3 Discrete Elements: Facets and Boundaries

From the different definitions given so far, we may now introduce the notion of discrete boundary
elements, which are the voxels and voxel-faces that separate foreground from background (under
some labeling process) in a scene. We state this notion in the form of an existence theorem in what
we shall see is the “6-connectivity”, but may be extended to other connectivities (to be introduced
later):
P ROPERTY 2.1 (Boundary Voxels, Boundary Faces (Facets))

V
Let a binary segmented scene. Let V V V
such that is a set of 1-voxels and c its complement V
of 0-voxels. Let = ∅, V6
c = ∅, V6
then,
9 2V 2V 2
( v1 v 0 c k 0 5] ) such that v 1 v 0 = k k U ; u^ u^ 2
thus, kv ; v k = 1 in unitary grid coordinates.
1 0
and,
9 voxel faces f i 2 v f j 2 v with i j 2 0 5] such that j = i + (;1)i:
1 0
In fact, i k (face and unit vector indices). We call

✦ the ordered pair f = (v f i ), a facet of V (or boundary oriented face),

f + 1
✦ the ordered pair f = (v f j ), a facet of V c ,

; 0
✦ the 1-voxels v , boundary voxels of V , and
1
✦ the 0-voxels v , boundary voxels of V c .
0
Remarks. The rule “j = i + (;1)i ” is only a way to code face indices into pairs of opposed orientations:
f(f i f j )g5i=0 j=i+(;1)i = f(f 0 f 1 ) (f 1 f 0 ) (f 2 f 3 ) (f 3 f 2 ) (f 4 f 5 ) (f 5 f 4 )g
Indices i j could be related following any look-up table. See for example f 0 f 1 in Figure 2.1d-g.
By construction, boundary oriented faces (hereinafter simply denoted facets) satisfy the following
properties issue from the existence property. The proofs are trivial.
C OLLORARY 2.1 (Facets as Pairs of Voxels) A facet, without regard to orientation ( ), can also

\ ;
be defined as f j j = (v0 v 1); an orientation (+) or ( ) can be assigned from the expression
; u^ 2
sign((v0 v 1) k ), with k 0 5] such that (v 0 v 1) k ) = 0. ; u^ 6
When orientation is assigned, the facet f + = 1

(v f i ) i 2 0 5], can be also uniquely associ-
ated with the ordered pair of 0- and 1-voxels (see example of Figure 2.1f,g, in page 88):
f+ () (v0 v1 )
conversely, the opposite facet f; = (v0 f j ), with j = i +(;1)i can be associated with the ordered
pair:
f; () (v1 v0 ):
f g
Thus, if we know f , we know v1 v0 (see below the facet-to-boundary-voxel operator ). A choice
f+ is called outwards-oriented. We have now the elements for the practical implementation of facet
representation:
C OLLORARY 2.2 (Facet Representation) A facet f = (v fk ) of voxel v (x y z ), at oriented face

2
f k k 0 5] is uniquely specified by the vector (x y z k), or more explicitly by the pair ((x y z ) k), û
u^ 2
with k U , the signed unit vector which is the normal to the oriented faces f k .
Remarks. In terms of discrete boundaries, a facet is most of the times a “boundary element” or bel, or also a
surfel for “surface element”, in the multidimensional generalization introduced by Udupa in [Udupa94c]. Since a
set of facet elements alone may constitute ribbons or open surfaces (not boundaries, which are closed), we preserve
the term “facet”. We also use voxels as boundary elements (see below, Definition 2.12, page 93). While there are
some analogies with 2D pixels and pixel borders, 3D rectangular facets possess two relevant attributes: orientation
and an associated set of lateral traversal circuits, which are assigned in function of facet orientation, and introduced
later.
Rosenfeld et al. and Udupa used in [Rosenfeld91, Udupa90] an alternative notation to de-
scribe oriented boundary faces. It recalls the set U of Definition 2.2, but refers to the ordered
set (f 0 : : : f 5 ) “combined” with the coordinates of the boundary voxel v (x y z ) of a given facet.
We change slightly some details for clarity; in essence, they defined
F 6 = (x; x+ y ; y + z ; z + ) (2.1)
as a partition of any set of facets into six subsets, in function of orientation. They further identified
F
directly a boundary face with a pair (v 0 v1 ), with one of x y , or z in 6 as follows: F6
Coordinate notation with F 6 Facets (v1 f k ), or f = (x y z k)
(x; y z ) (x y z 0)
(x+ y z ) (x y z 1)
(x y ; z ) (x y z 2)
(x y + z ) (x y z 3)
(x y z ;) (x y z 4)
(x y z +) (x y z 5)
With this classification, facet f (x y z 2) is a “y ; -facet”, for example. Notation using “ 6 ” is F
;
not always clear (neither the one used by Udupa, and Rosenfeld et al., with “ x +x : : : ”), but we
explain it for compatibility with literature where surface tracking implementations are proposed and
F
use 6. This partitioning is also used by Udupa to describe boundary opposed facets, for run length
F 6 ;
coding. We use 6 mainly with this connotation. Notice that x ; = x+ , etc., the sign indicating
;
only opposed face directions on the axis X . Thus, we avoid the use of “ x +x, etc.” in this notation.
2
The symbols f and subindexed f n , n N+ are reserved to indicate any facet of the boundary without
reference to its orientation (however comprised in its description by (x y z k) ).
opface()
D EFINITION 2.9 (Opposite-Face Operator)
Let v1 2V , v0 2V
c a 1-voxel and an adjacent 0-voxel, such that f + = (v1 f i ) and f; =
;
(v0 f j ), with j = i + ( 1)i. We define a mapping opface( ) between facets, such that f =
opface(f ). We call it the opposite face operator.
Remarks. Operator opface( ) swaps the face-orientation interpretation of face f i (thus, the sign of the facet
i
normal), and the face index of f from i to i i , and the associated pair v 0 v 1 is substituted by its mirror
+ (;1) ( )
( )
v1 v0 . This operator allows to interpret a foreground boundary as the negative of a background boundary, and
V
conversely. In discrete convex objects, they always enclose runs of voxels of , but in non-vonvex objects, they
may enclose voxels of the foreground (concavities, holes, tunnels or cavities).
At this point we can define the boundary of an object in a scene (volume representation) in at
least three ways:
✦ Continuous point boundary @^ . The (continuous) set of points defining the boundary.
@
✦ Discrete Face-Based Boundary . The (discrete) set of facets (boundary-oriented voxel faces).
✦ Discrete Voxel-Based Boundary . The (discrete) set of boundary voxels (or grid points).
In the following paragraphs we provide a precise definition of each b-rep, their relationships, and
how to pass from one to another. Applications, advantages and limitations are mentioned on the way.
D EFINITION 2.10 (Continuous Point Boundary)

V
Let be a binary scene and VV
a 1-object. Then, the set 3
@^ V @^ V =

f(x y z) 2 V j 9 v 2 V c 9 v 2 V such that (x y z) 2 (v \ v ) g
0 1 0 1
is called continuous point boundary of V .
If V V (the cubic grid), @ ^ V consists of all points at intersections between 1- and 0-voxels. There
are three ways in which the condition “(v \ v ) = 6 ∅ ” arises in the cubic grid. Voxels v v (the
0 1 0 1
object foreground and its background) share either:
kv ; v k = 1 ), or p
✦ a face (i.e., 0 1
✦ only an edge (i.e., kv ; v k = 2 ), or
p 0
✦ only a vertex (i.e., kv ; v k = 3 ).

1
0 1
This distinction introduces different “K” connectivities in discrete representations (K = 6 12 8 in

the above cases, with strict equalities). We examine more closely adjacency and connectivity in
Subsection 2.3.4. For the moment we consider only face intersections, since the surface area of the
\
set (v 0 v1 ) is not zero when v 0 v1 = 1. k ; k
^V
Remarks. Even if the voxels correspond to grid points, @ is a continuous boundary, since 9( x y z ) 62 N3,
(
such that x y z)2( \ )v 0 v1 . A discrete boundary is then specified not by the totality of its real points but by
enumerating either the facets or the boundary voxels. Notice that most definitions given in Section 1.1, pages 23-
^V
28 and Appendix A apply to @ , and some can be translated directly for discrete boundaries. Facet orientation
(using either U or U ) provide the means to introduce oriented boundaries and allow a formal definition of solid
interior for discrete objects.
D EFINITION 2.11 (Discrete Face-Based Boundary)

V
Let a binary scene, VV be a 1-object. The set
@V @ V = f f = (v f k ) j 9 v 2 V 9 f k 2 v f k @^ V g
1 1 1
is called face-based boundary or facet boundary of V .

Setting N = card(@ V ), we also write @ V = ffn gnN . facets
If facet orientation is outwards (choice U ), then @ V = @ V is a positive oriented boundary.

facets =1
+
V
Remark 1. @ is a finite set of Nfacets subsets f k , that is, of oriented voxel faces contained in the continuous
^V
boundary @ . Face-based boundaries are illustrated in the Figure 2.2a.
Remark 2. When the operator opface( ) 2 V

is applied to all f @ , the boundary orientation is inverted allowing
to define negative boundaries also as: @ ;
V @ + , and conversely (see Definition A.4, page 232).
= opface( V )
This definitions allow to characterize and manipulate discrete cavities.
3
For simplicity, we used symbol @ to denote continuous and generic boundaries in Chapter 1.
D EFINITION 2.12 (Discrete Voxel-Based Boundary)

V
Let a binary scene, VV be a 1-object. The set
V = fv 2 V j 9 f k 2 v k 2 0 5] such that (v f k ) 2 @ V g V

is called voxel-based boundary or solid boundary of V .
Setting N vox = card( V ), we also write V = fvm gNm . vox
=1
V , the geometric interior of Definition

V
Remark 1. Using the solid boundary 1.5 (page 25) in the discrete case

is the set V= Vn V . There may be nonempty objects for which V = ∅, or it consists of several connected
components, but a discrete version of the Jordan property about closed, simple boundaries [Udupa94c, Herman96])
allows to consider these cases. No discrete geometric interior is defined with face-based boundaries.
Remark 2. The 2D equivalent of V

are classic contours formed by pixels. The 2D equivalent of @ are V
edge-based boundaries, which are mentionned in some contour extraction methods, active contours, Markov-field
segmentation and cell complexes. The present work should be easily adapted to 2D applications.
Remark 3. No orientation was attributed to V in our implementation, but boundary voxels could be orientable
if their facets remain adjacent (a non-simple point is a counterexample). If orientable, an average normal could be
assigned. We conjecture that orientability is related to satifying or not the Jordan property.
Since there is one and only one voxel at p = (x y z ), the boundary V
is isomorphic to a list
of point coordinates (x y z ). An algorithm to extract V V
, without passing by @ , is presented in
[Voss93]. Voxel-based boundary representation is illustrated in Figures 2.2b,d and the three bound-
V
^ @ of a sphere r are compared in Figure 2.3. Comparison of @ and is also illustrated
aries @
in Figures 2.2c,d by removing aside a (thin) wall of facets and a (thick) wall of voxels in each case.
Conversion between the two discrete b-reps is possible, and we introduce two operators to do it.
We first observe that a unique boundary 1-voxel is obtained directly from f = (x y z k) @ 2 V
as the voxel v at (x y z ). To obtain the 0-voxel v 0 “at the other side”, we recall that face-index k is
u^ 2
the index k U ; thus v 0 = v1 + k . u^
D EFINITION 2.13 (Facet to Boundary-Voxel Operator)
Given a facet f (x y z k) we define the facet to boundary-voxel operator as
facettovox()
(v0 v1 ) = facettovox(f (x y z k)) = ( v(x y z ) + u^ k v(x y z ) )
Remark 1. As defined, this operator is consistent with the definition of f + as the ordered pair (v 0 v1 ).
Remark 2. Since several facets may share a single boundary voxel, it follows that card(@ V) > card( V). We
conjecture that the case “=” corresponds to an infinite wall of voxels. In our implementation of the facettovox( )
operator, redundancy of boundary voxels v 1 is eliminated during conversions by labeling in a scene these v 1 ’s. If a
voxel has not been visited, it is un-labeled and we add it to the list of boundary voxels. This process is independant
of the voxel order chosen.
For the inverse operation, given a 1-voxel v 1 2 V

, there is at least one 0-voxel in contact with
2
it, determining one facet f . To obtain all facets fn v 1, with n 6, we identify all v 0 c suchf g2V
k ; k
that v 0 v1 = 1, by neighbor examination (up to 6 cases). In other words, the corresponding
2 u^
indices k of each face f k are those k 0 5] such that v 1 + k is a 0-voxel.
(a) face f 5 (b) voxel v

5
facet f = ( p ,f )
p p
(c) V ={ facets f n } (d) V ={ voxels v m }

fa f
a
f
b
Z
fc Y fb f c
V
Figure 2.2: Two boundary representations (b-reps) of object . (a) A point p = (x y z) and an oriented face
2
f k , k 0 5], for example, f 5 ; the boundary element is a facet f . (b) The voxel at p is a different, “3D” kind
V f g
N
of boundary element. (c) Face-based boundary @ , made by facets fn 1 facets ; the (thin)“wall” of facets
V
with face f 1 has been removed to show how @ is composed of facets. (d) Voxel-based boundary V
f g
, made
by voxels vm 1Nvox ; the (thick) “wall” of voxels corresponding to facets with face f 1 , has been removed to
show how V is composed of voxels (becoming a “double wall” of facets). Notice the corresponding tagged
facets fa fb fc in both representations, with facet f a invisible in (d). Facets fb fc share the same voxel.
D EFINITION 2.14 (Boundary-Voxel to Facet Operator)

Given v1 2 V and all v 0 n1 f g 2V
c , with n 6, such that v 0 v1 k ; k = 1, the faces f k =
\ 2 f g
(v0 v1 ) k 0 5] determine the set of m facets f n nn==1m = (v1 f k ) k 2 0 5] 1 m 6.
Such a procedure is called boundary-voxel to facet operator:
voxtofacet() voxtofacet(v(x y z )) = f fn (x y z k) some k 2 0 5] gnn==1m
( )
Remark . Facet index n of f n x y z k enumerates all facets of a boundary voxel (at least one, at most six). It
is not related to index k indicating face orientation (f k ).
P ROPERTY 2.2 (Boundary Conversions)

The following equivalences hold, when applying the conversion operators boundary-voxel by
boundary-voxel or facet by facet, with redundancy eliminated:
@ V = voxtofacet( V ) (2.2a)
V = facettovox(@ V ) (2.2b)
(b)
∋
f(x,y,z,k) V
(a)
p=(x,y,z)
∋
V
(c)
v(x,y,z) ∋
V
Figure 2.3: Boundary representations of an object V and frontier elements for each b-rep: (a) points p =
(x y z) (symbol “ ”) for continuous boundaries @^ V ; (b) facets (romboids, triangles, and oriented faces
f(x y z k) ) for face-based boundaries @ V ; (c) voxels v(x y z) for voxel-based boundaries V .
Remarks. If V;is considered as isolated, it may have N int cavities V r r 2 1 Nint ]. Thus, it has inner, negative
boundaries “@ r V ”, and the last relations are unions of all components.
V
Solid Interior of a Face-Based Boundary Let @ composed by one single component; or take the
Vj
outmost boundary @ out (see Definition A.9, page 235) such that all boundary components of are V
Oj
contained inside @ out . For simplicity we consider the first case (no cavities). Then, the discrete
V V
solid interior of is the set itself, as defined operationnally (“traversed”) from its continuous
boundary @ V
^ (see Notation A.2), when a traversal method exists. In N 3, the discrete solid interior is
expressed in terms of its solid boundary and its geometric interior: interior( ) = V
. We give

V V

V V
now a way to express in terms of the face-based b-rep of ; that is, how to traverse using facet V
V
information. When cavities are present (thus @ is multiply-connected) we then consider @ out for Vj
V
the solid interior of , filling out all its cavities.
V
A traversal method to define all solid interior points of , given its boundary @ , is now de- V
scribed.
Consider runs of voxels between opposite facets f = (x y z k) of a boundary @ , sharing two V
coordinates (e.g., y,z, thus colinear in axis X ). We consider only runs starting at a boundary voxel
of a given facet, running in the opposite direction of its normal, and ending at the opposite facet;
V
thus the runs lie inside . These runs may consist of at least one voxel. We could equally take other
V F
partitions of @ , as explained in page 91, using 6 (Equation 2.1), e.g., all the pairs “(y ; y +)” and
“(z ; z + )”. Sorting of facets into corresponding opposites is done easily during surface tracking, as
explained later, since all x y z k are available. These runs constitute all the interior of @ (hence, V
V
of ), including V . We have then:
D EFINITION 2.15 (Discrete Solid Interior of @ ) V

V
Let @ be composed by a single connected component. Let also
F = f(xa y z 0) (xb y z 1) 2 @ V j xa xbg

01 (2.3)
be a subpartition of @ V into opposite facets f (x a y z 0) and f (xb y z 1); then the set:
interiorx interior (@ V ) = f v(x y z ) 2 V j (xa x xb ) ^ ( (xa y z 0) (xb y z 1) 2 F ) g
x 01
is called the x-solid interior of @ V (or solid interior by x-runs (x a y z ) (xb y z )]).
Remark 1. Solid interiors by y- or z -runs of voxels are similarily defined. In the “x ”-notation, opposite facets
in 01 are pairs of type x; x+
F ( )2F 62 . Note that the direction of runs (two, from x to x ) are defined to
2
^ k U of the ending facet.
match the normal u
V
Remark 2. When the boundary of is constituted by several connected components, i.e., @ V = SNk @ @k V , then
V
each component interior defines a ”fragment” or ”cavity” of .
P ROPERTY 2.3 (Volume Traversal)

V V are equivalent:
The x-, y -, and z -solid interiors of @ and
interior (@ V ) interior (@ V ) interior (@ V ) = V
x y z
Hereinafter, we drop the subindex, and use by default x-runs from facets with orientation f 0 (i.e.,
x; ) to facets with f 1 (i.e., x+ ). Demonstration of this property is trivial and very similar to the
f g
Property2.1, using either the ordered set of face orientations f k 50, or the partition 6 , of facet F
coordinates, which are equivalent. Cavities have not been considered here, but if @ is composed V
of several parts (nested boundaries), internal facets can be found to match by pairs with indices
;
j = k + ( 1)k . The way to find such nested boundaries is treated in Section 2.4. Since all voxels
are visited, we have thus defined a volume traversal method.
To simplify discussion, we have employed till now a strong voxel-adjacency condition: bound-
k ; k
ary voxels share a face, or equivalently a boundary pair (v 1 v0) satisfies: “ v 1 v0 = 1”, in grid
units. In particular, this condition was required in several definitions about boundary voxels as sets
\
of points (i.e., v1 v0 is a facet). It is a special case of K -adjacency, with K = 6, as presented in
the following paragraphs. Several concepts need to consider the type of connectivity and adjacency.
2.3.4 Discrete Adjacency and Connectivity

A set of voxels with the same label (representing objects or background) may form one or more
connected components. In discrete topology we must define what connectivity means, as in the
2D case, because the number of components may change in function of the initial choice of fore-
ground and background connectivities. This is equivalent to the mathematical assertion that cardi-
nality of a set depends on its topology, and topology changes in function of connectivity relationships
[Kovalevsky89, Voss93]. Thus a consistent choice must be made and preserved during analysis. A
(a) (c)
" x - wall"
y
V
x
x- (b) x+ N xfacets
V V = { ( x - , y, z, 0) j }j=1
x-
u0 u1
Figure 2.4: Facet walls. (a) Facets of V

@ are classified by their orientation u^ k , forming opposed pairs
(x; x+). V
Object is fully contained between any of its three sets of opposed facet walls. (b) Traversal
direction from x; to x+ . (c) A ”facet wall” is the subset of all facets fj = fj (x y z k) k = 0 : : : 5 in
F
partition ; for example, @ x; .Vj
convenient solution is to introduce K -adjacency and K -connectivity , with K a parameter depend-
ing on the geometric properties and the ways that volume elements are organized in a discrete space.
The term connectivity is broadly applied to regions, subsets of objects (for example a discrete path,
or a discrete submanifold), or sets of voxels, and adjacency denotes connectivity in the immedi-
ate neighborhood of a voxel, that is, at the minimum discrete distance (grid resolution). Discrete
distances are in turn defined for each K , in function of space tessellation.
Since we adopted the cubic grid for our model, connectivity in 3D is an extension of the 2D case
(the square grid): pixels, contours and regions with 4- or 8-connectivity become voxels, boundaries
and regions with K -connectivity. Adjacency between voxels depends on neighborhood relations.
They may either:
✦ share one face and then possess up to 6 neighbors (6-adjacency), or

✦ share only an edge, and contact up to 6+12=18 neighbors (18-adjacency), or
✦ share only a vertex and contact in this way up to 6+12+8=26 neighbors (26-adjacency).
Thus, K 2f g
6 18 26 in the cubic grid intersections. With these intuitive notions, we proceed
with the following definitions. Facet and voxel adjacency and connectivity relations are illustrated in
Figure 2.5.
D EFINITION 2.16 (K -Adjacency of Voxels)

Let va vb 2V
be two voxels. We say that
✦ va vb are 6-adjacent iff kv a ; vbk = p1,
✦ va vb are 18-adjacent iff kv a ; vbk p2,
✦ va vb are 26-adjacent iff kv a ; vbk 3.
Remark 1. The latter definitions are equivalent to those given above, since Euclidean distances between faces,
edges and vertices satisfy the indicated inequalities. In n a K -adjacency is defined by v a vb 2 n, with K
N k ; k
the number of induced neighbors in the orthogonal grid and n < K < n
2 3 ;1 [Malandain93].
Remark 2. Other connectivities are possible; for example, Gordon et al. defined a “T u ” connectivity where the
voxels are adjacent if they share an edge parallel to any two fixed coordinate axes orthogonal to axis u2f X Y Z g
[Gordon89]. The justification for such anisotropic connectivity is that some faster implementations avoid a natural
redundancy found in the isotropic K -connectivity (see [Gordon89b, Perroton93]. Several problems arise when the
same object is rotated because the anisotropic version of the surface tracker is not orientation-invariant. While this
drawback may be irrelevant in some applications (mainly visualization, using strictly cubic voxels), it is critical
for homotopic shrinking, normal estimation, slice-interpolation and other processing and morphometry operations,
specially when dealing with fine structures. We have thus restricted our implementation to the original choice of
isotropic connectivity used by Artzy et al. in [Artzy81].
Remark 3. In some applications, the above definitions are often defined as strict equalities. In such a case,
Figures 2.6c, e, and f illustrate minimum K -connected paths between two points, with K = 8 12 6
, respectively
(see also below, Definition 2.19). Cellular complexes generalize these connectivity possibilities, counting edges
and vertexes as candidates for boundary elements, besides voxels and their faces.
Remark 4. Voxel adjacency can be also defined from grid coordinate differences of 1
between K -adjacent
voxels; for example they differ in one or two coordinates for K = 18
, and in exactly one coordinate for K . =6
Adjacency of the facets is defined in terms of their boundary voxels. The number of adjacents
may vary in terms of voxel configuration.
D EFINITION 2.17 (K-Adjacency of Facets)

Let v a vb 2V be two K -adjacent boundary voxels. Let f f 2 (va vb) (at least one per
voxel, at most six per voxel). We say that f f are K -adjacent if
✦ for K = 0, f and f share the same 1-voxel (v a = v b ) and one edge (their face
orientations are orthogonal and the associated 0-voxels are 6-adjacent),
✦ for K = 6, f and f share an edge (they are edge-adjacent, and they belong to 6-adjacent
voxels),
✦ for K = 18, f and f share an edge, and belong to 18-adjacent voxels (they share the
same 0-voxel),
✦ forK = 26, f and f share a vertex (they are vertex-adjacent, and each one belongs to
26-adjacent voxels.
Since facets are boundary elements, facet adjacency is also called geodesic- or surface-
connectivity.
Remark 1. Adjacency refers to neighboring voxels or facets sharing at least a point. Note that voxel and facet
adjacency is a symmetrical, but not transitive relation. K -connectivity is the condition of pairwise K -adjacency
in a path bewteen voxels or facets, and turns out to be a symmetrical and transitive relation (thus, it is a reflexive
relation [Klette98]).
D EFINITION 2.18 (Connected Facets)

2 V
Let fa fb @ be two facets. We say that fa fb are K -connected iff
9 n 2 N 9 ffk gnk 2 @ V such that

=1 (2.4)
(f = fa ) ^ (fn = fb ) ^ (8 k 2 1 n ; 1] fk is K -adjacent to fk )
1 +1
where K 2 f6 18 26g. The sequence ffk gnk which is the shortest among all such paths, is
=1
called a geodesic K-connected path between fa and fb , and n is the length of the path.
Remark 1. True geodesics imply a notion of shortest length, which is better defined in terms of a metric defined
^V
on @ . In discrete spaces, the metric depends on the choice of K -adjacency and K -connectivity, since different
paths arise between surface elements.
D EFINITION 2.19 (Connected Voxels)

V
Let va vb be two voxels of object . We say that v a vb are K -connected iff
9 m 2 N 9 fvk gmk 2 V such that =1 (2.5)

(v = v a) ^ (vm = vb ) ^ (8 k 2 1 m ; 1] (vk is K -adjacent to v k ) )
1 +1
where K 2 f6 18 26g. The sequence fvk gm

k is called a K -connected path (or K -path) be-
=1
tween va and v b .
Remark 1. It may happen that for some other j k 2 0 ]
n facets f j and fk are also K -connected (idem for v j
and v k ). Multiple paths are useful to define ”non-simple” paths.
0-adjacent facets 18-adjacent facets

26-adjacent facets
6-adjacent facets
(a) (b) (c) (d)
Figure 2.5: Adjacency relations between facets and between voxels: (a) single voxel, (b) voxel adjacency
by face (6-adjacent voxels), (c) by edge (18-adjacent voxels), (d) by vertices (26-adjacent voxels). Facet
adjacencies are also indicated. A 0-voxel (background) is shown in (c).
Remark 2. Cardinality of a set VV depends on connectivity and adjacency relationships. For example, in
Figure 2.5, the number of K -connected objects depends on K :
(a) and (b): 1 object 0

for all K > ;
(c) 2 objects if K=6 ,
(c) 1 object if K 18 ,
(d) 1 object if K= 26 ,
(d) 2 objects if K 18 .
Analogously, Figures 2.6c,e,f have one object for K = 26, three in (c) for K 18, and three in (e) for K = 6.
In summary, an object connectivity is defined by local adjacency of its elements. Several combina-
tions of background connectivity (K 0) and foreground connectivity (K 1 ) are possible, but to avoid
connectivity paradoxes 4, compatible choices are proposed:
4
e.g., a 18-connected ’wall’ do not separate a 18-connected background.
(a) (b) (c)
(d) (e) (f)
Figure 2.6: Connectivity relations between voxels tagged with a “ ”: (a) both, 18- and 26-connected, (b)
6-, 18- and 26-connected, (c) 26-connected only, (d-e) both, 18- and and 26-connected, (f) 6-, 18- and 26-
connected at the same time. Tagged voxels are K -connected if there is a path of pairwise K -adjacent voxels
foreground K 1 -connectivity background K 0-connectivity

18 6
6 18
26 6
6 26
18 26
26 18
The combination “(6 6)”, even if consistent, is not very useful, due to loss of information and be-
cause it does not allow to define surfaces satisfying the Jordan property (simple and closed, partition-
ing the space into interior and exterior). Combinations such as (18 18) or (26 26) are not useful,
too, causing holes and tunnels where separability should be expected. We denote the choice of a
specific ordered pair as (K1 K0)-connectivity . If the opposite is also used, then we denote both as
f g
K1 K0 -connectivities (idem for adjacency, in the immediate neighborhood).
Toriwaki et al. also introduced a conditioned 18 0-connectivity [Klette98]. Serra, Morgenthaler
proposed choices of (K1 K0) 2f g
(6 26) (26 6) , which are compatible with mathematical the-
orems on discrete Jordan paths in the orthogonal grid [Serra82, Morgenthaler81], while Kong and
Rosenfeld further applied an algebraic topological approach to homotopic transformations in N 3 and
f g
proposed to use 6 18 -connectivities [Kong89]. For Zn, Malandain provided a formal characteri-
zation for a choice of discrete connectivities in voxel surfaces (or solid boundary components) K V
and cell complexes [Malandain93].
Face-based boundary representation is better suited to edge-sharing adjacency, with 18- or 6-
connectivity for voxels, which is also a choice free of topological paradoxes. Since cavities are back-
ground connected components, we prefered to treat them as similar as possible to foreground objects.
We thus excluded vertex sharing as a connecting property and worked with choices (K 1 K0) 2
f g
(6 18) (18 6) for boundary extraction and representation using mainly the pair (18 6). Thin,
filamentary structures (blood vessels) and medial axis transforms (skeletons) require a different
treatment (thin fragments), where connectivity should be restored and topology preserved during
thinning. In that case a choice (K1 K0) = (26 6) enhances particle connectivity under “strict”
segmentation. We will come back to these issues in Section 2.4.4 and in Chapter 4.
Another restriction arises if K 1 = 6, since facets can have different adjacents if 18-connectivity
V
is choosen for @ . This is illustrated in Figure 2.6a, where two points are not 6-connected, but
they are 18-connected. When facet connectivity is analyzed, Rosenfeld and Kong distinguish 18-
connectivity in Figure 2.6a from the “stronger” 18-connectivity of Figure 2.6b, where a 6-connected
path of voxels exists between the tagged points [Rosenfeld91]. These voxels have at least one facet
in the 18-connected boundary.
In the rest of this chapter, unless otherwise stated, we use (K 1 K0) = (18 6) connectivities for
facets and voxels, and recall it explicitly ( K ) where connectivity for other entities (neighborhoods)
are also used, or a particular property is only valid for that connectivity. Face-based boundaries @ V
are always defined as 18-connected (voxels sharing only a vertex are not connected).
We are now able to count all connected components of a scene.
D EFINITION 2.20 (A Scene as a Set of Objects)

fV g
Nobj
Let i i=1 be a set of K -connected 1-objects in V. If
0 N 1
@V = ViA ^ ; Vi \ Vj = ∅ 8 i j 2 1 Nobj] (i 6= j )
obj
i=1
then we say that scene V is described by its N obj disjoint, K -connected components V i, with
i = 1 : : : Nobj.
Remark 1. In this definition the properties that scene components share are: ”being disjoint, 1-objects”, and
”K-connectivity”. Other kind of decompositions and descriptions of a scene are possible, in function of the specifi-
V
cation of the sets i , which depend on re-labeling operations on a binary scene, that is, the attributes of two voxels
in order to be K -connected. Since different labels arise from different data processing (filtering, dilation, selection,
sort-by-size,...), a sequence of scene decompositions can be obtained, in which the connected components change,
and re-group into new sets.
We introduce in the Section 2.4 the means to extract the connected components i of a (binary) V
V
scene , detecting their boundaries @ i , or V V
i by using a facet-based or a voxel-based representa-
tion.
To quantify morphometric properties by different b-reps, we also need to distinguish the volume
and surface measures that arise from each b-rep as set cardinalities, and then find its measure in
world coordinates (usually one or more scaling factors).
D EFINITION 2.21 (Voxel Cardinality (Discrete Volume))

V V
Let be a K -connected object in a scene . Then, = vk N V f g
k=1 is a set of N V
V K -connected
V
voxels, that is, the voxel cardinality, or discrete volume of is the integer: card( V ) = NV .
Remark 1. Recall that Nvox denotes the number of boundary voxels, i.e., the cardinality of V
, while N is the
number of boundary connected components (cavities and nested boundaries) of V
, i.e., the cardinality of the set
f Vg = 0
j j : : : N . Similarily for the number of boundary components N@ .
D EFINITION 2.22 (Facet Cardinality (Cardinality Surface Area))

V
Let as above, with K = 18. Then, @ = fk k=1 V f g
Nfacets
is a set of N facets 18-connected facets, that
V
is, the facet cardinality, or cardinality surface area of is the integer: card(@ ) = Nfacets . V
Remarks. The discrete surface area Surf @ (V)
in a cubic grid and scaled to world coordinates, is: Surf @(V) =
Nfacets L2 , with L
2R being the side of the voxel faces (grid step). For the physical volume: Vol (V) =
NV L3 . For anisotropic voxels, see Subsection 2.5.1. A solid-surface area is defined as Surf vox

(V) = Nvox
=
in grid units. Since N ;
Nfacets Nvox depends on the shape of an object, it could be useful to quantify in a
cubic grid the compactness of an object. We rather used discrete shape factors, as presented in Subsection 1.2.2.
Other measurements and analysis require the concept of discrete neihborhoods, which are intro-
duced in the next subsections for voxels, facets and boundaries.
2.3.5 Voxel (Euclidean) Neighborhoods

We saw in Chapter 1 that local information is needed to define or measure specific shape features of
any object. Several problems in 3D require to traverse, analyze or modify not only points p , or 2V
2 V
p @ , but also its neighborhood. In discrete space the smallest neighborhoods are the K -adjacent
voxels (or facets), and a neighborhood can be restricted to points in , @ , V V V
, or other sets. They
can also be generalized in several other ways: in the XY -plane, along the surface, along the local
normal, or other direction. Discrete neighborhoods are related to important analysis methods, such
as Mathematical Morphology (MM) in classical 2D- and 3D-image processing.
One of the principles of boundary-based processing, is the making of decisions about operations
or parameter adjustement at the instant of visiting each facet of a list (usually a list per object). These
decisions can also been made at a higher level, i.e., per whole objects, since the traversal of a list of
V f
selected objects comprises the traversal of the list of their facets @ = f n n = 0 : : : Nfacets . g
While scanning the boundary or the interior of an object, analysis of neighborhood information (e.g.
configuration, mean orientation, labels), for each facet or voxel, allows:
✦ to perform filtering,
✦ to modify a voxel label,
✦ to tag specific facets,
✦ to alliviate discretization problems in visualization (e.g., a local average allows to estimate

surface normals).
✦ to create special lists, or
✦ to accumulate a count or sum for a measurement, in function of facet or/and neighborhood

characteristics, which may determine the weight of the contribution.
Eventually, a whole object is modified, re-labeled or selected as result of a boundary-based anal-

ysis. All such possibilities and boundary-conditioning of 3D processing or analysis can be called
generically boundary-driven, filtering or analysis, belonging to the more general concept of shape-
, morphology-, feature- or geometry-driven filtering, analysis, etc. Related examples are given in
[TerHaarRomeny94]. We present in these subsections Euclidean and geodesic neighborhoods for
volume and boundary elements and boundaries themselves.
From the adjacency relation between voxels we obtain sets of natural nearest and near neigh-

bors that form the basis for MM operations as erosion ( ) and dilation ( ), as well as for local
measurements.
D EFINITION 2.23 (First-Order Voxel K -Neighborhoods)

Let v 2Vbe a voxel. If v0 9 2V
, such that v 0 is K -adjacent to v, K 2 f6 18 26g, then, the set
NK (v) = fvj j (vj is K -adjacent to v) j = 1 : : : K g
is called the immediate K -neighborhood, or first-order K -neighborhood of v.
In some applications the central voxel is not included in the neighborhood definition, and denote
N
by K (v) the set N
K (v) ;f g
v . We use K E N
K (v) to denote neighborhoods K (v) used as N EK
structuring elements for MM filtering operations. Figure 2.7 shows the possible neighborhoods in
2D and 3D for K = 4 8 and K = 6 18 26 in 3D.
Figure 2.7: K -adjacent voxel neighborhoods, with (a) K = 4 8 in 2D, and (b) K = 6 18 26 in 3D (the
central voxel is included in EK , but not in K N
(v ) = EK ;fg
v . These neighborhoods constitute also
structuring elements for Mathematical Morphology operations.
Remark 1. A voxel neighborhood of a -voxel may or may not contain -voxels. We usually are interested in
neighborhood voxels sharing a particular label. However, see in Section 5.7.3 a four-label example in the study of
atomic species interpenetration in amorphous-deposition simulations.
Remark 2. In MM operations E26 is a cubic structuring element, E 6 is an octahedral structuring element and
E18 is a cube-octahedron structuring element. These sets are used in literature for approximations of Euclidean
distance transformations, and region growing for constructing Voronoi regions and zones of influence [Klette98].
Remark 3. In the terminology of Crystallography, solid and surface Physics, voxels may correspond to sites,
the orthogonal grid V to a lattice, all v
18 va 6 va are named the
2N( )
6 va are the next-nearest neighbors
nearest neighbors of v a , while all v
26 va
2
(N ( ) ; N ( )) and v 18 va 6 v a are the next-
2 (N ( ) ; N ( ) ; N ( ))
to-next nearest neighbors.
B
Higher-order neighborhoods of a voxel comprise discrete balls rM (v) of radius r and some
parameter M which is related to the shape of the ball, since discretization allows for different ap-
E
proximations. Sometimes M relates to structural elements K to dilate a voxel into a “sphere”,
2
alternating different values of K . Let q = (x y z ) R3. In the discrete approximation of an Eu-
clidean sphere, voxels v are computed at integer samples (int(x) int(y ) int(z )) to obtain r (q ) as B
an approximation of the continuous ball B r (q ). Then the difference (under some metrics) between
Br (q ) and samples5 of the continuous boundary @^ B r (q ) is minimized, but depends on positions q ,
which are clipped or rounded to discrete grid points.
In our applications we used the following discrete approximation of an Euclidean sphere of radius
2
r R in a cubic grid : V
Br (q) = fp 2 V j round ( kp ; qk ) rg
(
; int(x)) < 0:5
with
int(x) if (x
round (x) =
int(x) + 1 if (x ; int(x)) 0:5
Sets of discrete-ball neighborhoods were implemented as precalculated offsets from a given center q .6
B B
These balls comprise r (q ) r (q ), with r 2f g B
0 : : : Nr (for r = 0: 0(q ) = q , 0 (q ) = ∅ ). B

The maximum radius Nr depends on applications; we used up to N r 25 (see Chapter 3). We also
added means to read or write on B
r (q ) for update operations in sliding windows (or rolling ball
buffers), as described in Section 3.3.3, page 156, and for the design of a discrete tubular-structure
detector, as described in Section B, page 242. Other applications (e.g. local measurements and
filtering) are described later.
Facet Euclidean Neighborhoods of a fp 2 @ V , with the associated voxel v at p = (x y z) could

be defined as sets:
EK (fp) = ffq 2 (@ V \ NK (p))g (2.6)
with K 2 f6 18 26g. In general, in a r-ball region centered at fp (recall facet centers are shifted to
1=2u^ k + (1=2 1=2 1=2)):
Er (fp) = ffq 2 (@ V \ Br (fp))g (2.7)
Since boundary faces are placed on a surface, it makes more sense to define their neighborhood
V
along @ , in the following Subsection. See later comments on surface density, in paragraph 2.3.7,
page 108.
2.3.6 Facet (Geodesic) Neighborhoods

Besides Euclidean neighborhoods, which do not depend on the shape of an object, we now con-
sider geodesic neighborhoods, which are defined along (or tangential to) the surface boundary of a
connected set.7 8
There are three ways to generate geodesic neighborhoods:
✦ By defining a discrete geodesic metric dgeo(p ; q ) and then to estimate surface curvatures to
establish a local reference system. Then:
N@ (r p) = fq 2 @ V j d geo (p ; q ) r g
p
5
A mapping such as z = r2 x2 y2 gives z from grid samples xy .
;( + ) 2R 2N
6
+ (1 2 1 2 1 2)
recall that voxel centers are at q 2 B ( + (1 2 1 2 1 2))
= = = , which adds a constant offset to all p r q = = = :
7
Geodesics in general can also be defined with respect to any set.
8
Strictly speaking, surface “geodesics” are only defined in continuous surfaces with a local reference system based on
principal curvatures, a metric measure, and a minimal-path condition under this metric.
✦ As in Definition 1.8, by using the approximation (similarly for V ):

N@ (r p) Br (p) \ @ V
✦ By using a MM approach with geodesic K -adjacent boundary elements (facets or boundary
voxels) and dilations (iterated adjacents of first-order adjacents).
The first approach is very accurate but difficult to implement and many applications require small
values of r (up to r = 3 in geodesic neighborhoods). The other two are very similar and well adapted
for boundary-based operations, thus we made an implementation using facets in a very simplified
way, as explained in the remaining paragraphs (the voxel version was not tested, but it is presented
in the next subsection).
V
Since a facet has four edges and a face-based boundary @ was defined as a closed surface,
any f 2 V
@ has always one facet adjacent per edge. They may belong to the same or to another
boundary voxels v 2 V . Connectivity relations allow several other neighbors. Discretization limits
f g
orientations for faces f k 50 to only three orthogonal directions (i.e., the discrete normals k U ). u^ 2
Some local averaging is required to approximate local Euclidean normal vectors of @ , and other V
properties of discrete surfaces (e.g., curvature). The following property restricts what facet neighbors
are possible and allows to organize the neighborhood, in function of facet orientation k : u^
D EFINITION 2.24 (First-Order Neighbors of Facets (or Geodesic 4-adjacents))
2 V f g
Let f = (v k) @ , then its four 18-adjacent facets f m 30 satisfy :
8 m 2 0 3] 9 vm 2 V 9 i 2 0 5] such that:

fm = (vm i) ^ (i =
6 m + (;1)m):
ffm g 3
0 are called geodesic 4-adjacent neighbors of f .
Remark 1. Some of the v m may refer to the same voxel.
Remark 2. 8 26
Strictly speaking, “geodesic -adjacent” (or Euclidean -adjacent) facets may or may not exist
4
(consider a single voxel, for example). There is a way to define them in terms of geodesic -adjacents of the facets
fm 30 themselves (excepting the central f ). It may then happen that some of the geodesic -adjacents are identical
f g 8
to some fm (see Figure 2.8c). To have a way to visualize this and other local configurations of facets, we introduce
a “cut-and-fold paper” representation of boundary patches, illustrated in the same figure.
Remark 3. 4
For each facet edge ( ), there are 3 possible facet neighbors (imagine three positions of a door,
m 90 m = 1 2 3), thus, a total of 12 possible facet neighbors. Notice that the condition i 6= m + (;1)m
6 18
warranties that in voxel - and -adjacency, any facet has only one 18-adjacent neighbor when considering the
example in Figure 2.5c (see also remarks of Property 2.1, page 90).
V
Orientability along @ is also needed, in order to introduce the traversal of @ . We also complete V
the full definition of geodesic neighborhoods after definition of lateral directed circuits along @ , in V
Subsection 2.4.2, which allow to select pairs of facet adjacents as “incoming” and “outgoing” facets
V
to traverse @ . We introduce however a preliminar definition, in terms of a partition of the four
geodesic neighbor facets into:
4
✦ 2-adjacents: A choice of two -adjacent facets ff left frightg at orthogonal edges of f (they
may be at the same voxel; see Figure 2.8a,d).
✦ co-adjacents: The remaining two facets, ffright-co fleft-cog.
(a) 2 right adj (b) 6
F 2 5
left adj 0 1 left co-adj
F
right co-adj 0 1 4
3
(c)
(d)
F
F
order of face
neighborhoods:
1th
2nd
3th
> 3th
Figure 2.8: Geodesic facet neighborhoods in a “cut-and-fold paper” representation. (a) First-order neigh-
bors, 2-adjacent and co-adjacent facets, relative to a starting voxel-face F . Numbers indicate the exploration
order for the adjacency subset. (b) Facets 3 to 6 are second-order neighbors (only 2-adjacents and second
adjacents are numbered). (c) Third-order facets are included (“semi-adjacent”) in a higher-order neigh-
borhood. A local-facet configuration example in 3D is shown (d), where color indicates face-neighborhood
order. Dashed facets in (c) are not necessarily “the same” facet in 3D, as shown in the example (d). See also
Figure 2.9
The terms “left” and “right” are just to distinguish locally each facet 9 . There are up to four possible
partitions of the four neighbors to obtain 2-adjacents. The choice is latter done by introducing a
local reference system trihedron with normals U and lateral circuits with an in-edge and out-edge
direction.
Remark 1. Geodesic K -connected paths and geodesic K -connectivity could be also defined with -adjacency 4
and 2-adjacents, in order to define and manipulate connected subsets (geodesic patches) along a boundary @ . V
Thus, hereinafter the first-order neighbors are either 2-adjacent facets, co-adjacent facets, or all 4-
adjacent (see Figure 2.8).
2.3.7 Voxel Geodesic Neighborhoods

For completeness, we include in this subsection some definitions of geodesic neighborhoods on . V
We did not use them in the present work, since facet neighborhoods were employed as described in
the last subsection, and other local calculations used a MM approximation, by erosions and dilations
9
This notation used by various authors is moderately misleading when considering local displacements: a sequence of
choices alternating ‘left’ and ‘right’ facets on a plane turns out to be a straight path (not a ‘zig-zag’). In the other hand, a
sequence of ‘lefts’ tends to be (correctly) a closed circuit
(voxel Euclidean neighborhoods) following voxels of the facets of a discrete boundary @ , or its V
equivalent V , using the face-to-voxel operator.
The next definitions are a special case of those introduced by Bertrand in [Bertrand94b] as dis-
crete geodesic neighborhoods related to simple point determination (those points whose removal
does not change object discrete topology), and to find topological numbers, which characterize fur-
V
ther topological properties of a cubic grid N3. Bloch et al. made a fast implementation which
still uses a volume approach to obtain a boundary representation [Bloch90, Bloch90b]. Recall that
neighborhoods K N (v ) and N E
K (v) v = K define also a structuring elements for MM operations

at v. In the following we are interested in voxels on the solid boundary V

, as a subset of . V
D EFINITION 2.25 (n-Order Voxel-Based Geodesic Neighborhood)
Let VV , and v 2V
. The n-order geodesic neighborhood of v inside V is defined
recursively as:
(
Nn (v V )
1 = NSn (v) \ V

Nnk (v V ) = fNn (w) \ N (v) \ V g:

w2Nnk;1 (vV)

26
In the context of the other definitions, n 2 f6 18 26g. Bloch as well as Bertrand express this
construction as a geodesic propagation inside N (v) \V (we are restricting their definition to V).

It becomes more intuitive when considering only the subset V ; then the propagation is along this
26
surface [Bloch90]. In general, the new set Nnk (v V ) may be expressed as a conditional MM dilation
(a) (b)
2 4
6
1 3
(f) n
adj
(c)
co-adj
7
(d) 2 (e) 6 8
1 3 5 9
12
4 10
11
Figure 2.9: Access to geodesic neighboring facets is achieved by adjacency (a) and co-adjacency (d) rela-
tionships, which assign a search order in first and second-order neigborhoods (b,e). An assignement is done
by LUT tables, following specific circuits. An estimation of the local normal vector is available from weighted
averaging of the normals of the neighboring facets (f). See also Figure 2.8, and Figure 2.12.
Nnk
( ) of ;1 (v V ), inside (restricted or conditioned to) N 26 (v) \
V , as:

Nnk (v V ) = Nnk (v V ) Nn (w) \ ; N (v) \ V
;1
26
N
where n (w) is the structuring element (excluding the center w).
The suitable geodesic neighborhoods for different connectivity pairs allow to minimize the num-
ber of possible candidates to simple points and compute several topological features. Since neihbor-
hoods so constructed are represented by graphs, they also allow to use standard algorithms for search-
ing connected components in graphs [Bertrand94b] (such as our boundary-traversal methods). For
the connectivity pairs (6 26) (26 K ) (18 K ) and (6 18), with K 2f g
6 18 26 , several require-
N V N
1 V N
2 V 3 N V
ments indicate that 6 (v ) 26(v ) 18(v ) and 6 (v ) are the optimal or compatible
2
choices of geodesic (voxel) neighborhoods, for each connectivity pair.

Geodesic distance fields may be obtained by geodesic propagation, as described by Bloch [Bloch90].
Generalized geodesic distances on gray scale images are described in [Soille94].
Other Neighborhoods of Boundary Voxels. As with facet “Euclidean” neighborhoods (Para-

graph 2.3.5, page 104), boundary voxels v(p) 2 V
, p = (x y z ) have Euclidean neighborhoods
defined as sets:
E K (p) = fv(q) 2 ( V \ NK (p))g (2.8)
where K 2 f6 18 26g. In general we can use r-balls and define:
E r (p) = fv(q ) 2 ( V \ Br (p))g (2.9)
which constitute small ROIs where discrete surface density of V at v(p) can be studied to extract
irregularity measures or 3D-roughness features in a neighborhood E r (p). We describe an application
of discrete surface densities in Section 5.6.
2.3.8 Discrete Boundary Neighborhoods

Geodesic neighbors of facets or boundary voxels were defined along the surface; i.e. in tangential
V
directions. We consider now neighbor elements in the normal directions of @ , that is, “inwards”
V
and “outwards” of . Since no restriction is applied in the tangential directions, the whole boundary
is considered.
V V
Once the face-based @ is extracted, further information of the shape of can be obtained from
V
boundary characteristics. Boundary @ , as a set of facets fj N f g
j =0 , can be specified even without
facets
V
knowing itself, for example as a transformation on the boundary of another object. In order to
VV
perform some analysis and processing operations on @ , or a small neighborhood of them, we
found convenient to define the following elements in the first-order neighborhood of a facet, in order
V
to consider internal and external layers of facets and voxels adjacent to @ . Figure 2.10 illustrate
some of these elements.
D EFINITION 2.26 (First- and Second-Order Neighbors of Boundary Voxels and Facets)
Let U = fu^ g
k 5k=0 be the set of unit vectors (Definition 2.2). Let f = f (x y z k) @ be a 2 V
facet, with (v 0 v 1), the corresponding boundary pair. Consider the neighborhood 6 (v1 ) of N
N N \V
6-adjacent voxels to v 1 . Let us partition 6 (v1 ) into: 6(v1 ) c and 6 (v1 ) , which are N \V
V
external and internal to . Consider also 6 (v0 ) N \V
c . Then10 :
f+ = f ((x y z ) + u^k k) is the front-facet11 of f (x y z k)
f; = f ((x y z ) ; u^k k) is the back-facet of f
f ;; = f ((x y z ) ; 2u^k k) is the next back-facet of f
v+ = v 0 (x y z ) = v((x y z ) + u^k ) is the main front-voxel of v 1 at f
v; = v ((x y z ) ; u^ k ) is the main back-voxel of v 1 at f
fvj gj<j
+ 6
=0 = N (v ) \ V c

6 1 are the front-voxels of v1
fvj gj<j
; 6
=0 = N (v )\ V

6 1

are the back-voxels of v1
fvj gj<j
++ 6
=0 = N (v ) \ V c

6 0 are the next front-voxels of v1 at f .
Remark 1. The voxels v +

f g 0 j 5 in front of all boundary faces of v 1 are also defined as the set:
j
fv 1 ((x y z ) + ) 6= kg.
^ j , with j
u
Remark 2. No front-voxel and no back-voxel is a boundary voxel (v

j 62 V j < 6).
Remark 3. Consider facets of v ; . Then, the next back-facet f ;; of v1 at f is also defined by: f ;; x y z k
( )=
opface( (( ); )
f xy z u^ k i , with i k = +(;1) k ; i.e., these facets have opposite orientations (Definition 2.9). With
this alternative definition, only the first-order voxel neighbor v ; is required ((see Figure 2.10b)).
Remark 4. By a similar argument, the back-facet of v 1 at f

k . Thus: f ;
(x y;z k), that is, f ; has thek opposite
orientation
(( ) )2
that f xy z i v1 , with i k = + (;1) = opface f ((x y z ) (k + (;1) ) .
Only the last set constitutes a second-order neighborhood. In practice, all these elements are obtained

from offset coordinates (x y z ) (x0 y0 z0), with 1 ;
x0 y0 z0 +1 and look-up tables,
usually in function of the k index of each facet. The implicit restriction to K = 6 comes from
V
the available information from a face-based boundary @ , from which the front facet and the back
facet are directly accessible, while other facets require to know the local voxel configuration. Similar
arguments apply for the front, back and K -adjacent voxels, and an application constituting a personal
constribution is a facet-driven implementation of region growing segmentation, using neighboring
voxels and facets, as described in Figure 4.23, Chapter 4. We now proceed to define several boundary
sets obtained from the above neighboring elements:
10
0
Recall that given only a boundary voxel v 1 , several facets may exist, as well as adjacent -voxels v 0 .
11

We used notation f + f; to denote the choice of face orientation u ^ k . Here f indicates the oriented face positioned

at offsets u (
^ k . Recall that face centers are located at x y z) + 1 2 + (1 2 1 2 1 2)
= u^ k = = = .
^
u v1 foreground (label 0 )
0
background (label 1 )
v0 0
f
Z
(x,y,z) X
(a) Y
^
u 5 v 5+
f --
f-
^
u 0 v +0
(b)
f v1
(c)
f+
v-
(d)
v1
v+
^
u 4 v+4
Figure 2.10: Neighbors of boundary voxels and facets (example). (a) Voxel v1 2 V
at (x y z), boundary
pair (v 0 v1) and unit vector u 2 2 V
^ 0 U . (b) Facet f = f(x y z 0) @ , its front-facet f + , its back-facet
f ; , and its next back-facet f ;; (the four facets share the same orientation u^ 0). (c) The main front-voxel
;
v+ ((x y z)+ u^0 ) of v 1 at f and the main back-voxel v ; ((x y z) u^0 ) of v 1 at f . (d) Three possible front-
voxels v+ + +
0 v4 v5 of v 1 (selection depends on the boundary neighborhood 6 (v1 ) N \V
c ). In this example, if
+
v4 v5+ 62 V ; ;
, then back-voxels v5 v4 do not exist inside . V
D EFINITION 2.27 (Discrete Boundary Neighborhoods)

Let V N3 be a discrete object formed by a set of (18-connected) voxels v i (x y z ) N V
i=1 and f g
V Nfacets
f g
@ its 18-connected face-based boundary f j j=1 , with NV Nfacets N the number of 2
voxels and facets, respectively. We define the following union of neighboring elements, for all
2 V
fj (x y z k) @ , assuming a 18-connected foreground, and 6-connected background:
@V = ffj gNj facets
=1 The face-based boundary.
@ V = ffj gNj
+ + facets +
=1 The front-face boundary or face-exoboundary.
@ V = ffj gNj
; ; facets -
=1 The back-face boundary or face-endoboundary.
V = fv j gNj 1 =1
vox
The voxel-based boundary or solid boundary.
V = fvj gNj
+ + vox +
=1 The front-voxel boundary or front solid boundary.
V = fvj gNj
; ; vox -
=1 The back-voxel boundary or back solid boundary.
V = fvj gNj
++ ++ vox ++
=1 The next-front-voxel boundary.
@ V = @ (V V
++ + ++ V) The next-front-face boundary.
where Nfacets Nfacets + Nfacets - Nfacets ++ Nvox Nvox + Nvox - Nvox ++ are the number of
neighbor-boundary elements of each set (facets or voxels), and depend on the shape and connec-
V V
tivity of the original object . We further denote by @ and all the above face-based and V
voxel-based boundaries, and in particular we denote the front- or back- boundaries by @ .
Remark 1. As defined, these neighborhood sets have not necessarily nesting relations with @ or V V
(child
or parent), and in general do not preserve topology (e.g., number of connected components). Verification of the
Jordan property allows to deal with such cases.
Remark 2. Given f 2 @ V as a pair (v 0 v 1 ), Udupa and Herman called [Udupa92, Herman98]:

✦ Surface S of V 2 Zn, the set of all pairs (v0 v 1 ) isomorphic in N3 to @ V ,
✦ Reverse-oriented surface S ~, the set of all pairs (v1 v 0 ) isomorphic in N3 to @ V ; = opface( @ V ),
✦ Immediate interior II (S ) all boundary voxels fv 1 g equal to V in N3,
✦ Immediate exterior IE (S ) all boundary voxels fv 0 g equal to + V in N3.

✦ Immediate neighborhood IN (S ) = II (S ) IE (S ) equal to V + V in N3.
n
Their generalization to Z includes two connectivities satisfying discrete Jordan-surface properties which
we do not consider here. Multidimensional surfaces are specified as -boundaries. We adopted a more specific
nomenclature, since we deal with various other boundaries, interiors and cavities.
Remark 3. The notation for the back-face boundary @ ; V is not to be confounded with negative boundary @ V ;
whose facets are reverse-oriented.
c f --
V V f-
f
f+
V v-
v1 v1
v+
(c)
1111
0000
(a) + - = 1111
0000
0000
1111
0000
1111
000
111
000
111
= 111
000
000
111
(b) ++ + -
000
111
000
111
000
111
000
111
000
111
000
111
Figure 2.11: Discrete boundary neighborhoods of an object V
V V
(2D view). (a) facet-based boundaries separat-
ing neighboring voxel layers around the standard surface boundary @ ; the faces in front of each face of @
V V
constitute the front-face boundary @ + ; the faces back to each face of @ constitute the back-face bound-
V
ary @ ; . (b) voxel-based boundaries: V V
corresponds to voxels with faces in @ ; front-voxel boundary
V V V V
+ corresponds to @ + and back-voxel boundary ; corresponds to @ ; ; an additional voxel layer can
V V
be obtained from @ + , the next-front-voxel boundary ++ , without knowing the next-front-face bound-
V
ary @ ++ . (c) Corresponding neighbors of boundary voxels and facets (3D view). All coordinates and faces
V
are directly obtained from @ , using look-up tables for a given K -connectivity (K = 4, in the 2D figure, and
K = 18 in our implementation).
It is clear that we could also use MM operators directly for some definitions, since examining
NK (v) = EK at each v 2 V defines an MM operation on V , excluding the voxel boundary. From

facet and voxel boundary equivalences we have for example:
@ + V = @ (V
E) 6 (2.10)
@ ; V = @ (V
E) 6 (2.11)
The difference in our approach is the method to obtain @ V V directly from @ V itself, thus we can

reverse the definition and effectuate voxel MM operations by adding V to V (“wrapping” a layer
+
of voxels), or subtracting V from V (“peeling” a layer of voxels).

A number of relationships and properties arise from the above definitions; for example:
✦ Definition of facets f as pairs of boundaries has a global equivalent, but orientation information
is lost: @ = ( V V \ V f
+ ) g
orientation of f . This information can be expressed as a
binary decision of assigning index j or k in the following set: f
f (v f j or k ? ) ( 2 V \
V ; 2 g
+ ) j = k + ( 1)k k 0 5] .
✦ Except for voxel labels, in (18 6)-connectivity we have +
V = V c, which may consist of
V 18 6
several connected components if has cavities. It is also the nearest global neighborhood of
an object and we explore it to detect contact with other objects, to extract interface boundaries,
label specific voxels and make morphological reconstruction.
;
✦ Chamfer distance fields (internal “ ” or external “+”) may be obtained from proper sequences
of sets W W
Ki j , where j =
+
interior( +Kj V ) , and the internal chamfer field from sequences
Ki (
;
Vn Kj ), with Ki Kj2 f6 18 26g being proper sequences of connectivities that ensure
the best chamfer approximation to Euclidean distance.
✦ For a 6-connected object W (Definition 2.28):

(W E ) = W n W
6 18 “peeling 18 ” W
(W E ) = W W
6
+
18 “wrapping +18 ”. W
Several other relationships and operations may be derived, such as morphological reconstruc-
tion for which we provide an example in Section 2.5.2, page 130.
✦ Fat-boundary neighborhoods are trivially defined; for example:

G V V V )
= (
G II V V V ) or
= ( ; +
G III V V V V )
= ( ; +
where G V equals the immediate neighborhood IN (@ V ) of Udupa and Herman [Udupa92],

+
the set of all boundary voxels f v v g. These fat-boundary neighborhoods may not have
0 1
useful properties from the point of view of discrete geometry (they may present holes and cav-
ities), but provide a dense sampling of space around @ V to measure local, statistical properties.
Also, their comparative volume and surface area may give estimations of local roughness.
✦ Irregularity shape properties at scale resolution can be studied globally from analyzing “resid-
ual sets”, such as + V \ V.
In order to better explain different ways to exploit these boundary-related sets, we present in the
following section the means to extract and traverse face-based boundaries.
2.4 Surface Tracking 113
2.4 Surface Tracking

We present in this section the stage of boundary extraction or surface tracking, in order to detect
V V
connected components in a scene , and our implementation of the method proposed by Artzy et
al. in [Artzy81].
Implicit Surface Extraction

The first surface-rendering methods for arbitrarily complex objects attracted much attention, as they
dramatically enhanced 3D visualization of any data volume, but without further representation or
analysis. A popular method is the one proposed by Lorensen and Cline, the marching cubes, which
is based on iso-surface thresholding and reconstruction, giving as output a list of triangles at the
vertices of a cubic mesh [Lorensen87]. In several ways, the marching cubes surface reconstruction
is like 2D thresholding with binarization, without contour extraction. It is thus an implicit method
for extraction and representation of object boundaries. Bloomenthal recently developed an advanced
version of the marching cubes, called a “polygonizer”; but it is still focused to surface and volume
rendering [Bloomenthal94].
The main criticism to marching cubes and similar algorithms for surface extraction is that it does
not provide directly an explicit representation of each particular object in a scene, and processing and
analysis require further transformation of data into structured meshes. The output of the marching
cubes is a raw list of triangles (or codes to triangle configurations), which does not isolate each indi-
vidual connected component; surfaces must be tracked from the list of triangles all over the volume
in order to separate and process individual objects. Another solution for single object manipulation
is to segment and label the scene beforehand, either by a human or by computer methods to detect
connected-components. The output is a volume where voxels bear information about the objects or
classes they are believed to belong to. Once a scene is labeled for object processing, the whole vol-
ume has to be either traversed several times (once per label, with marching cubes), or bear lengthy
codes per voxel (e.g., labels plus pointers to mesh configurations and surface normals) and case-by-
case examination has to be employed. It turns out to be efficient for preliminar visualizations (as
an interactive 3D-thresholding), or when one single object is easily localized, but information for
processing and morphometric operations has to be obtained apart.
Explicit Surface Extraction

There are methods to explicitly extract a 3D b-rep of each connected component in a discrete scene.
These methods are able to perform surface detection and tracking at the same time, and may work
on gray-level scenes, without previous segmentation (however, literature mainly reports binary im-
plementations of such extraction algorithms). In this way, the b-rep of the scene is accessed and
processed at a higher level, object by object. If morphometric characteristics are available (e.g. ob-
ject shape), selection criteria allow to process only relevant features or apply for example geometry
driven techniques for filtering [Romeny94].
The most representative of the explicit surface extraction methods is the surface tracking algo-
rithm from Artzy et al., based on directed-graph models of the surface of an object [Artzy81]. We
review it together with our implementation in the next subsection. Bryant and Bryant report a simi-
lar method for n-dimensions, but their description is very poor [Bryant90]. Shu and Krueger report
a faster implementation, which turns to be much more complex and oriented to CAD-like objects
with large planar surfaces [Shu91]. Other authors have proposed alternative discrete b-reps with
similar characteristics which are suitable for boundary-based processing, MM, and morphometrics.
We just mention cellular complexes [Elter92], which is well adapted for dealing with local-topology
problems in modeling and homotopic processing, since the data structure specification of a cellular
complex includes the incidence and adjacency relations among its elements [Rosi96]. This additional
information introduces the burden of managing complex and lengthy data structures for even simple
discrete sets, since not only faces and voxels are used as independent components of boundary ele-
ments, but also edges an vertices. The approach is however well adapted for physical models where
the cellular complex encodes model attributes that strongly depend on topology.
Since surface tracking methods proceed in a sequential progression to traverse a graph, a one-
dimensional list is obtained for the 3D-surface of the object; a K -connected path of facets (or voxels,
depending of the surface tracking method) which traverses the whole boundary. No preferential
order exists and there are several possibilities obtaining a list, depending on the starting point, and
the particular set of surface tracking directions 12. Once found, the list provides the means to traverse
the surface for purposes other than its initial detection, such as:
✦ local filtering (smoothing), either of the original gray-level information, or other local infor-
mation, such as normal vector calculations,
✦ collecting neighborhood information,
✦ labeling, either the surface boundary or the whole solid, and
✦ visualization with a Z-buffer or other object-rendering techniques for pipe-line processing.
In previous sections we introduced our facet-based model for b-reps; we now explain our implemen-
tation of the surface tracking method of Artzy et al. in the following paragraphs.
2.4.1 Surface Tracking Algorithm

Effective methods for detection and surface tracking of @V were first developed by the it Medi-
cal Image Processing Group (MIPG) of the Pennsylvania University [Artzy81, Herman83b], and
later justified and enhanced by discrete-topology advances [Herman83, Kong92, Udupa94]. Several
variations and faster implementations have been reported in the bibliography [Gordon89, Udupa90,
UdupaOdhner91, Shu91, Perroton93, Perroton95].
V
In a facet-based model the extraction of @ relies on a depth-first or breadth-first exploration
of the graph model of the surface. The facet-based approach allowed Artzy et al. a significant
improvement, since their method retains only the nodes (facets) that are reached at most twice. The
traversal properties of the graph representation are described in the next section.
We first describe the steps of the surface tracking algorithm, as implemented for 18-connectivity.
Candidates of adjacent (or co-adjacent) facets are examinated in a specific order similar to contour
tracking. It is illustrated in Figure 2.12 for the current detected facet in @ . V
All facets to be explored are added to a queue Q. Those which have been already put in Q but
which could be reached once more by another path are put into a second list P , since each facet has
two incoming edges and two outgoing edges. If a new facet is encountered, it is searched in P , if it
is not there, it is added to the queue Q and output to the list of boundary facets (the “else” in step (3)
of the following table).
12
We estimate per face-based boundary no more than N facets (8 6)Nfacets different paths, having 8 possibles circuits
per facet, and 6 face orientations
The header of the algorithm, summarizes the relevant data structures, where the volume array
V
design for is described in Section 2.6.2, page 2.6.2:
f g 2
INPUT: Binary scene V = voxelsz ]y ]x] ; optionally, a facet f0 @V , or a starting point near
a boundary component. Other parameters: (K0 K1)-connectivities, and thresholding method.
V
OUTPUT: List @ of facets f whose voxels are 18-connected (all f is 18-connected with f 0 , either
V
given or found). @ is the face-based boundary @V .
KEY STRUCTURES:
Queue Q (circular FIFO), “left” and “right” faces adjacent to f0 .
List P of marked faces (nodes of a bintree), which are the left and right adjacents to a
!
new face f . In the following, arrows ( ) indicate queueing (unqueueing), or link insertion
(unlinking) of an element in a queue or a linked list.
Look-Up-Tables with coordinate offsets of neighborhood voxels to search, for each face
fk 2F6 with some k 2
0 5]. Adjacents are detected from pre-calculated LUT’s indicating
facet candidates.
Voxel connectivity, face-adjacency and special cases (such as the “Tu ”-connectivity of Gor-
don et al. [Gordon89]) are handled in the LUT design and specific local tests.
S URFACE TRACKING (face-based boundary extraction).
2
1. Find initial facet f0 = (v0 f ) @V f 2F
6 . It is either
found by user (interactive selection in cross-sections), or
found by automatic scanning if a ROI (thresholding, labels, local segmentation).
2. f0! ! V ! !
Q, f0 @ , f0 P , f0 P (notice two copies).
(Collisions are avoided with a hashing table and a linked list)
6
3. while( Q = ∅ )

f Q (unqueue one f from Q)
find fleft left adjacent to f withf left 2 @V
4
= (offset LUTs).
if( fleft 2P )
fleft P (unlink from P )
else
fleft ! Q, fleft ! @ V , fleft ! P
find fright right adjacent to f withf right 2 @V
4
= (offset LUTs).
if( fright 2P )
fright P (unlink from P )
else
fright ! Q, fright ! @ V , fright ! P
4. endwhile: @ V is a list of the external boundary of V , a 18-connected body.
V
Remark 1. At the input, the access mode to @ , which is being extracted, is random access, since a list is not
available and the whole 3D scene must be present in memory. At the output, the boundary is organized in a linear
V
list @ of facets, and can be accessed in sequential access (boundary traversal).
Two modes of surface-tracking operation were implemented, with several options.

(a)
(b)
F
F 3
(c)
F (d)
5 (e)
6 2 F
1
4 F
F (f) ?
?
?
(g) unqueue F from Q
(a) V [1] = F
/*** Adjacency : search the LEFT-adjacent facet to F ***/
(b) If facet=1 V [2] := (c)

else if facet=2 V [2] := (d)
? (h) else V [2] := (e) /*** facet = 3 ***/
queue V [2]
F /*** Adjacency : search the RIGHT-adjacent facet to F ***/
(f) If facet=4 V [3] := (g)

else if facet=5 V [3] := (h)
else V [3] := (i) /*** facet = 6 ***/
(i) queue V [3] in Q
F
Figure 2.12: Facet tracking order. Three possible candidates of the right-adjacent facet are examinated per
edge in (a,b,c,d,e). The shaded facet (not visible in case (c)) is the next facet, if the queried voxel (shaded
V
in gray) belongs to the object. The left-adjacent facet is searched (f,g,h,i) if no more “right” facets remain
unvisited. The output list “@ k]”, with k = 1 : : : N facets ” constitutes the extracted boundary. The pseudo-
code illustrates one-single cycle (two adjacent facets). Attending candidates are queued in a list Q.
f
✦ In the first mode, a starting coordinate (a facet 0 on an object) can be given (found by the
user), or the user may let the algorithm scan the whole scene (or a ROI of it) to extract all
objects satisfying selection criteria (size, gray-level value range, or having a specified label, if
assigned beforehand). The objective of this operation mode is to allow full automation of the
extraction process while performing a fast segmentation (such as thresholding).
✦ In the second operation mode, a scene previously labeled (segmented) can be scanned to extract
all boundaries of iso-label voxels, and the threshold value of segmentation is replaced by the
L
next object-label i found during scene scanning while instead of testing condition (or
L
> ) for boundary detection, the condition = i is tested, for i 1 Nobj ]. If several 2
connected components are present per each label, a third sub-mode (not yet implemented)
would organize connected objects in function of their labels. The turn-around solution is to
scan a scene with a given starting label as threshold (first mode), save the list, and repeat until
all labeled sets are extracted. This scanning mode allows to use the output of any segmentation
operator.
With either tracking mode, a set of 18-connected objects (connected components of a segmented
scene) can be described by a list of boundaries. The details are explained in Subsection 2.4.3. We
consider in the remaining a single object . V
V
The extracted boundary @ (a list of facets fi ) may in turn be organized in different ways. When
only the space coordinates of a facet (x y z k) are retained and redundacy checked out, we obtain
a 18-connected voxel-based boundary V
, as the list of 1-voxels in contact with the background (6-
c V
connected with ). Another organization is possible when sorting facets by orientation type k, that,
F f g V
is by using the face partition 6 = x; x+ y ; y + z ; z + to represent @ by six lists of point
f u^ g
coordinates corresponding also to oriented faces (f k k ) 50 (see Definition 2.7).
Any operation employing boundary traversal visits voxels or neighborhoods corresponding to
all fi 2 V F
@ , or a subset, such as the subpartition 01 (Equation 2.3). Facet visualization is the
perspective or orthogonal transform of the coordinates of each f i , using either Z-buffer or back-to-
front rendering. We examine these topics in later sections.
2.4.2 Facet Traversal by Lateral Circuits

Until now we have not explained how “left” and “right” adjacent and co-adjacent facets are assigned,
and how is constructed the surface graph model. To establish a mathematical model of discrete
surfaces in the boundary tracking algorithm, a discrete orientation is assigned to facet traversal,
2
besides unit normals U , to oriented faces f k , in function of k 0 5]. A full trihedron is formed
and facets have a back and a front (U ), but also their edges are in-edges (incident) and out-edges
(adjacents). Figure 2.13 illustrates this trihedron per voxel face, including normals, the reference
index k 2 F
0 5], and the alternative notation with the set 6 (see Equation 2.1), which helps to
indicate which axis direction is concerned, but does not describe the nature of these sets of points as
voxel faces.
Recall that Figure 2.9 in page 107 showed the access to adjacents through such circuits (white
arrows are interchangeable by black arrows in the opposed sens). Each facet has two orthogonal
traversal circuits assigned from one edge to the opposite and an adjacent edge, in function of its
orientation U and a choice.
Boundaries themselves possess an overall lateral orientation, 13 analogous to orientation of con-
tours in 2D which have only two possible traversal directions: hourly (–), and trigonometric (+). In
3D, we have 6 contour orientations in planes XY Y Z ZX .
Thus, each facet has 4 edge-neighbors; traversing in one sense or the opposite gives 8 possibilities
for assigning the “next” and “previous” facets. Since there are three possible adjacent faces per
border, we have 12 possible faces (next and previous) in all (see Figure 2.12b).
We talk of lateral circuits, and directed circuits relative to the coordinate axes X Y Z , to avoid
confusion with orientation of surface normal vectors, which remain orthogonal to circuit directions.
It would be logic to specify “geodesic” circuits, but literature avoids the term to avoid cumbersome
notations. Boundary traversals are constrained to follow these circuits. With a predefined circuit
direction, in relation to XYZ, a consistent traversal order is introduced.
13
not to be confounded with the discrete normal orientation of the facets, given by the set U
z+ x-
f5
y-
f3
f1
y+
x+
z-
Figure 2.13: Face orientations and lateral directed circuits. Pairs of directed circuits are assigned to each
face f k (note that f 0 f 2 f 4 are at the opposite sides). Long axes represent the 6 face normals, and the two
remaining directions, tangent to each face, determine traversal circuits across the edges, to search the next
two adjacent faces. Recall that the ordered set of faces (as a vector) (f 0 : : : f 5 ) and assigned orientations
U correspond to face orientations (x; x+ y; y+ z ; z + ), in the alternative notation of Rosenfeld et al.
Outgoing edges of facet with face f 1 are bolded.
In Section 2.3.6, we introduced geodesic facet adjacents for closed objects. Lateral traversal
circuits consist in specifying two adjacent facets (left and right) 14 as outcoming or successor facets
when the circuit crosses an edge from the facet under consideration to the adjacent. The other two
are co-adjacent (left and right) which constitute incoming or predecessor facet. Here, “right” and
“left” do not have anything to do with “left- or right-handed coordinate system”, being only a local
choice of direction.

Note that there are (6 face orientations 4 circuit combinations =) 24 possible sets of directed-
circuit choices, which can be organized into 2 complementary sets corresponding to left-hand or
right-hand coordinates X Y Z . We call the 12 possible choices of the left-hand set orbits, and
its complement, co-orbits. If consistently chosen, orbits provide positive measures of volume for
foreground objects (and negative for the internal boundary of background cavities), and co-orbits
change the sign. Otherwise, the difference between orbits is the permutation of surface directions
followed during surface tracking of traversal. As with the coordinate system (left-handed or right-
handed), the co-orbit set corresponds to a specular inversion of the orbit set.
Surface tracking and most processings are all implemented in a “successor” direction, following
adjacent facets and one choice of directed circuits (one orbit out of 12 possibilities). A complemen-
tary alternative is to use the co-adjacent facets, that is, those found following the “previous” direction
of facet traversal (the co-orbit set of directed circuits). In our implementation adjacency rules and
possible decisions for each possible configuration of successors/predecessors, were thoroughly pre-
calculated and coded into LUT’s in function of the 6 possible face orientations. This allowed to
make available the two directed-circuit sets (orbit and its co-orbit), but a single set has to be chosen
14
If the coordinate system is itself exchanged from axes permutations XY Z ] to XZY ], left and right are inter-
chanched.
for most operations. We remind that the net difference in traversing a boundary by adjacence or by
co-adjacence, results in a change of sign in signed-surface or volume measurements, in a similar way
to 2D signed area and perimeter extraction of contours, in hourly or trigonometric senses. A duality
exists when the scene is 1-complemented and the tracked object is background, (a cavity, instead of
F
foreground), orientation sign is inverted from ! to ! for ! = x y z (set 6); that is, from set of
orientations U to set U , and facet traversal behaves as if using co-adjacency. To calculate signed
surface and other morphometrics, each term contribution is weighted by the facet sign.
Directed circuits for facet traversal allow to use directed graphs (digraphs) to represent and tra-
verse discrete surfaces. Then, boundary extraction becomes a full-digraph traversal problem. The
facets are then represented by the digraph nodes, and arcs are constituted by directed-adjacence rela-
tions between pairs of facets [Artzy81, Voss93]. One or more Hamiltonian circuits‘, that is, circuits
passing through every node, may exist, but there is no warranty than nodes are visited only once,
which is only desirable for optimization purposes. There exist conventional techniques to traverse
such graphs, as described in [Knuth68], and most implementations are equivalent to traversal of a
binary tree spanning the digraph. Left branches correspond to left adjacents and left co-adjacents,
and similarly for right branches (Figure 2.14).
The surface of object of Figure 2.14a is tracked by the algorithm, starting at facet number 1.
The 2D-digraph represents connectivity and adjacency of all facets and it is traversed, building a tree
(Figure 2.14d). Different trees are generated if the starting facet is other than facet 1, or traversal
circuits are inverted and lefts and right adjacents and co-adjacents are exchanged. In a planar surface
the tracking follows a stright path, but it turns at corners. Artzy described the traversal as “cloning
flies over sugar cubes” [Herman98], which means that a cellular automata algorithm duplicates it-
self at each facet (branching in the bintree spanning the digraph of the surface), searching for new
facets. Such duplication succeeds more often in irregular surface locations than in planar of concave
locations. This remark could be useful in future applications for feature extraction.
In digraph representation, four oriented arcs link each node (facet) to two facet-successors (out-
puts) and two facet-predecessors (inputs). This imposes four possibilities of traversal-order combina-
tions, and hence, exhaustive ways to traverse the digraph given: (1) a starting facet, and (2) a choice
of oriented circuits, to determine which edge is an in-edge (precessor facet) or an out-edge (successor
facet). A full traversal cannot be completed by just following the left successors of a given face or
just the right successors. The correct choice of which successor follows –left or right–, is done by
the circuit definition, which depends on the next facet orientation itself (for example, if it is an x +
facet, the right adjacent is chosen but if it is a x ; facet, the left is chosen).
Theory and justification of the surface-tracking algorithm has taken time to be satisfactory and
clear. Details and further discussion can be found in the bibliography.
2.4.3 Interior Traversal and Object Labeling

V V
When several objects k , k = 1 : : : NV are present in a scene , their boundaries are extracted
one after another by a simple algorithm described in the next subsection (the set fV gNV is also
k k=1
V
called the connected components of ). Since segmentation consists in labeling the interior of each
V
detected @ k , we explain in this section how such operation is performed and in general, how object
interiors are traversed. There are two labeling modes: Geometric and Solid Interior Labeling and
Full Interior Labeling.
Discret(a)
object V associated digraph to boundary
(c)
V := { facets 1, 2, ..., 14 } 10 9
3 8 3
4 12 14
2 (b) 4
11 5
6 1 2
11 13
13
1
6
9 7
8
5
1
14 10
7 2 X
4
12 (d)
3 8
4 9 X
3
5 10
6 11
7 12
1 X 13 "left" adjacent facet
"right" adjacent facet
14
binary spanning tree of a
hamiltonian path of the digraph
Figure 2.14: Discrete surface tracking as a directed-graph traversal. Nodes of the digraph (directed graph)
V
V
represent facets and links represent adjacency relations. (a) Discrete object , (b) traversal circuits to find
adjacent facets, (c) digraph associated to boundary @ , and (d) a binary tree that spans ONE Hamiltonian
path of the digraph (there are 2 only-left and 2 only-right paths in (c)). Other trees are possible.
3 9
x 8
4 2 5
y 6 1 x 14 10
z 13 y
z 7
11 12
Figure 2.15: Directed lateral circuits. Sequence of visited (detected) facets ffj g14j=1 following the LUT of
left and right adjacents reproduce paths of the digraph and the object in Figure 2.14a,c. Facet orientation
and object shape determine the paths, which are independent of starting facet f j0 (j0 = 1 in the figure). A
Hamiltonian path passes through all facets (not necessarily once).
Geometric and Solid Interior Labeling The geometric interior and the solid interior interior(@ V
V)
V
that constitute all the object can be both traversed from the extracted face-based boundary @ . In V
a first approach, labeling ignores present cavities and fragments (it “fills” them out). This opera-
tion is enough for most applications and we detail it after explaining a “conditioned” version, which
accounts for nested boundaries.
V
Full Interior Labeling The boundary of an object with several nested boundaries (cavities and
Vj
fragments inside those cavities) is in fact its outmost boundary @ out (see Definition A.9, page 235),
and has to be traversed in a different fashion to take into account background components inside V
(cavities). We do not avoid the traversal itself in these regions, but we either:
✦ disable labeling, or other volume operations during traversal of cavities and fragments, or
✦ the voxels of these regions are labeled differently, or
✦ their boundaries (i.e., nested boundaries) are extracted and incorporated into the ”full” bound-
V
ary @ (different conected components of the boundary), and cavities become true background
components.
The nested boundaries (cavities, fragments, etc.) can be also extracted later, in a second scan of the
V V
scene , making a list of boundary connected components @ j , with j = 0 corresponding to the
first detected, outmost boundary and then running iteratively for all nested boundaries, up to either a
V
maximum depth or a maximum number (we denote max(j ) = N@ ( ). To this end, scene traversal is
substituted by interior traversal, as done in the labeling process (see below), but for surface tracking
inside an object.
V
A full boundary @ is then specified by the list of all nested boundaries. The geometric interior
of this full boundary coincides with its solide interior, since all cavities and fragments are taken
V
into account. When traversing such full boundary, only voxels in are visited. When traversing
V
the interior of the outmost boundary, all voxels in are also visited, but also those voxels in c V
corresponding to cavities.
V F 2
Let @ be partitioned into 6 sets in 6, facets f (v f i ), with i 0 5] constant in each set (facets
Vj
“x ”, etc.). Each partition, such as @ x; , is called a facet wall (see Figure 2.4). Their voxels may
;
compose one or several connected components in non-convex objects or with nested cavities. @ V
has six wall sets. The interior traversal method starts from all voxels in a “x ; -wall”, reading (or
labeling) the scene, and advancing towards +X until the scene limits are attained (open or incom-
plete boundaries), or a special label is recognized. The special label can be previously marked; we
overlay a contention x+ -wall in the scene with a Stop label to each voxel, we can then examine
for foreground information, and cavities.
I NTERIOR T RAVERSAL (usually, for label operations).
Vj
Build a “stop” wall (partition @ x+ ):
(1) for all v = facettovox(@ x+ ) Vj
L (v) = Stop label
(2) 2 Vj
for all f @ x;
(3) L 6
While (v) = Stop label
u^
walk from voxel at f (v f 0 ) in the 1 direction
L
(optionally, (v ) := final label, or do other operations on v).
(4) L
f (v f 1) is such that (v) = Stop label
L
(optionally, (v) := final label, or do other operation).
Labeling (if done) can be further conditioned. If facets were previously sorted into opposed,
;
colinear pairs (f (v f i ) f (v f j )), with j = i + ( 1)i, traversal is even simpler.
Labeling of Connected Components Udupa proposed in [Udupa90] an algorithm consisting in

applying boolean operations (1-complement and XOR 15 , mainly) to mask detected objects whose
holes have not been detected. The mask serves to render each detected component “invisible” to the
surface tracking operation, while holes are treated as foreground. For large volumes it imposes an
overwhelming load, if parallel methods are not employed.
In our implementation of this feature we added some capabilities for dealing with many ob-
jects at the same time (the present limit is 32K objects, which have to share a maximum of 250
different labels). Udupa reports a recursive approach [Udupa90], in which boolean operations are
sequentially applied to the whole volume buffer to extract and label each connected component. Let
Nops the number of boolean and labeling operations as described by Udupa (typically, N ops 5:
scan-detection, label, XOR, label, XOR). These operations are iterated to treat nested bodies inside
cavities and conversely, exchanging background by foreground, until all nested levels are attained.
Real-case applications require usually one single iteration [Udupa90].
For a scene of size N 3 voxels forming up to N obj objects to detect and label, even if they are

one-voxel large, the method proposed by Udupa executes around N obj N 3 Nops total operations.
We label directly the geometric interior of each detected componend by a 3D-fill operation (or “3D-
flood”), using the boundary representation itself. Discrete fractal surfaces, with dimension 2 < D <

3, say D=2.5, have a surface composed of O(N 2:5) facets, for each object k 1 Nobj]. We 2
execute a total of Mops = 2 operations: scan-detection and label, thus M ops = 2=5Nobj. All this

gives a total average of Nobj N 2:5 2:5Nops. Even for a very complex, such as space-filling
fractals (a 3D checkerboard of one-voxel size), the performance remains 2.5 times superior.
Our labeling algorithm consists of the following instructions:
V L
INPUT: A scene (or ROI). Initial label 0 to detect. On a binary scene, usually ‘255’ represents
the foreground (1-objects), and ’0’ the background (0-objects). On a gray-level 3D image, it
may be a (local) threshold. On a labeled scene, it is defined by the first label found different
from background, and latter defined by each subsequent label found. Other inputs: number
of objects to detect Nobj , minimum size ‘min surf’ as number of facets, and optionally, an
output label (usually varying to indicate a different object). Other options: fill cavities and
erase fragments, or detect nested boundaries.
OUTPUT: Lis‘t of boundaries consisting of lists of facets with the corresponding label, the cardinal
surface area (number of facets per each object), and a labeled scene . Optionally, volume V
measures can be extracted since volume traversal allows to count visited voxels inside each
object.
C ONNECTED COMPONENTS (detection and label of connected components by boundaries).
1. L L Set = 0 , the current detection label (usually 255 in binary scenes).

Set k = 1, allocate and initialize list of surfaces @ k . V
L Initialize out , the output label, usually a sequence 1 : : : N obj , with out L 6= L.
2. 8 2 V v (or ROI),
9 if ( f0 at v , with label ) L
15
Given a b booleans, a XOR b = (a _ b) ^ (a ^ b); e.g., “one or the other, but not both”.
@ Vk = S URFACE TRACKING(f0 , L)
if( card(@ Vk ) < min surf) L := background.
L ABEL OBJECT( @ Vk Lout )
increment Lout ; increment k Nobj = k.
if( card(@ Vk ) < min surf) discard @ Vk
V
3. continue to scan all (the labeled object is now ’invisible’ to detection).
V
4. End. Nobj is the total number of connected components k found in V
The ”L ABEL OBJECT” operation consists of volume traversal of V using the extracted boundary
@V L
k , and labeling interior voxels with a target label out .
Other Capabilities. In our version of the original algorithm of Artzy et al. we have incorporated
the following enhancements, to take full advantage of boundary representations:
(a) Connected component labeling during scene or ROI scanning. This operation has already been
described.
(b) Concurrent operations. A number of processings, analysis and morphometrics is done on-the-
fly , while boundaries are being extracted, or just traversed when they are already known.
Processing can be a simple re-labeling , or include neighborhood operations such as MM di-
lation and erosion. Because of the enhancement described in (a), morphometric operations are
performed concurrently with the labeling operation (“on-the fly”), allowing to include many
object-feature extraction capabilities.
(c) Multi-label operations All operations were implemented to deal with different labels, (up to
250 in the present implementation). This possibility allows to treat as “invisible” objects with
a given label, or take a particular decision if one voxel or facet has a specific label. To this
end, “foreground” and “background” are relative, and defined in function of a specific goal,
such as common boundary extraction between two regions, which may produce open surfaces
(boundary patches). This allows to work also with several non-binary labels. We present an
example in Section 5.6, page 203 (see also Figure 5.9, page 204).
(d) Selectivity Most operations can be executed or not, by selecting specific criteria according to
the desired processing or measurement. Current criteria include size (volume-value thresholds
or windows), surface, form factor, center of mass, sphericity (or “spread”) or isotropy (see
Table 2.1).
(e) Non-solid objects. Some provisions have been taken to allow for manipulation of non-solid ob-
jects. These are constituted by sets of special facets that may not have all four adjacents and
f g
are not defined by a pair 0-voxel 1-voxel . For example: a single-facet cloud, a ribbon of
facets x+ , or an open subset of a boundary (a surface patch). Most morphological operations
only make sense with closed-surface boundaries, (solid filling, for example), but in some cases
particular manipulations with surface patches are useful. A specific example is the label and
visualization of the contact interface between two objects.
Most of these operations use the boundary information available at each processing stage. If an
operation modifies the scene in such a way that the boundary-information update is not available for
one or more objects, then a new boundary is completely re-extracted, given a starting point in the
interior or at the boundary of the target objects. If no starting point is known, the scene can always
be re-scanned entirely in few minutes (1-5) for volume resolutions of the order of 256 3.
2.4.4 Run-Length Interpretation of Interior Traversal

Definition 2.15 of solid interior and Property 2.3 about volume traversal defined runs of voxels
between colinear facets with opposed (antiparallel) orientation 16. There are however two differences
with real run-lengths: first, we indicate the initial and final voxels plus their oriented face. This
allows to know the direction of the codification. The second difference is that, from the point of view
of data compression, our full representation is redundant, because run-length coding can be done
in only one direction, while we keep three sets of run-lengths (from sets of walls x ; to walls x+ ,
and the same for walls y + y ; z + z ; . It would not be difficult to add a routine to eliminate this
redundancy and to recover, if needed, the orthogonal sets of run-lengths.
(c) x +
x k- k
...
(a)
...
... (b)
(d)
...
...
(d)
...
...
(e)
...
...
(d)
...
Y
X
(f)
f (x +,y,z, 1)
(f)
f (x - ,y,z,0 )
V V
Figure 2.16: A run-length representation of a 3D object . (a) profile of @ ; (b) a slice perpendicular to
axis Z ; (c) pairs of Nx facets facets (x; + V
k x;k ), +from @ encode x-runs of voxels that fill the solid interior of
V ; the kth x-run is the closed interval xk xk ]. Shaded voxels indicate first and last voxels of each x-run.
(d) Cavities and concavities are taken into account by multiple x-runs for given values y z (a set of bars); (e)
a single x-run is compressed into two border voxels (two facets x; +
k0 xk0 ); (f) a full specification of oriented
; +
boundary-face pairs ( f(x y z 0) f(x y z 1) ) delimits starting and ending voxels in x-runs. Storage
and volume traversal are possible by specifying the set (x; f
+ Nx facets;1 .
k xk ) k=0 g
16
A step towards justification of our ad-hoc condition of Definition A.2, page 229
F ;
Using the facet partition 6, a facet pair with opposed oriented faces (f i f j ), with j = i +( 1)i,
for example, with i = 0 j = 1, the set of opposite facets of the form f (xa y z 0) f (xb y z 1),
with xa xb, gives all information needed to identify an x-run of voxels (a ’bar’) between co-
F
ordinates (x; y z ), and (x+ y z ), where we use the notation of Udupa and partition 6, as in
Definition 2.15 (see Figure 2.16).
Since the whole volume is represented, and pairs of sorted facets that differ only in x ; x+ (i.e.,
V
forming an x-run, and representing the interior(@ )), the information supplied by these facets is
enough to calculate the volume of the object. These and other morphometrical parameters will be
presented in Section 2.5.
2.5 Boundary-Based Processing and Analysis of 3D Objects

Applying the Gauss Theorem 17 , volume-integral calculations such as the volume itself, the center of
mass and higher-order moments can be obtained from surface-integral calculations [Udupa90b]. Let
f n
~ a vector function, ~ the normal vector of a surface element ds. The set is any spatial region in V
V
3D (the object interior, for example), and @ is its continuous boundary. Then, the continuous Gauss
Thorem states that:
ZZZ ZZ
V
r~f (x y z) dxdydz = @V
~f (s) ~n ds (2.12)
Volume integral surface integral
This theorem expresses a relationship between a volume integral of a region in the space, and a
surface integral, measured along the boundary of that region. It is the 3D equivalent of the Green
Theorem in 2D, which allows to extract the surface area of a region from information of theR
C R n
contour = @ . In a discrete form, normal ~ corresponds to the three axes of orientation, plus sign,
F
justifying the importance of data partition acoording to 6. Equation 2.12 gives rise to the following
formulae to calculate the volume and the first central moment (Center of Mass or “centroid”) for each
object (see Figure 2.17):
NX
x facets ;
Vol = x+n ; x; n Ly Lz (2.13a)
n=1
NX
x facets ;
XC = 2N1 x+ n ; x; n (2.13b)
x n=1
NX
YC = 2N1
y facets ;y + ; y ;
n n (2.13c)
y n=1
NX
z facets ;
ZC = 2N1 z+n ; z; n (2.13d)
z n=1

Vj
Vj
where Nx facets = card(@ ) x ) Ny facets = card(@ ) y ) Nz facets = card(@ ) z ), i.e., the

Vj
total of facets of types x; x+, etc. We deduce the equation 1.13a from the Gauss Theorem, but it
~ C and the run-length
should be obvious from Figure 2.17, as well as the equations for the centroid X
interpretation of the facet partition.
Several methods we use come from a general interpretation of the Gauss theorem: analysis and
manipulation of a 3D object can be accomplished by analysis and manipulation of its boundary. In
the cases where such correspondence is not possible, we complement our boundary-based paradigm
with a volume traversal method, which takes advantage itself of boundary-representations, since
facets constitute starting and ending points of voxel runs.
V V
At each step j of a series of (pre-)processings over a scene j , (with 0 the starting scene), the
lists of objects and their boundaries can be updated, allowing to extract morphometrical information
useful for processing, before final quantification, and allowing to select the objects to be further
analyzed. Surface rendering visualization at each step j is also feasible.V
17
also known as Ostrodgradskiı̂’s Theorem, or Divergence Theorem
2.5 Boundary-Based Processing and Analysis of 3D Objects 127
face
Boundary
Volume element
Object
face
Slice axis
Figure 2.17: Volume calculation of a discrete object V using the voxel face in @V . Volume elements are built
from face couples in opposite orientations.
Once all objects identified in the 3D scene are properly represented, the processing, quantitative
analysis and visualization can be effectuated through their boundaries. We have already seen how
to take advantage of the discrete Gauss Theorem to calculate the volume, centroids and moments of
inertia of the object. Processing operations can be thus simplified and made selectively on a single
object, or on a list of them, rather than performing the operation in the whole volume. This selectivity
allows to introduce a priori information concerning the kind of objects to be analyzed, or even on
subsets of their boundaries (e.g., concavities). Binary mathematical morphology in N 3 is an example
of boundary-based processing:
D EFINITION 2.28 (Morphological Boundary)

Let WV W
N3 a discrete object in a 3D scene. Let @ be a full boundary (all cavities and
fragment sub-boundaries of W
must be included). Then, the morphological erosion of Wby a
E
structuring 6-connected element 6 can be defined in terms of the 18-connected voxel boundary
( W ) of the object because (see for example [Jain89, page 388], for the 2D case):
18 W = Wn(W E ) 6 (2.14)
thus, W is also called a morphological boundary. Given W , the converse relation holds:
18 18
(W E ) = Wn W6 18 (2.15)
The erosion of W by E is the 18-connected geometric interior W . We call peeling this erosion-

6
by-boundary operation.
The dual operation, that is, “wrapping the front-voxel boundary” comes from definition of W +
in terms of a dilation by N = E :
6 6
W = (W E )nW
+
18 6 (2.16)
Then, a dilation is done by wrapping W to W :

+
(W E ) = W W
6
+
18 (2.17)
W
Recall that boundary neighbors p m are defined and found in terms of @ (a facet boundary; see
Definitions 2.26 and 2.27, pages 109-110. Thus, discrete morphological operations of an object in
the cubic grid can be effectuated by boundary traversal operations.
2.5.1 An Example of Boundary-Based Morphometry: Euclidean Area Estimation

Several morphological measures can be obtained or estimated from boundary information. We il-
lustrate what can be done introducing a correction of non-Euclidean measures, based on geodesic
neighborhoods (adjacent or next-neighbor face on the boundary), which are analyzed on a boundary
traversal.
A discrete estimation of Euclidean surface area, for cubic voxels with discrete steps L x = Ly =
Lz = 1:0, is obtained from (see Figure 2.18) [Russ90]:
4
S=
+
p21 number
number of othogonal-adjacent voxels
+
p3 number ofof 3D-diagonal-adjacent
2D-diagonal adjacent voxels
voxels:
(2.18a)
(a) (b) (c)

Figure 2.18: Euclidean approximations of area for staircase configurations of boundary voxels. (a) Orthogo-
nal voxels (no correction), (b) two-dimensional diagonal adjacence, (c) three-dimensional diagonal adjacence.
Light shadowed facets indicate the corresponding facet configuration.
Another approximation was proposed and tested by Smeulders and Beckers for 3D line lengths,
which is directly applied to 3D surface area [Smeulders89]:
S = 0:877 number of othogonal-adjacent voxels

+ 1:342 number of 2D-diagonal adjacent voxels
+ 1:647 number of 3D-diagonal-adjacent voxels
(2.19a)
Prismatic voxels of arbitrary physical dimensions L x Ly and Lz demand more complex corrections.
2D-diagonal and 3D-diagonal planes are formed from orthogonal faces in their six possible configu-
rations (see Figure 2.19). Facet-adjacency information is obtained from the boundary representation
and provides 2 adjacent and 2 co-adjacent next neighbors for each facet. A 3-bit code of their relative
orientation and a lookup table of correction factors allow us to device an Euclidean approximation of
local surface area. Higher-order corrections with second-next neighbors are feasible, but codes and
configuration combinations become much more complex. If higher precision is intended, it seems
more appropriate to build mesh models of the discrete surface (marching cubes, adaptive triangula-
tions or fitting of polynomial surface patches).
Sabcg = Ly Lz (2.20)
Scdeg = Lx Ly (2.21)
Sagef = Lz Lx
q (2.22)
Sacdf = 1=2Lx L2y + L2z (2.23)
p
Sabde = 1=2Ly L2z + L2x
q (2.24)
Sbcef = 1=2Lz L2x + L2y (2.25)
q
Sace = 1=2 L2x L2y + L2y L2z + L2z L2x (2.26)
2.5.2 Boundary-Based and Volume Processing (Examples)

These are some examples of 3D processing tools that make use of the principles already mentioned.
Figure 2.19: Prismatic voxel of sides Lx Ly and Lz and its 2D and 3D diagonals. Surface diagonal elements
(equations 2.20) help to obtain Euclidean approximations of area for staircase configurations of boundary
voxels.
✦ Post-labeling of segmented objects. This secondary labeling , after segmentation, can be em-
ployed to mask the object on the original (gray-level) scene for densitometric measurements
V

(as a free-shape ROI). The geometric interior can be traversed, thus labeled or simply exam-
inated, guiding the interior traversal from boundary traversals of the facet subsets x + f g
n and
f g
x;n which form the extreme points of an internal “run” of voxels. An entire object is filtered
out from the scene by being re-labeled with the same value of the background by using a LUT
and then by excluding its from the boundary traversal list.
✦ Separation of weakly-connected components. This tool exploits the boundary representation

to create discrete watershed surfaces, in a similar fashion to 2D clump splitting, as explained
in Section 1.2.3, and detailed in [Bloch90b, Mangin95, Marquez93b, Marquez94b, Lopez95,
Marquez96a].
Using the morphological equivalence of boundary trimming and discrete erosion by struc-
E
tural elements K K = 6 18 26, one or more erosions are firstly made on the object to
decompose by simply relabeling to background the boundary voxels, and re-extracting the
new boundaries. These erosions are non-homotopic, giving rise to several fragments which are
labeled as different objects. Then, a number of conditional dilations are applied, preserving
labels locally (homotopic dilation) and extending the separating interfaces to the whole object.
Conditional dilations are applied until all original object is filled with the new labels. More
compact components are obtained with this method. The total number N of required erosions
is function of that of the minimum neck-size of the connections to break. In the biological ap-
plication described in [MarquezCON91a, Lopez95, Marquez96a], serial images of cell nuclei
form touching chromatine bodies with different shapes. In this example, we set N 4, with
E 6 , corresponding to the estimated size of the connection neck [Lopez95]. In general, the
number of reconstruction dilations N depends on thin structures present and is determined
by convergence (no more new voxels are added). In the same biological application it was

N 11. The reason that N > N and sometimes N N is that a single erosion can
disappear a thin run of several voxels (a filament for example), and each conditioned dilation
will restore only one voxel at a time.
✦ Label manipulations. Two objects can be associated to be always treated together by being
assigned the same label. The opposite manipulation would consist in breaking a single object
into two or more volume components that are weak connected. Such separation can be done
by watershed segmentation, marking each component with a different label (see Figure 2.20).
This operation creates discrete interfaces constituted by the facets shared by each labeled com-
ponent. In general, a voxel label can serve as special marker, be transparent to some particular
analysis, serve as “contention wall” for propagation processes or have other meanings. Ob-
ject labeling is done by traversing the object’s volume by series of voxels comprised between
;
facets x; and x + ; this replaces interior-fill (or “flood”) algorithms which do not exploit
boundary information and require specification of an internal point to work.
Figure 2.20: Separation of weakly-connected components. (a) A subset of cross sections of

chromatine clumps in animal cell nuclei; the gray-marked regions are seen as background (in
a b
black) by the watershed segmentation. (b) Output subset; color labels indicate each of the 26
c d weakly-connected objects that were detected (operations are done in 3D space). (c) View (POV)
of reconstruction. (d) Another POV, selecting-out the biggest 3 components. Data from the
Microscopy Laboratory, Facultad de Ciencias, Mexico University.
✦ A more precise measure estimation of surface area. Facet representation imposes an important
error in area calculations due to 2D and 3D staircases. A proper correction in function of
adjacency relations is possible, as explained in Section 2.5.1.
✦ Estimation of the Euclidean normal vector for each facet. This calculation is described in
section Section 2.5.1.
Table 2.1: Some morphometric features calculated from boundary representations. R is a 2D region under analysis (e.g., a contour from a 2D slice or image) and
W 2 V is a 3D object from scene V . In 2D, (xn yn) are vertices of contour @R. In 3D, ~xn = (xn yn zn) X~ C = (x y z) are point coordinates of @W . Note that
for fractals in 2D and 3D, perimeter P and surface S are functions of scale .
Morphometric feature Symbol and definition

Z Z I I
Continuous contour area A= dx(t)
dxdy = y(t) dt dt ; x(t) dy(t)
R @R @R dt dt
vertex
NX
Polygonal contour area A = 1=2 (yn xn;1 ; xnyn;1 )
n=1
vertex
NX
Polygonal contour perimeter P= k(xn yn) ; (xn;1 yn;1)k
n=1
18-connected boundary of W W Wn(W
E6)
Eroded W by ’peeling’ W
E6 = Wn W
Dilated W by ’wrapping’ W E6 = W +W
(isotropic) Surface area of W S = cardf orthog-adj voxs
g + p2 cardf 2D-diag-adj voxs 3D-diag-adj voxs
g + p3 cardf g
faces
NxX
Volume of W Vol = (x+n ; x;n ) Ly Lz)
n=1
2.5 Boundary-Based Processing and Analysis of 3D Objects
voxels
NX
Coordinate x of the Centroid X C = x = 2N1 (x+n ; x;n )
x n=1
voxels
NX
Mean radius = 1=N ~xn X ~C
jj ; jj
n=1
voxels
NX
Standard deviation of 2 = 1=N ~xn X~C 2
jj ; jj;
n=1
Sphericity (compacity measure) Sph = =
Shape factor in 2D and 3D
p
f
f f = 4A=P 2 f 3D = 3 4V=S 3=2
133
Minkowski fractal Dimension of W W n EK ) i n = 1 2 : : : K 2 f6 18 26g

DM = h ∂ logV (∂ logn
Figure 2.21: (Top) Complex interfaces example from a biological application: analysis of invagina-
tions and endoplasmic reticulum interfaces with the nucleus of a dopaminergic neuron as described in
[Anglade93, Marquez94b, Anglade95, Anglade97]. (Bottom) Use of voxel and facet boundary neighbor-
hoods (V ) and @ (V ) to extract, analyze and display internal boundary components (nucleolus, periph-
eral chromatin, nuclear wall, endoplasmic reticulum and invaginations). These examples are from displays at
low-resolution, with dithering on only 7 colors.
2.6 Visualization of Complex Structures 135
2.6 Visualization of Complex Structures

Visual interpretation of voxelized objects can also be done using discrete boundaries. A conic-
perspective transformation is used, and a diffuse illumination model is applied for each of the discrete
normal vectors. In the simplest approach, three discrete normal directions give three gray-levels
precalculated in function of light direction. Back-to-front rendering was used to solve the hidden-
surface removal problem in our first implementations. Z-buffer techniques are much more efficient,
and have been recently available as public library functions [Karinthi95], or hardware-implemented
in graphics workstations. At present we have not incorporated such techniques, but our boundary-
based approach is compatible with Z-buffer rendering.
Common color displays have a limited number of colors (256 minus the colors allocated by the
X-Window system). In order to have color shade gradations and be able to display a high number of
distinct color labels, a dithering technique was employed to synthesize interpolated colors. Given
two color shades C1 C2, this technique allows to interpolate 15 shades (plus two original extreme
f g
values C1 C2) denoted by c^k 16 0 , between C1 C2, with c^0 = C1 and c^16 = C2 . In this manner, the
f g
system allocates only 7 original shades C k 0 for each color label, without noticeable Mach bands
6
or textural effects [Ulichney87a]. Edge sharpeness is also respected, since dither masks are applied
per pixel, preserving resolution at edges (see Figure 2.22).
Figure 2.22: A 4x4 dither matrix set of 17 patterns, used to interpolate between black and white. The size of
the patterns has been exagerated (scaled by 3).
2.6.1 Surface Rendering

2.6.1.1 Hidden Surface Removal and Surface Shading
In visualization of complex structures, simple perspective projection does not provide an effective
depth illusion. In our boundary-based approach, hidden surface removal is performed by simple
back-to-front displaying of single facets. This technique is compatible with Z-buffer techniques and
special graphics architectures, which avoids the need of depth-sorting of facets. Depth or distance
shading cueing is done by letting the back-to-front rendering yield the coordinates of the surface
voxels along the viewing axis instead of the encoded surface normal vector. A blending factor allows
to combine both shading techniques (depth shade and the normal orientation shading). Several light-
sources are possible, because discrete normals are precalculated in function of facet orientation.
2.6.1.2 Discrete Normal Estimations
In a more general approach, discrete normals are assigned per voxel or per facet in function of local
neighborhood averaging. The nearest facet neighbors (18-adjacent facets) allow for 34 possible nor-
mal orientations, because at a given facet, three neighboring facets are possible per edge, and each
facet has four edges. Second- and third-order neighbors determine a higher number of discrete nor-
mals. Our implementation and data structures have taken into account this higher-order information.

Figure 2.25 shows 3D rendering of a CT skull (resolution 512 512 146), with normal estimation
by first-order facet neighbors (geodesic 4-adjacents, Definition 2.24). Discretization artifacts are only
Figure 2.23: Smooth-gradations rendering using dither interpolation of 7 colors, at real display resolution.
There are 120 interpolated shades. Note that dithering texture is almost of the same order than the printer
halftones.
Figure 2.24: Same as Figure 2.23, zoomed detail (X4). Edge borders are scarcely distorted and textures
remain minimal.
visible in the Z axis, where resolution is the smallest (146). Our facet-based approach for rendering
presents some advantages in comparison with several existing rendering methods; for example:
✦ Rendering is discrete-oriented; individual voxel details and inter-connections can be made

visible. At the same time, a smooth appearance is available. In continuous-oriented approaches
(splines, traingle meshes and Phong smoothing) voxel information is lost or distorted.
✦ Only lists of boundary elements are stored and traversed.
✦ Traversal and display may be very selective: it can be organized by ROIs, by objects of interest,
by topological features such as cavities, by sub-boundaries, or specific sets of facets. This
selectivity allows also for labelling specific facets.
2.7 Summary and Conclusions 137
✦ Discrete-normal estimations may be dependent of other local informations (shape, curvature,

and neighborhood characteristics).
✦ Boundary traversal for visual rendering can be combined with object processing and morpho-
metric feature extraction.
2.6.2 Three-Dimensional Data Structures.

We found illustrative to give some few examples of implementation details. In particular, when

dealing with huge volumes (832 640 200 bytes for one database), we find useful the following
strategy that we could not found properly reported in the literature.
During boundary extraction and volume processing (e.g. region growing, thresholding, back-
ground noise remotion and volume MM operations), a volume dataset, such as coordinates with
labels, a computer-simulation output, voxelized surfaces, or a set of image slices, is read into a 3D
data structure. Several data structures have been reported, such as:
Spatial array of voxels (or ”spatial occupancy enumeration” [Foley92]). A straight N x Ny Nz

array of numbers (or vectors). This is a conveniently indexed 3D structure, but very expensive
in terms of storage, since a single continuous block of memory is allocated (for example a
cubic volume of 2563 =16Mb). We used these arrays in some small ROI operations, and
voxel neighborhoods, where radius is limited to no more than 40 voxels.
Octrees. This 3D-structures are difficult for implementing traversal and neighborhood operations.
We did not use them at all.
Run-length encoding. This compact representation is implicitly used in our b-rep, as already de-
scribed. During volume operations, an explicit run-length compression does not allow random
access which would require lengthy decoding and encoding to update linked lists (see how-
ever the permforming methods reported in []). Run-lengths are implictly produced during
the boundary extraction (”encoding”), even without pairing opposite facets; data also behaves
as run-lengths during the boundary-based operations (”decoding”) and when boundaries are
re-extracted, if needed (equivalent to re-encoding).
Marginal indexing. This is a hierarchical pointer-based sparse representation, which allows all ran-
dom access operations as spatial arrays of voxels. It is illustrated in Figure 2.26, and described
for 2D images in [Foley92]. We made a 3D-implementation consisting of:
V
✦ a pointer to a volume ” ” (a scene),
✦ which consists of an array of pointers to slices (images ” V z ]” in the Z -axis);
✦ these slices are also constituted as a ”wall” of pointers ” V z ]y ]” to
✦ rows of voxels V z ]y ]0] : : : V z ]y ]x max].
2.7 Summary and Conclusions

We described in this chapter a discrete boundary-based representation (“b-rep”) of objects in N 3, and
provided definitions and tools for several manipulations and analysis.
From Raw Data to Models in N3: A Boundary-Based Approach
1 x 6 discrete normals 81 x 6 discrete normals

fk ∋
V fk , { fm}03 ∋
V

Figure 2.25: 3D rendering of a skull at 512 512 146. Left: Voxel rendering with depth-cue rendering and 6 normals per facet fk . Right: Idem, with 81 normals
per facet estimated from four geodesic 4-adjacent facets. Color dithering is also applied to interpolate 16x8 color shades; each color label uses only 8 entries from
the palette of 256 colors.
138
pointer to array V array of N z pointers to slices V[z]

Z Z
(a) . . . (b)
Y X
. . .
X Y
. . .
(c)
wall of pointers:
. . .
. . .
. . .
. . .
N y columns V[z][y]
of pointers to
rows of Nx voxels . . .
(e)
voxel at V[z][y][0]
(d)
. . .
voxel at V[z][y][x]
voxel at V[z][y][N x -1]
Figure 2.26: Marginal index arrays. 3D-data structure to access a discrete scene in a sparse representation.
(a) A pointer V to “a volume” as an array of pointers; X Y Z indicate dimensions and coordinate axes. (b)
Array of pointers V z] to slices (dimension Z ). (c) A “wall” of pointers V z]y] to rows of voxels. (d) Rows of
voxels V z]y]0] : :: V z]y]x max]. (e) an object in scene V .
A key concept of digital spaces is K -connectivity, which partitions a scene into K -objects V
(K -connected components), whose frontiers or boundaries can be represented by points, facets or
V
voxels. We used in particular the face-based boundary @ as the basis of several manipulations and
V
analysis of discrete sets. Of particular importance is the partition of @ into sets with facets of the
F
same orientation (6 sets 6 ). The voxel-based boundary V
allows to define and make possible
morphological characteristics (e.g., geometric interior, neighborhoods). Passage from one b-rep to
the other is done by examination of the immediate neighborhood (from boundary voxels to facets)
and redundancy elimination (from facets to boundary voxels).
Several concepts can be grouped together; we have traversal operations in a scene, the interior of
an object, a facet, or a boundary. Facets have a trihedron of discrete orientations assigned, (normals
F
and lateral circuits) and are partitioned in 6 orientation sets ( 6 ). Neighborhoods appear in Euclidean
and Geodesic modes (along a surface), but also in the surface normal and tangential directions. They
are also defined for voxels, facets and boundaries.
We started early implementations of the boundary extraction method of Artzy et al. for biomedi-
cal applications (electron microscopy, [Marquez94b] in PC computers, and this lead us to review the
theory of digital spaces and discrete representations, as well as the manipulation of several objects
at the same time. We have dealed with other problems related to complex objects and boundaries.
Some of these are presented in this manuscript, in Chapters 3-5. At present the system was ported
to UNIX, working under a Motif user interface. We have tested most algorithms in resolutions up to
832x640x220 voxels.
A substantial part of the work in this chapter has been already done by other groups, using
sometimes different notation, or claiming generalizations to n dimensions, or faster algorithms (see
for example [Shu91] for a comparison table). They usually are reported to work for one single
object which has to be indicated or isolated by the user. We describe synoptically our work and our
contributions:
✦ We stated the b-rep model in terms of boundary elements: oriented-faces and voxels, and devel-
opped a consistent description of objects in discrete space and several characteristics towards
complex shapes, as presented in Chapter 1. Some of these definitions are not always clear in
the literature, such as partitions of face-orientations, and lateral circuits, and the difference in
treatment between voxel faces and boundary elements (facets or voxels).
✦ We have built and optimized several Look-Up Tables (LUT) to look for facet adjacents and co-
adjacents, and to be able in the future to work with different sets of traversal circuits (orbits),
as a mean to sample in different ways a given surface.
✦ Our volume-traversal method using a subset of @ V (a containing wall of facets x + and a start-
ing wall of facets x; , not necessarily paired) is very simple and original, and we avoid the
computation of logical operations on the whole scene (a method still used since its introduc-
tion in [Udupa90]).
✦ Besides a paper of volume calculation of Udupa ([Udupa81]), and the original suggestion
of Rosenfeld et al.[Rosenfeld91], we have not found actual applications of morphometrical
parameter extraction from boundary information. We implemented some MM operations, and
V
neihborhood analysis on @ , and applied them in Chapter 4 for local segmentation, region
growing and tubular detection, and in Chapter 5.1 for interface analysis.
✦ In particular, we proposed a better Euclidean estimation of boundary surface area, using the
nearest facet neighborhood configuration. This information also provided a normal vector
estimation that allows smoother visualization of voxel-based volumes, and the means to probe
the object, from its boundary, in the normal direction.
In the other hand, we did not study, tested, finished or incorporated the following topics and
features in the present work:
✦ The discrete Jordan property of surfaces.
✦ Topological considerations (homotopic operations, simple point removal, Medial Axis Trans-
form, which is only briefly described in Chapter 4).
✦ Full validation and comparison of different measures and Euclidean approximations. Some of
these were done, but not presented in this report.
✦ Nested-boundary trees, adjacency graphs, hierarchical decompositions and other descriptive

structures for several objects (having common boundaries and neighboring relations).
✦ Extension to the discrete case of all definitions in the preliminaries Section 1.1 and Ap-
pendix A.
The latter list opens a very vast field of perspectives; but these will be summarized in Section 5.8
”Conclusions and Perspectives”.
Chapter 3
Radiometric Homogenization of the

Color Cryosection Images from the VHP
Lungs for 3-D Segmentation of Blood
Vessels
Abstract
This chapter deals with the problem of radiometric inhomogeneities found on the physical color im-
ages of the anatomical cryosections from the Visible Human Project (VHP) male body. Our goal is to
extract very thin structures, like the blood vessel tree from the lungs. Current segmentation methods
applied to VHP color images are disturbed by discontinuous, inter-slice radiometric variations; we
thus devised an adaptive correction that is propagated along a series of parallel slices, taking ad-
vantage of structural coherence between consecutive slices [Marquez96b, Marquez98]. No blurring
is introduced, and fine details and texture are respected. Results of 3-D segmentation of fine blood
vessels on the corrected volume are presented.
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144

3.2 Problem Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
3.2.1 Gamma Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
3.2.2 Visualization of radiometric inhomogeneities . . . . . . . . . . . . . . . 146
3.3 Local Adaptive Homogenization . . . . . . . . . . . . . . . . . . . . . . . . . 150
3.3.1 Inhomogeneity Characterization by an Auto-regressive Model . . . . . . 150
3.3.2 Local Coherence Hypothesis . . . . . . . . . . . . . . . . . . . . . . . . 152
3.3.3 Correction Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
3.4 Discussion and Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
144 Radiometric Homogenization of Color Images from the VHP Lungs
3.1 Introduction
Many laboratories have extensive experience of the three-dimensional reconstruction of structures
from data collected from transmitted, emitted or reflected radiation (X-ray computed and emission
tomography, nuclear magnetic resonance imaging, ultrasound, confocal and electron microscope
images, etc.). This is not always the case with traditional, physical, cross-section reconstruction,
which is lengthy and requires block fixation and destruction of the specimen. Even if physicians are
familiar with anatomic slices of the human body, until very recently there were no large color data
sets to reconstruct whole organs for anatomy atlases and models.
”VHP” I Cryosection techniques have been used in the Visible Human Project (VHP) [Ackerman95,
Spitzer96] of the National Library of Medicine to make a high resolution volume of anatomical
information available to scientists. 1871 axial-plane slices spaced at 1mm have been sampled at a

resolution of 0.33 mm, with 2048 1216 pixels of 24 bits. Three sets of images corresponding to the
three channels RGB have been recorded. The three channels are spatially well registered and a signal
of one byte per pixel and per channel is available. The complete data files occupy 15 Gigabytes.
Computer tomography and magnetic resonance imaging sets are also available.
This chapter deals with the problem of radiometric inhomogeneities that we have found on phys-
ical color images from the VHP male body. These images correspond to anatomical cryosections1 of
the pulmonary region. Interest for the detection, display and compensation of such inhomogeneities
in the VHP is timely, since automatic procedures for feature extraction and elaboration of reference
atlases require volume data to be homogeneous and isotropic. Hence, any noise or artifact compo-
nents must be properly identified or estimated.
We consider in the following our data subset or Region Of Interest (ROI) which is the cropped

sub-volume which encloses both lungs. This ROI consists of 160 cross sections of 832 640 pixels
of 24 bits, corresponding to slice numbers 1320-1479. In the following sections we describe the
problem of specific inhomogeneities encountered in the ROI, and present several methods which
we have developed to visualize and characterize them. Then we detail the correction algorithm for
which we use the fact that consecutive images are very similar in structural features. We finally
present results of the correction and the automatic extraction of blood vessels by 3-D segmentation
techniques.
3.2 Problem Description

In order to obtain three-dimensional segmentation of the bronchial blood vessels or any other struc-
tures in volume data from cross sections, the images must be spatially registered, but they must also
be radiometrically registered or homogenized, i.e., color intensity distorsions must be eliminated or
properly compensated through the ROI. The VHP color images are correctly registered in rotation
and translation, except for some images in which small translation offsets have to be corrected. To
ensure radiometric homogenization, each color image was digitized by the VHP team including a
gray-scale test card for color camera calibration, to allow for gamma correction [Poyton96], and
homogenization of a stack of color images (see Fig. 3.1). The test card was used to homogenize
f g
intensities in each image I n of the ROI, n = 1320 : : : 1479, and to obtain a set In in which in-
1
Hystological slice or polished tissue previously congelated.
3.2 Problem Description 145
tensities are normalized with respect to an average gray scale in each channel RGB. This correction
consists of:
(i) a measurement of the 20 RGB gray-scale values2 (which present a non-linear response varying
between channels and between images),
(ii) a curve fitting of the average gray scale (a spline),
(iii) a gamma correction by using a specific 256-entry look-up table, for each I n , and each channel
2f g
u R G B (see Fig. 3.1c).
In each image and for each gray-scale bar i = 0 : : : 19 of the corresponding test card, the extreme

values (over a window of 5 13 pixels) were not taken into account in averaging operations as they
were considered as outliers due to acquisition artifacts or noise.
3.2.1 Gamma Correction

We observed that, even after a separate gamma correction of each image by using the accompanying
gray scale, there remained some radiometric discontinuities between slices which affect the three-
dimensional segmentation of small blood vessels and bronchi (see Figs. 3.2 and 3.3). The origin
of these inhomogeneities is unknown, but they seem to be unrelated to acquisition artifacts (camera
calibration or variations in lighting, causing an uncontroled reflectance factor). Spitzer et al. noted
in [Spitzer96]: “previous experience with willed cadavers who have died by court-ordered lethal
injection had revealed that such remains may undergo massive deterioration within 24 hours of
death”. Even if measures were taken to delay this deterioration and the body was frozen two days
after death, some tissue degradation could have taken place during the 20 days of cutting sessions.
Hence, radiometric inhomogeneities could be evidence of an irregular oxydation of the sliced surface
of the frozen body between two image acquisitions. Furthermore, these acquisitions could have
been unevenly spaced in time, or taken under different temperature conditions; but these are only
hypotheses. Lung tissue differs from other parenchyma, since it has a porous structure. Thus, a high
sensitivity to air exposure is expected. We have found no other regions of the VHP male body, except
the lungs, where a similar radiometric inhomogeneity problem is noticeable.
In a sequence of slices, a radiometric homogenization could be sought by a histogram registration
where the main features, in particular the principal mode, are more or less aligned for small, medium
and large regions in each image. Since a shift of the main peak corresponds to an average color offset,
radiometric inhomogeneities can easily be visualized by coronal or sagittal cross-section images
resampled from the slices in the ROI (see Fig. 3.2). Inter-slice inhomogeneities then appear in such
cross-sections as horizontal artifacts.
f g f g
Let I n be the original color data subset and I n the subset obtained by gamma correction,
using the gray scale provided for each image. Figure 3.3-left shows a coronal slice sub-image from
f g
I n ; each of its rows corresponds to one of the successive axial-plane images. Figure 3.3-right
shows the corresponding resampled slice from In . f g
Even if some global homogenization has taken place, we observe that the most important re-
maining horizontal discontinuities can not be interpreted as just a global color offset between two
successive acquisitions. This is further demonstrated by exhibiting inhomogeneities, before and after
correction, in the different visualization modes which we will now describe.
2
A “gray” level is not perfectly colorless for a camera.
n
I γ − correction I nγ
color-gray scale n
(a)
255
gray bar mean value u^
(b)
0 gray bar index i 20

255
look-up table entry
(c)
0 gamma-corrected value u 255
Figure 3.1: Global gamma correction. (a) A gray scale (in color) is used for a global radiometric
f g
homogenization of the image set I n . (b) Each gray scale image provides three RGB intensity
curves, with i the gray bar index from 0 to 19 and u ^ the mean value of their measured RGB values
(u2f g
^ R G B ). (c) A 256-entry look-up table is built to gamma-correct each channel of each slice
with the linear scale defined by the gray bar indices.
3.2.2 Visualization of radiometric inhomogeneities

The remaining inhomogeneities as well as coherent features along the slices may be further studied
with three modalities of visualization that we proposed consisting in images of
✦ stacked color histograms of the slice set (see Fig. 3.4),
✦ co-occurrence color images (see Fig. 3.5), and

sagittal
n cross sections
γ
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slice I γn
coronal cross sections
Figure 3.2: Residual inhomogeneities. Display of sagittal and coronal cross sections resampled from
axial images I n reveals clearly residual homogeneity differences between slices.
✦ checkerboard displays of adjacent slices (see Fig. 3.6).
These techniques were applied to exhibit and understand the radiometric inhomogeneities present
in our set of gamma-corrected color images. They allowed us to design a correction method. At first,
before we realized the local character of inhomogeneities, we aimed at a global homogenization of
color intensities and developed two approaches which gave rise to correction strategies that did not
work. However, we consider it illustrative to describe them briefly.
For each color image In , we obtain three histograms H n (u) u 2f g
R G B (see Fig. 3.4a),
which may be viewed in radiometric space as a row of a 2-D color image (see Fig. 3.4b). The
horizontal axis corresponds to the intensity levels u for each color channel RGB, the vertical axis
Figure 3.3: Residual inhomogeneities. A coronal sub-image of the original volume set (left), and after
gamma correction (right). Remaining inhomogeneities appear in the right as horizontal artifacts
pointed by arrows. Only 40 slices are displayed to show the inhomogeneities more clearly.
corresponds to the slice number n, and the pixel color at abscissa u represents the three frequencies
(maximum value normalized to 255) of the three intensity values u in slice n. Thus each horizontal
row represents the color histogram of a cross-section image. Global inhomogeneities are then easily
visualized as color shifts between rows. Alignment of extrema was attempted for a global homoge-
nization by histogram manipulation, with a crest-line tracking technique (see Fig. 3.4c). Important
local extrema of RGB-color histograms were detected and linked to form continuous ridges, and his-
togram stretching operations were then applied to each image. Unfortunately, this operation did not
remove some local discontinuous variations.
Co-occurrence color images were also useful in exhibiting RGB-intensity disparities between
two consecutive images In In+1 (see Fig. 3.5). Both axes correspond to traditional histogram ordi-
2f
nates, that is, intensity values u n un+1 g
0 : : : 255 . In conventional histograms, the height of the
function at location u indicates the frequency of pixels with that intensity value u. In co-occurrence
color histograms, RGB intensities are plotted directly as a colored pixel, instead of coding them as
height profiles. Thus, the pixel at location (u n un+1 ) indicates the frequency of coordinate pairs
2f
(x y ) in images In and In+1 , having values un and un+1 respectively, with un R G B . When g
both images are exactly the same, the co-occurrence color plot consists of a diagonal colored line,
whose RGB intensities correspond to the conventional color histogram of the image. When both
images are highly uncorrelated, no diagonal appears, and the plot consists of scattered points. Im-
ages from a series of thin slices should present co-occurrence images with predominant diagonal
features. Radiometric inhomogeneities appear as an irregular scattering of point clouds near the di-
agonal, which is also distorted. Biases from the geometric diagonal reflect the presence of significant
populations of pixels with systematic shifts in RGB values. A second global correction method could
then be devised on diagonal properties, similar to crest-line alignment in stacked histograms, but it
would not allow us a correct homogenization which has to be performed locally in our case.
Checkerboard displays of adjacent slices allow us to exhibit local disparities more clearly before
and after a correction method is applied. A checkerboard pattern is used to interlace two consecutive
images, which are displayed alternatively in the ”black” and ”white” squares (see Fig. 3.6). The
presence of remaining inhomogeneities notably enhances the perception of the checkerboard pattern
n n
H (u) = Histo(I γ )
(a)
0
slice n
u
∋
u { R,G,B }
255
1440
(b) slice n
1459
0 127
1400
(c)
1470
0 255
Figure 3.4: Visualization of slice-set histograms. (a) Each curve H n (u) u

n
2f g
R G B is the
histogram Histo (I ) of the image corresponding to slice n. Only one channel component per slice
histogram is plotted for clarity. (b) Misalignments of histogram features; each row n is a color
line defined by the three histograms H n (u) of the corresponding image I n . (c) Global histogram
registration by a crest-line tracking technique with alignment of detected local extrema.
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I γn+1
I γn
0 un 255
Figure 3.5: Co-occurrence color image. Pairwise comparisons of consecutive gamma-corrected

images In and In+1 allow us to visualize radiometric inhomogeneities as an irregular scattering
around the diagonal. The RGB values of the co-occurrence image pixel situated at coordinates
(un un+1 ) represent the frequency of the pixels with the same spatial coordinate (x y ) in images I n
and In+1 and having the intensity values u n and un+1 , with u 2f
R G B . g
(see Fig. 3.6-left). This pattern becomes unnoticeable when we apply the local adaptive homoge-
nization method described in Section 3.3.1 (see Fig. 3.6-right).
3.3 Local Adaptive Homogenization

3.3.1 Inhomogeneity Characterization by an Auto-regressive Model
Co-occurrence images took us naturally to consider pairwise differential images and to study the
peak features of their local, stacked color histograms. To correct the discontinuities observed, we
have adopted the following first-order autoregressive model:
In (x y) = In;1 (x y ) + n (x y ) (3.1)
where In (x y ) is the gamma-corrected RGB-intensity vector of pixel p = (x y ) in slice number
n, and n (x y) is an offset vector (see Fig. 3.7a) that includes at least three kinds of radiometric
discontinuities that may arise between two axial-plane slices:
✦ The first kind of discontinuity is the real texture and 3-D structure feature innovations between
slices (see Fig. 3.7b). This is the information that must be preserved.
✦ The second kind are smooth gradients due to lighting changes between image acquisitions,
gradual specimen alterations during slicing and inhomogeneous blood distribution at the time
of freezing (see Fig. 3.7c).
✦ The third kind corresponds to the residual inhomogeneities which we need to remove. It con-
sists of noise and some artifacts due to regional variations caused by an unknown physical
process which has altered the color of the tissue before digitization (see Fig. 3.7d). In some
n
Image I γ
n+1
Image I γ
Figure 3.6: Checkerboard color displays clearly exhibit whether regional differences are present or not in consecutive images I n and In+1 . Two
consecutive slices, after the gamma correction (left), and after the adaptive homogenization described in Section 3.3.1 (right).
151
imaging modalities such as MRI [Zijden95], this component of n (x y ) can be further sep-
arated into inter- and intra-slice intensity variations, but some a priori knowledge would be
required for an explicit formulation.
(a) (b)
. ..
. .
(c) (d)
Figure 3.7: An ideal, simulated decomposition of inter-slice radiometric inhomogeneities. (a) Dif-
;
ferential image I n = In In;1 + k128 (see footnote 1 in page 152); (b) 3-D structure innovations
and texture (to be extracted); (c) smooth 2-D and 3-D gradients (lighting mismatches and speci-
men spatial and temporal variations); (d) inhomogeneity artifacts and noise due to discontinuous
alterations. Unfortunately, in practice, such a decomposition can only be approximated.
3.3.2 Local Coherence Hypothesis

In order to correct the third kind of inhomogeneities, we have taken advantage of structural coher-
ence (see Paragraph 1.2.5, page 40). First, a differential image In (x y ) is obtained by subtraction
between two consecutive color cross sections 1. Only innovations corresponding to anatomical dif-
ferences between successive images, give rise to significant positive or negative deviations from the
ground level (0,0,0). They appear as contrasted thin features at the boundaries of 3-D structures
such as organs, bones or vessels (see Figs. 3.7a and 3.7b). Large colored regions in the differen-
tial images should then reveal radiometric discontinuities. As we are interested in segmentation of
fine structures such as the blood vessels, large unexpected innovations which suddenly appear must
be removed. In the lungs such inhomogeneities will color differential images unevenly, as can be
observed in Figs. 3.7a and 3.9a.
1
In order to display and distinguish negative and positive deviations from (0,0,0), a constant offset k 128 is added to
each channel; but in the discussion we refer to the ”ground level” as (0,0,0).
3.3 Local Adaptive Homogenization 153
n n
Hp (u) := Histo( Np )
n n
δI γ }
∋
where Np = { q : |p-q| < R, q
n n n-1
and δ I γ := I γ - I γ
n
Np R
p
n
Hp (u)
u(p)
u=0 u
∋
{ R, G, B }
Figure 3.8: Local coherence hypothesis: when consecutive color slices are radiometrically reg-
istered, their differential images In have local histogram modes aligned around (R G B ) =
2
(0 0 0), for all pixels p In .
For radiometric homogenization, our coherence hypothesis consists in having the modes of local
2
histograms of In (x y ) centered at (R G B ) = (0 0 0), for all pixels p In (see Fig. 3.8). Even
if very complex fine structures are present, two consecutive thin cross sections are similar enough
to expect that, locally, In (x y ) will have a histogram centered at (0,0,0). The local histogram at
2 N
point p In is measured over a small circular region pn in the differential image, pn = q N f j
j;j 2 g
p q < R q In . The radius R of this neighborhood is chosen large enough to guarantee
meaningful statistics (e.g., the histogram mode should be easily detectable). Furthermore, secondary
peaks present in this histogram correspond to innovations which represent the end or beginning of
a different tissue region between two slices (a slanted vessel, or the transition between two organs,
for example). Any shift of the central mode from (0,0,0) implies a radiometric discontinuity of
the third kind at that pixel. In our implementation the region radius R was chosen larger than the
local area occupied by an innovation such as small blood vessels that we want to extract and which
have a diameter of 1.0 to 6.0 mm; thus we set R > 20 pixels. The coherence hypothesis can also
be stated as follows: if no inhomogeneities are present, the area of innovations (thin, high-contrast
(black) features in Fig. 3.7b) is negligeable compared to the area of all inter-slice common features
(white background in Fig. 3.7b). Innovations are also highly contrasted, that is, their peaks in the
differential histogram are far from (0,0,0), which facilitates further automatic detection of the central
mode (see Fig. 3.8). This property also applies to large discontinuities at the top or the bottom of
well-defined objects (vertebrae, for instance). Thus, if the mode is too far from (0,0,0), no correction
is done and the inhomogeneity is treated as a large, natural discontinuity. The decision threshold for
correction was fixed at (30,20,20), because no radiometric inhomogeneity higher than (26,12,8) was
f g
detected in the worst case. This was found around slice n = 1451 of the set I n when we checked
parenchyma transitions with other organs.
3.3.3 Correction Algorithm

Thus, we perform a local adaptive correction, for each color channel, which is propagated along the
images In . Figure 3.9 shows difference color images, plus a global offset in order to display negative
values also. The dominant gray value (R G B ) = (k128 k128 k128) corresponds to ground level
(0,0,0), and darker or lighter pixels represent innovations or inhomogeneities. A local histogram is
obtained for each channel and for each pixel p(x y ) of the difference color image In ; the pixel
N
neighborhood pn of radius R = 20 consists of 1250 pixels. The main peak is detected and its shift
from zero is calculated for each pixel p:
err u (p) = argmax

u
(Hpn(u)) u 2 fR G B g:
This shift represents the local mismatch between images I n;1 and In at pixel p. A partial correction

of amount a err u , with 0 < a < 1, is made on the corresponding pixel p of the second image I n .
Once In is corrected, the third image In+1 is subtracted from In to obtain I n+1 , and the process is
repeated, until all images of the ROI have been processed. Figure 3.10 summarizes the algorithm.
A second pass is performed backwards to ensure a minimal deviation from original undistorted
values while rejecting inhomogeneities which are not innovations. The fading memory constant

a 1 that we have introduced weights the error correction. Such a constant comes from a general
autoregressive model of the form:
In = a0 + a1 I n;1 + a2 In;2 + a3In;4 + : : : (3.2)
from which we have only retained the first-order term. Constant a plays the role of a1 , and the
combination of a0 together with the error of the first-order approximation is assimilated to the term
n (x y ) in Equation 3.1. We have found that a partial correction of 60% (a = 0:6) in one direction
and another of 60% of the residual difference in the backwards direction (making a total of 84% of
the original difference), perform better than a full 100% correction (a = 1:0) in one single pass, as
this may produce some color artifacts. The reason is that the starting slice I n0 for error propagation
may be too inhomogeneous in relation to its neighbors, and a full correction may thus introduce
unnatural color shifts, even if the final set is radiometrically homogeneous. Besides the memory
fading constant, a proper choice of In0 can be devised using homogeneity testing techniques [Wu93].
The goal is to start at an image with low distorsion, and a simple criterion is to choose the slice with
+127
+95
+63
+31
0
-32
-64
-92
-128
Figure 3.9: Difference image between two cross sections (slices 1450, 1451) before (left) and after (right) local adaptive homogenization. Small,
high-contrast deviations from (R G B ) = (k 128 k128 k128) represent innovations. Larger, low-contrast zones are inter-slice inhomogeneities. The
gray-scale at the left is the same for each channel R G B .
155
n = n0
n n n -1
δ Iγ = I γ - I γ Auto-regressive model of order 1
R > size of innovations

A n
Np = { q: |p-q|< R }
n Hpn (u)
δ Iγ
∋ n n
p H p(u) = Histo( Np )
n
erru (p) = argmax( H p (u) ) u
u 0,0,0
local histogram
A ∋
u(p) u(p) - a erru(p) 0< a <1, u {R,G,B}
I γn
∋
p
n n+ 1 forward propagation
Figure 3.10: Adaptive correction algorithm. Starting at slice n = n 0 selected as the slice whose next
difference image is closest to ”zero” (Equation 3.3), shifts in the mode of local histograms H pn (u)
on differential images are compensated on image number n, for every pixel p. Neighborhood size
R for Hpn (u) is chosen greater than innovations. Corrections are propagated forwards and then
backwards along the ROI.
minimal differences between its neighbors. In our case, we select the slice number n0 for which the
;
differential image In = In In;1 has the smallest contrast contents. A simple way to ensure this
condition is selecting an image I n0 for which the area of the differential histogram is minimal:
0 Z 1
@ X
n0 =4 argmin
n n
Histo(In) A (3.3)
u2fRGB g I
Finally, to optimize the local histogram calculations, a rolling buffer (or sliding window) tech-
nique has been implemented (see Fig. 3.11). It consists in updating the neighborhood information
by adding to the local histogram only the next entering front of pixels, subtracting the leaving pixels,
and updating the central pixel information 2. Updates of the buffer are done as long as window pn N
2
The central pixel p itself is excluded from pn in order to enhance statistical robustness when radius R is diminished.
N
This improves the local radiometric homogeneity around small details such as in the extreme case of one-pixel width blood
vessels.
is slid on each row of the input image; the neighborhood is fully read only once per row to initialize
the buffer. Local operations other than histogram measurements can also be performed.
Fig. 3.12-left is equivalent to Fig. 3.3-right. Figure 3.12-right shows the same coronal sub-image
as in Fig. 3.12-left, but after our local adaptive homogenization. Previous horizontal artifacts have
f
almost disappeared. We call the new color data subset IHOMOG n g . Other coronal and sagittal images
f n g
resampled from IHOMOG show similar performances of the radiometric correction (see Fig. 3.13).
n
N p = { q : |p-q| < R } => precalculated list of offsets {q}
...
p = (x, y) p’ = (x+ 1, y)
Histogram update:
n n
Hp’ H p + {new list } - {old list }
Figure 3.11: Rolling buffer technique for fast local histogram calculation. Only the boundary pixels
N
(new or old) of the sliding neighborhood pn are considered for the update of the histogram.
f n
Let IGRAY g f n
be the set of gray-level images, taking the luminance from IHOMOG g. Using local (or
f n g
”adaptive”) thresholding [Castleman90] on IGRAY , we have obtained a binary volume IBIN f gn , where
fine blood vessels can be isolated for three-dimensional reconstruction. A volume rendering view
f gn is shown in Fig. 3.14-left, using a back-to-front approach with depth cueing [Frieder85,
of IBIN
Tiede93]. An improper choice of the neighborhood radius R for the analysis (too small or too large)
or of other parameters as the constant a may affect homogenization results. But these results remain
very robust for a wide interval of the parameter values, as observed when setting the neighborhood
radius from 15 to 40 pixels, and the constant a from 0.6 to 0.85. In order to evaluate the performance
f n
of the 3-D segmentation of the volume set I HOMOG gwith different homogenization parameters, we
use the inverse of an axial Maximum Intensity Projection (MIP) image [Udupa93, Napel92], as J ”MIP”
shown in Fig. 3.14-right. MIP color images allow us to visualize the projection of the blood vessels
traces present in the volume and to verify their presence after the 3-D segmentation.
f
Simple local thresholding on I GRAYn g was useful for evaluation of the homogenization results
with the help of coarse volume renderings, as shown in Fig. 3.14-left. Besides a more realistic
visualization, we aim at obtaining morphometric analysis and explicit representations of anatomic
structures. Since lung parenchyma and blood-vessel images present texture and partial-area varia-
f n
tions, local thresholding on I GRAY g is inadequate for fine blood-vessel extraction, and does not take
Figure 3.12: Local adaptive homogenization result: (left) coronal resampled image of the gamma-
f g f
corrected set In ; (right) the same cross section taken from I HOMOG
n g
, i.e., after local adaptive
homogenization.
Figure 3.13: Local adaptive homogenization result: (left) another coronal resampled image of the
gamma-corrected set; (right) the same cross section after local adaptive homogenization.
full advantage of 3-D homogenization and color information. Thus, a more robust method was used
for thin-structure segmentation.
Using the gamma-corrected and radiometrically homogenized ROI we have obtained realistic
reconstructions of the bronchial tree after different stages of segmentation and 3-D image processing
(see Fig. 3.15), using a 3-D region growing method, and a 3-D surface tracking with boundary rep-
resentations [Pavlidis90, Artzy81, Udupa82, Thurf95]. These methods are described in Chapter 4.
Correction of the inhomogeneities proved to be useful for the automated 3-D segmentation by region
growing because this method relies on local statistics of RGB values (mean and variance). With
Figure 3.14: Volume rendering: (left) back-to-front display with depth cueing of blood vessels traces
detected in the radiometrically homogenized sub-volume; (right) axial minimum intensity projection
image of slices 1420-1429.
this approach, the red channel information was enough to discriminate most bronchial blood vessels
from lung tissue. Gray-level luminance was also tested, with no evident improvement. Blue and
green channels carry less contrast information, and linear combinations with the red channel tend to
diminish the discriminating power of the latter, at least for blood vessels in the lungs of the VHP.
Further work must be done to confirm these observations and to explore segmentation approaches
using Principal Component Analysis (PCA) of color distribution in parenchyma, and using color
spaces other than RGB.
Figure 3.15: 3-D Visualization. Two views of bronchial blood-vessel tree extracted from the VHP
data set after radiometric homogenization.
3.4 Discussion and Conclusion

We have proposed and tested a non-linear, local adaptive algorithm for radiometric homogenization
of cryosection image series from the VHP dataset. The high resolution of the thin slices allowed
us to exploit local coherence, in order to distinguish changes in 3-D structures from radiometric
artifacts. This was done by: (i) selection of an image I n0 as reference, (ii) calculation of the color
;
differential images I n from two consecutive slices n 1 and n, (iii) calculation, for each pixel, of
a local histogram of I n , (iv) examination of the RGB shift from zero of the principal mode of the
histogram, and (iv) correction of the error and setting the resulting image as a new reference in order
to propagate the correction from slice to slice.
An important advantage of the adaptive homogenization method is that no blurring is introduced
f n g
in the resulting set I HOMOG of corrected images. Since no low-pass filtering is done, fine 3-D details
and textures are preserved. Pixel modification consists of local RGB offsets which depend only on the
coherence mismatch between regions of two adjacent images. The use of a fading-memory constant
allows us to preserve smooth gradients across the volume set (inter-slice variations), while the local
character of our correction impedes the filtering of smooth variations inside an axial image (intra-
slice variations). For these reasons, local thresholding or region growing techniques were needed
to segment fine structures such as the blood vessels, as shown in Fig. 3.15. However, classical
segmentation problems such as non-additive noise, sub-sampling, partial volume, etc., remain to be
solved.
Remaining inhomogeneities still visible in Fig. 3.12b could be entirely smoothed out if smaller
neighborhoods of lung tissue were analyzed or a higher-order autoregressive model were used (Equa-
tion 3.2)v. This type of very local analysis is difficult in the proximity either of important innova-
tions or of parenchyma other than the lung tissue, because local histogram analysis works better with
medium sized regions where the radius is much larger than blood vessel innovations. A possible
solution would be to perform first a coarse segmentation of large innovations, such as those from
the heart and the stomach, in order to mask them out from differential images. In this way, differ-
ential histograms could be freed from large innovation components, improving mode detection and
measurement of its local shift from zero.
Our segmentation methods used only the red channel, as explained in Chapter 4. The homo-
geneization method allows the correction of each color channel, which would permit a data-fusion
approach. Another solution is to work in an adapted color space in which blood-vessel characteriza-
tion uses PCA.
There are many image processing and pattern recognition techniques designed for motion image
sequences. It is common practice to apply such techniques to 3D volume analysis or vice versa.
The homogenization method presented in this paper may be applied to correct or detect certain in-
homogeneities in time sequences; for example, in old motion film restoration where local distorsions
and artifacts appear often in individual frames or short sequences. This example is just a glimpse of
potential applications of the techniques developped for VHP-imaging to other fields.
Chapter 4
Extraction of Bronchial Blood-Vessels

from Color Cryosections of the VHP
Abstract
We describe in this chapter the extraction of the bronchial blood vessels in the lungs of the male sub-
ject from the Visible Human Project (VHP), as an example of complex 3D data. We review first some
anatomical facts of the lungs, useful in any computer analysis. Then, we examine the characteristics
of the VHP database concerning the lungs, the general approaches for vessel segmentation found in
the literature and the extraction methods we propose. We also present the results of the implementa-
tion of three of these methods, as well as the visualization of the 3D reconstructions from anatomical
color images of the VHP database.
4.1 Anatomy of the Branching Structures in the Lungs . . . . . . . . . . . . . . . 161

4.1.1 Tree Structure of the Pulmonary Artery . . . . . . . . . . . . . . . . . . 164
4.1.2 The Lungs of the Visible Human Male . . . . . . . . . . . . . . . . . . . 166
4.2 Blood-Vessel Extraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
4.2.1 Other Imaging Techniques . . . . . . . . . . . . . . . . . . . . . . . . . 174
4.2.2 Detection Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
4.2.3 Fusion of Cross-Sectional Segmentation . . . . . . . . . . . . . . . . . . 176
4.2.4 Local Thresholding with Hysteresis . . . . . . . . . . . . . . . . . . . . 179
4.2.5 Region Growing Segmentation . . . . . . . . . . . . . . . . . . . . . . . 185
4.3 Conclusions and Perspectives. . . . . . . . . . . . . . . . . . . . . . . . . . . 187
4.1 Anatomy of the Branching Structures in the Lungs

The lungs in mammals are constituted by three systems of highly branched trees: the blood-vessel
trees of the Pulmonary Artery (PA) and the Pulmonary Veins (PV1 and PV2), and the airways or J ”PA, PV”
bronchial tree which ends in the alveoli, the small air compartments (less than 0.3 mm in diameter)
where gas exchanges have place. Under normal conditions, carbon dioxide (CO 2) and other gases
162 Extraction of Bronchial Blood-Vessels from the VHP
pass from minute venules to alveoli while oxygen (O 2 ) and other gases (mainly azote (N)) pass from
alveoli to arterioles. Oxygen-rich blood is collected from all capillar vessels up to the PV into the
heart during dyastole (dilatation), to be redistributed in the circulation network of the body at systole
(contraction). The venous blood, charged with CO 2 from all the organism, is then pumped to the
lungs by the heart. Connective and supporting tissue encase the alveoli, the airways and the blood
vessels. This structuring tissue has a porous texture and is known as the lung parenchyma . A detailed
characterization of this texture would allow segmentation and analysis of important structures in a
texture-based analysis (see for example [Morris88]), but this was not the case of the present study,
and we used only the first-order statistics to characterize tissue as the background for blood vessel
structures.
The lungs are inflated and deflated during the respiration cycle to exchange air with the medium.
This cycle implies an important change in volume that demands a global deformation of the whole
structure. A first consequence of this dynamical behavior for computer analysis is the impossibility,
with present technology (e.g. spiral computer tomography, the fastest available technique), of high
resolution digitization of the whole respiratory system in vivo, specially in patients with respiratory
defficiencies. At the same time, deformable models, atlases and a better understanding of the struc-
ture of the lungs is needed to study “thick-slice” samples at specific regions of interest, conventional
radiographies, two-dimensional CT axial samples, and three-dimensional reconstructions from se-
rial slices or CT scans of post-mortem specimens. In the following subsections we present some
details of the structure of the lungs and indicate the relevance of this knowledge for segmentation,
three-dimensional reconstruction and analysis.
In function of energetic needs, there are high changes in the rythm of the cycle and the volume
fraction of the lungs deformation. A large volume of air (up to 3 liters in a health adult) has to
traverse and fill the airways in less than half a second during extreme physical efforts. At the resting
state, all the blood of the body passes through the lungs each minute. The fractal structure of the
lungs allows this rapid gas exchange by a cascading phenomenon [Armin94]. Such a structure is
illustrated in Figure 4.1.
Air and blood follow similar pressure patterns during the respiration cycle in each tree, facilitat-
ing their fast distribution through the lungs, but also enabling the expulsion of CO 2 and the diffusion
of O2 into the blood. There are predominantly-only dychotomic ramifications 1 (or bifurcations).
In fact, Horsfield and Cumming report exclusively bifurcations in their resin cast of the airways
[Horsfield68]. Bifurcations are not symetrical in both lung sub-trees (dychotomic asymetry). Con-
sidering only bifurcations, a tree node has 2 n branch daughters at branching order n. Since the flux
of the three substances (arterious and venous blood and air) remains more or less constant along
the trees (however, it gradually changes with time), the cross section of each ramification follows a
/
mass-conservation law of the form: An 2n , where An is the cross section at branch generation
order n, with n 2f g
1 2 : : : 10 for the airways, and is the flux (mass of fluid (air) per area unit).
There exists however up to 23 generations of bronchioles and 28 generations of blood-vessel bifur-
cations, but the power law does not take into account molecular diffusion and other gas-transport
considerations. When experimentally measuring average diameter of bronchial segments and blood
vessels, Weibel and Gomez report an accurate potential law:
d(n) = d0 2;n=3 (4.1)

with d0 17mm, and n 2f g
1 2 : : : Norder , up to branch generation Norder = 10 for airways and
for blood vessels up to order N order = 28, down to the capillary network [Weibel62]. Figure 4.2
shows this relation up to order n = 20.
1
Those directly modeled by a binary tree.
4.1 Anatomy of the Branching Structures in the Lungs 163
Figure 4.1: A resin cast model of the bronchial tree in an adult human (reproduced from [Weibel79a]).
From these considerations, a simple a priori estimation of the relations of branch diameter at order
n is available, and can be useful for reconstruction and morphometrical analysis of the lungs, from
anatomical slices. Assuming no partial-surface effects (“one-pixel diameter vessels”), and assuming

neither deterioration nor geometric distorsions of the specimen, then, at pixel resolution of 0:33 0:33
mm, branches from orders 16 and 17 (0.42 and 0.33 mm in diameter) indicate the finest vessel
resolution (see also Table 4.1). With a knowledge of the minimum detected vessel, and its relation
with resolution, we can generalize these estimations. Let f : R ! R an invertible monotonical
function relating resolution L and average diameter: L = f (d). Usually, f reduces to a multiplicative
constant. Let d(n) as in Equation 4.1. In this case, the bifurcation order n at resolution L is given
by:
f ;1(L)=d0)
n = 3 log(log 1= 2
(4.2)
where d0 can be measured from the slices in a particular specimen. Thus, in a more realistic approx-
imation (blur, noise due to texture and partial volume), we can expect to detect 7, 5 or 3 pixel-wide
vessels. In these cases, L = 7d, L = 5d, and L = 3d, and from Equation 4.2, we obtain the corre-
sponding orders: 8, and 10 to 12, and vessels from 2.68 to 1.06mm in diameter. In this conditions,
in order to detect the smallest capillars (0.1 to 0.03 mm at orders 22 to 28), an optical-microscopy

resolution of less than 0.01 mm (magnification 30) would be needed.
Another observation of Horsfield and Cumming, and Weibel and Gomez is that no monopodial
branches exist, neither in the airways nor in the PA or PV trees, that is, there are no small arterioles
or venules branching from stem or large vessels; thus diameter reduction is gradual and small struc-
tures do not connect directly to large segments. A consequence in segmentation methods of vessel
components of the lungs is the a priori knowledge that small vessels or airways cannot lay too close
to large branches.
vessel average diameter d (mm) -n/3

d = d 02
bifurcation order n
Figure 4.2: Power law of average diameter d of vessels at bifurcation (or binary branching) order n. Diameter
at order n = 0 (pulmonary artery from the heart) may change. The airways follow the power law up to n = 10.
In conclusion, anatomical models and their experimental validation provide some quantitative
relations useful to evaluate segmentation and branch extraction at a given resolution, provided that
the power law of Equation 4.1 holds. In the following paragraphs we review the structure of the
vessel and bronchial trees, and examine the particular characteristics of the lungs from the database
of the Visible Human Project.
4.1.1 Tree Structure of the Pulmonary Artery

Arteries and veins in the lungs extend from bifurcation sites known as hilar points, following a
divergence principle, described by Yamashita in [Yamashita78]. Recursive division of the three tree
structures proceeds in similar ways: for the airways this hierarchy begins at the trachea, leading
through bronchi, bronchioles, acinar airways, respiratory bronchioles, alveolar ducts and alveolar
sacas, comprising up to 23 levels or generations (from which only 10 follow closely the power
law). Vascular structures begin to run almost parallel, connected by the airway wall but then PA
and PV run independently. The PA and the airway tree follow a similar branching pattern (see
Figure 4.4 running more or less parallel, separated by the airway wall, and both follow almost the
same diameter distribution down to generation 10th. This hierarchical organization enables vessels to
carry and collect blood very efficiently, and constitutes for physicians an a priori information to infer
vessel localization in any lobe. A particular notation system has been attributed to label main arteries
with a capital “A”, veins with “V”, and bronches with “B”, each one with a superindex indicating
the segment number, and a lowercase letter for identifying sub-segments. Thus, A4 b refers to sub-
Anterior Posterior Anterior
(c) (g)
(a)
(f)
(b) (d) (h)
(e)
Left lung Right lung

Figure 4.3: Lateral view of the lungs: costal surfaces of main features. (a) Left upper lobe; (b) left lower
lobe; (c) right upper lobe; (d) middle lobe; (e) right lower lobe; (f) left oblique fissure (also known as left
major fissure); (g) horizontal fissure (also known as minor fissure); (h) right oblique fissure (or right major
fissure).
segment b of the fourth segment of the PA. In some anatomical books this notations changes slightly
(e.g. A4B for A4 b).
A tree-like representation in 3D of the pulmonary blood vessel anatomy was first proposed, for
the aid of computer reconstruction from CT scans, by Inaoka et al. (1991) [Inaoka91]. Their model
consisted of a tree with regular dichotomy, without regard to length and branch diameter. Using
a 3D vector representation, and the 26 combinations of 3D opposite directions (up and down, fore
and back, right and left), a knowledge base is encoded as a frame-type representation. An expert
physician validated such a structure in the work of Inaoka et al., where position, direction, and length
have been integrated later.
Other anatomical information useful for description and location of branching subsets (sub-trees),
is segmental and lobar anatomy, in which segment and lobar organization are taken into account.
Lobe organization is shown in Figure 4.3a-e. Internal interfaces of the lobes (see Figure 4.3f-h) also
serve as landmark structures, and are known as the major or oblique fissures in the left lobe and
the minor or horizontal fissure. We did not use this information, which needs to be extracted by
a semi-automatic method from the VHP images, due to low resolution (1mm per slice) and tissue
degradation. In better conditions, it should be valuable for a specific application in which each
branch would be labeled in accordance with its lobar location, and identified with a specific bronchial
segment from atlases.
Other structures in the Thorax Between the lungs and over the diafragm membrane and the
stomach, lies the esophagus duct, the heart cavities, the Aorta artery, the Cava vein and other im-
portant vessels other than the PA and the PV. When extracting the contours of the lobes of the lungs
or the airways and blood-vessels, these structures must be identified and separated. As the diafragm
area is concave, a substantial part of the upper liver and its blood-vessel systems accomodates under
the diafragm, as well as a portion of the stomach. Vertebrae, sternum and ribs appear in the borders
of the ROI of the lungs, and occupy several cross sections of the lungs of the VHP database. As
their volume is large in comparison with the ramified structures, simple mathematical morphology
reconstruction (a conditionned closening of a convenient size) suffices to isolate most of them, in
order to mask them out from analysis. A more difficult task is the identification of the interfaces of
T+2
A1a A a
T+2
A b
2 A1 b
Aa T+2
A rec. A c
2
Ab 3
A2c
Aa A2a
6
Ab
6 5
Aa Ab
4 4 3
Aa Ab Ab
6
Ac
A asc.
Airways
Pulmonary Artery
Figure 4.4: Notation system to address primary blood vessels of the Pulmonary Artery (PA), which runs
parallel to the airways. The pulmonary vein (PV) is not shown. The labels An m indicate sub-segment m of
Arterial segment n. “Rec.” stands for recumbent, “asc.” for ascendent (labels are not exhaustive). Diagram
redrawn from [Inaoka91].
each lobe, since they may appear as unconnected thin structures from one slice to another, in contact
with small vessels.
4.1.2 The Lungs of the Visible Human Male

Tiede et al., reported in [Tiede93] several problems concerning the available information from IRM
and CT images of the VHP in general when considering soft tissue, in particular the lungs, which
are particularlly porous, and vulnerable to fast deterioration. Airways are scarcely visible in IRM
images, and only some of the most important blood vessels appear. As resolution was also limited

(256 256 in the CT, and 128 128 in the IRM images when considering the ROI of the lungs), we
opted to analyse the color images, and more precisely the blood-vessels which are still much more
visible. At the other hand, only the main airways appear because the specimen lungs were collapsed
after death [Spitzer96]. Moreover, a substantial quantity of blood was drained out, and many small
blood vessels are difficult to track. This is not a disadvantage as it would appear, since without
circulation, all blood concentrates in the lower parts of the body, deforming vessels, organs and
tissue, and expanding during freezing, with the consequent damage of small structures. Resolution

for the ROI comprising the lungs is 640 832 170 in these images. As the VHP database was
created very recently, we have not found much information in literature about the lungs of the VHP,
because we ourselves (Marquez and Schmitt) were in 1996 the only group working in the color
images of the lungs, discovering the radiometric inhomogeneities reported in [MarquezVHP96].
slice#
1297
1305
1342
1365
1388
1415
1430
1453
1483
1504
Figure 4.5: Coronal view of the thorax in an adult and approximate position of the axial cross sections
comprising the lungs of the Visible Human Project (VHP) database. A coronal slice of the axial cross sections
is shown at the right.
Figure 4.6: Color slice number 1408 of the VHP.
Even by using manual segmentation slice by slice, with editing assistance, several groups work-
ing with the VHP dataset have reported in [Imielinska96, QuackenbushVHP96, SchiemannVBC96]
a very difficult extraction of small branches of blood vessels and other fine structures when working
with the physical color cross-sections. They also report work only with the red channel. Despite
all mentioned limitations, information from these slices is still very valuable because voxel size is

0:33 0:33 1:0, and color resolution is 8 bits per channel.
Local and Global ROI Statistics To approximately locate the axial slices of the thorax in a human
being, refer to Figure 4.5, where the position of cross sections are indicated in a coronal view of
the thorax. Figure 4.6 is the red-channel image component of slice number 1408, after correction
of radiometric inhomogeneities with a suitable stretch function for clarity (the original image is
too dark). Details are shown in Figure 4.7. An intensity profile for each color channel is shown
Figure 4.7: Slice number 1408 of the VHP (detail). Note that most cross sections are elliptical. Rectangle
samples with (left) and without (right) vessel cross sections are shown in Figure 4.9.
in Figure 4.8, with the image of the red channel superimposed. Note that useful information (the
“valleys” corresponding to vessel cross sections) is found mostly in the red-channel profile. An
intensity histogram including mainly parenchyma and a second one including several blood vessels
are shown in Figure 4.9. An exhaustive exploration of blood vessel characteristics through local
histograms, gave us the following information for each color channel R G B . These measures were
taken observing each separated channel image and the color image on three consecutive images at
a time, in order to ensure that a thin vessel was present at the selected pixel area. We give these
measurements in the form of a vector of components (R G B ), rounded to half integer values:
✦ The mean value < ~u > with components (R G B ) varies along the volume, in function of
global illumination characteristics. After gamma correction and radiometric inhomogeneity

filtering (see Chapter 3), the minimal value found was (7 2 4) (1 0:5 1) pixels, and the

maximal value of (46 12:5 17) (7 4 4:5). The last incertitude is high because manual
classification of what is vessel or texture features is subjective, and partial surface effects
produce a one-pixel wide “halo” around some “one-pixel” vessels, or a false vessel (a texture
artifact introduces the incertitude; in both cases the feature or noise is of sub-pixel size). The
global mean value was found to be < ~ u >ROI = (39 10 13). By using this value as a global
threshold one cannot obtain a ’maximum’ area of segmented valid fragments of blood vessels.
Most of the segmented fragments turned to be either over-segmented (background frgments are
labeled as blood-vessel foreground) or under-segmented (blood-vessel fragments are labeled
as the background), as shown in a single slice sample in Figure 4.10.
gray-level intensity 250

(a)
200
150
100
(b)
50
(c)
0 x axis
Figure 4.8: Gray-level intensity profiles of the red (a), green (b) and blue (c) channels on a line parallel to
axis X (indicated by arrows). Note the correspondence of valleys in the image across the horizontal line, with

vessel cross sections in the red-channel profile (a). Image intensities have been stretched by an exponential
transfer function (gamma a 3:0) to make details visible.
✦ The local standard deviation of gray-levels inside blood-vessels was found to be much more

consistent: ~ in = (11:5 6 8:5) (3 2:5 3:5). The same value was obtained for windows of
3x3 and 5x5 pixels (small vessels).
✦ The local standard deviation of parenchyma regions around vessels, was found to be: ~ out =
(43:5 26 31) (8 3 4:5). This value was the same for large regions (up to 30x30 pixels),
where none or only few small vessels were present. The local mean value has also high intra-
slice and inter-slice variations (from 0 to 160, even if the local standard deviation remains
lower). Nevertheless, gradients were qualitatively found to be very smooth, after the inho-
mogeneity corrections (these corrections filtered discontinuous variations which could be mis-
taken as transitions from vessel material to tissue). The only exception is a single slice, number
1454, where some illumination problem must have happened during the slicing session, since
saturation at 0 is attained for channels blue and green at the bottom of the image.
We noted that parenchyma of the lungs has a stronger green and blue component than blood
vessels in most areas, as expected, since it is more flesh-colored. Unfortunally there remain very
dark areas where green and blue channels have darker values than red. Figure 4.11 shows the sum
of the blue and green channel of one of these slices, in which there is no under-saturation, but red-
channel information is much richer and reliable. No information is useful, specially at the bottom
part of the image (slice 1451) because parenchyma is darker than blood vessels in the blue and green
channels (the opposite occurs in most part of the slices).
56
pixels
pixels
54
40 40
30 30
20 20
10 10
intensity R intensity R
0 0
0 50 100 150 200 250 0 50 100 150 200 250
Figure 4.9: Intensity histogram of parenchyma ROI (red channel R) without blood vessels (left) and intensity
histogram of a second ROI with cross sections of blood vessels (right). The insets show the ROIs (See also
Figure 4.7).
For the given reasons, in the present tests we used only the red channel, but Principal Component
Analysis may be applied in the future, as reported by Schiemann, for bone and skin segmentation of
the VHP [SchiemannVBC96].
Partial Volume Effects Any time a voxel (pixel) corresponds to the interface (transition) between
two (or more) regions with different gray-level information, it will contain information about both
regions (parenchyma tissue and blood-vessels or bone and tissue, air and tissue, tissue with contrast-
agent and normal tissue, etc.). In 3D this phenomenon is named the partial volume effect, and in 2D,
the partial surface effect, and it is present in most imaging modalities with discrete representation
of spatial information. In some modalities it is easier to determine subvoxel (subpixel) location of
the interface or boundary, from gray-level contents (e.g. 255 for bone, 0 otherwise). There are other
”PSF” I sources of gradual transition between regions, such as blur and the Point Spread Function (PSF) of
the acquisition system.
In the present study, since cross-section images come from physical, anatomic cryosections of
1mm-thick, no blur exists (ideally) in the axial (Z ) direction, that is, for each voxel in slice z k no
information is convolved with the adjacent voxels at slices z k+1 zk;1 . Mechanical image aligne-
ment in cross-sections and camera callibration have been warranted to have at most 0.1 mm, which

corresponds to 1=3 pixel error [Spitzer96], thus a net partial volume error should comprise only
the PSF of the CCD camera and partial surface effect (i.e., only in 2D). All observed edges and the
three RGB channel alignement show just one to two-pixels wide transitions. This is difficult to verify
quantitatively in lung parenchyma, since texture features are fuzzy by nature, but a key feature is the
fractal nature of the lungs. Equation 4.1 predicts the presence of blood vessel sub-trees at scales
much smaller than image resolution (0.33 mm). The observed texture of parenchyma is already com-
posed of partial-surface pixels (per slice), with assorted contribution from several scales. Figure 4.12
Figure 4.10: Global thresholding of slice number 1408 (red channel). The threshold value (38) was selected
from local statistics in a small ROI with vessels and tissue.
illustrates partial volume effects. Compare subfigure (d) with the pixels of the zoomed vessels in the
right inset of Figure 4.12.
To estimate the importance of this contribution, let us calculate the average density of sub-pixel
blood vessels at order n, by assuming binary bifurcations and a maximum of 28 bifurcation orders.
There are 2n branches at order n, with diameter d given by Equation 4.1. Since the adult normal lungs

(parenchyma) occupy a volume of Vlungs =5 liters. (or 5 106mm3 ), the density of blood vessels of

order n, is: = 2n =Vlungs. Densities for orders n = 1 : : : 28 are given in Table 4.1. This is only
a global average estimate and a local measure (per slice) would take into account length between
bifurcations. It predicts however, that if vessels of order n are intersected on a given slice, their
expected number, per cubic millimeter, is of the order of that found in the table.
Considering pre-processing degradations, the radiometric-correction method presented in Chap-
ter 3 does not introduce any blur: in difference images, a pixel value coherent with its slice-neighbors
either remains equal, or is shifted by a small quantity (R G B ) to make the mode location of its
image-neighborhood match the mode location of the neighborhood in the precedent slice (same co-
ordinates x y ). No information is convolved with the neighboring pixels, whether the image neigh-
borhoods are large or small. The only possible source of error are very weak-intensity innovations.
These innovations must be considered as under-sampled structures and true partial-surface pixels:
alveoli, parenchyma texture, nerves, connective tissue or collapsed airways and very small blood
vessels (less than a pixel-wide) traversing in a skewed angle, in order to produce such innovations.
By hand tracing some contours in a sample of ten slices from the ROI, we found an average
surface area of lung tissue of about 32300 mm2; which confirms the 5-liter volume measure of the

lungs used to estimate densities in column 4th of Table 4.1 (recall the ROI is 832 640 160). The
Figure 4.11: Contrast-streched image of slice number 1451: combined information of blue and green chan-
nels (R+B ). Note that many vessels (but not all) present higher values of blue and green than the surrounding
tissue, making the red channel a better choice for segmentation. The original image is almost “black” and a
stretching with an exponential transfer function (gamma of 4:5) was applied to allow visualization.
average number of vessels per slice is more difficult to estimate, since we have to take into account
vessel lengths and their natural bending towards the root [Weibel62]. A very rough approximation

and lower bound is the vessel density divided by each branch volume ( (diameter=2) 2 length)
multiplied by the slice volume. This measure turns out to be approximately 2 n itself, since lengths
follow a similar power law.
Just by hand-counting the smallest and darkest visible dots from 3 to 5 pixels-width, correspond-
ing (after the branching law) to generations 10 to 12 in the Table 4.1, we found in three samples
(slice 1408 shown in Figure 4.6 and slices 1347 and 1450) a much lower number of them: 312 42

and 191 68. A plausible reason is that vessels are contracted by tissue deformation or colapsed
(recall that blood was drained before freezing), and thus the expected diameter corresponds to earlier
branching generations: 7 to 9. This implies an error (from the image capture and partial surface
effects) of up to 7 pixels, if the law holds strictly (the difference of diameters between generation

7 and 12 is 2.4 mm, and each pixel is 0:33 0:33 mm). If this diameter difference holds also for
those corresponding (from the 2n law) to generations 16 and 17, then pixel resolution corresponds
to generations 13 and 15, and the observed texture includes tens of thousands of subsampled vessel
components (deformed by colapsation) of at least one-pixel diameter, and hundreds of thousands of
smaller capillars.
We stress the fact that many branching generations (a natural fractal), which tend to fill available
space as already noted, make an important contribution to background nature, making the blood-
vessel tree a very difficult structure for segmentation, since there is one “cut-off” generation 10 in
which foreground is no more resolved and is treated as a textured background. Some of this texture
is visible in Figure 4.8.
(a) (b) (c) (d)
Figure 4.12: Partial volume effect. (a) Original object and superposed grid for discrete sampling. After
digitization, each voxel contains both, information of foreground (black) and background (white), coded as

gray-level densities corresponding to the mixture (c); plus the effect of the Point Spread Function of the acqui-
sition system (here represented by a 3 3 convolution). Only the largest branches are noticeable in (c). Note
the partial surface effect (d) on tubular cross sections (b), when diameter is about two pixels.
We did not continued this kind of analysis for other vessel diameters, since the objective was
only to have a rough idea of how useful could be the 2 n and the 2;n=3 laws (number and density
of branches and their diameter), and the importance of the fractal structure in partial volume effects
and background texture. We were looking forward to obtain three dimensional reconstructions to
measure directly diameters and branching orders in the VHP database before realizing, by the latter
disussion, that background is noised by the same structure details we want to extract!
Two different consequences are drawn from all these observations:
✦ Background segmentation of the bronchial vessel tree may be difficult by 2D image analysis
and contour extraction. Coherence can be an advantage, against a textured background in a 3D
approach (adjacent voxels with similar gray-levels possibly belong to the same structure), but
thin structures reduce the number of pixels per vessel, per slice. The coherent property was
already exploited with success for radiometric homogeneization.
✦ Neighborhoods for analysis of local standard deviation ~ 2 have to be small, since they may
include gray-level information from sub-sampled vessels of several diameters.
Table 4.1: Densities of blood vessels of branching order n for volume of 5 106mm3 and initial diameter of
d0 = 17:0mm. orders 16 and 17 correspond to pixel resolution in the VHP images.
Order n Diameter (mm) 2n Vessel Density (1=mm3)

0 17.000 1 0.00000020
1 13.493 2 0.00000040
2 10.709 4 0.00000080
3 8.500 8 0.00000160
4 6.746 16 0.00000320
5 5.355 32 0.00000640
6 4.250 64 0.00001280
7 3.373 128 0.00002560
8 2.677 256 0.00005120
9 2.125 512 0.00010240
10 1.687 1024 0.00020480
11 1.339 2048 0.00040960
12 1.062 4096 0.00081920
13 0.843 8192 0.00163840
14 0.669 16384 0.00327680
15 0.531 32768 0.00655360
16 0.422 65536 0.01310720
17 0.335 131072 0.02621440
18 0.266 262144 0.05242880
19 0.211 524288 0.10485760
20 0.167 1048576 0.20971520
21 0.133 2097152 0.41943040
22 0.105 4194304 0.83886080
23 0.084 8388608 1.67772160
24 0.066 16777216 3.35544320
25 0.053 33554432 6.71088640
26 0.042 67108864 13.42177280
27 0.033 134217728 26.84354560
28 0.026 268435456 53.68709120
4.2 Blood-Vessel Extraction

4.2.1 Other Imaging Techniques
X-ray Digital Subtraction Angiography and similar techniques rely on vessel identification of ac-
quired images before and after intra-arterial injection of a radio-opaque contrast agent. In 2D these
techniques provide the highest resolution available (from 0.06mm per pixel to 1mm) [Sun89]. Vascu-
lar networks in general and bronchial blood vessels in particular pose different problems to classical
segmentation methods. These are mainly due to poor contrast of very thin structures. Complex vas-
cular abnormalities, aneurysms, stenosis and tortuosity demand high resolution 3D imaging, and a
large scale analysis with CT imaging of the lungs cannot be done in vivo, because of the high dose
4.2 Blood-Vessel Extraction 175
of X-rays required, and the movement of the lungs during a long acquisition session. Costello et al.,
and Paranjpe and Bergin [Costello92, Paranjpe94] examine and compare spiral CT images for 3D
segmentation of lung structures and blood vessels at small, local ROIs or very low resolution samples
(1.5cm appart), allowing assessment of only transversal segments of blood vessels and the overall
disposition of main arteries.
Magnetic Resonance Imaging in two dimensions is suitable for airway tracking, in vivo, up to the
fourth or fifth branching generation [Portman92]. With the introduction of contrast agents, Magnetic
Resonance Angiography provides projections in several planes and allow reconstruction in 3D of
large arteries. A systematic analysis of the best blood vessel imaging techniques is given by Verdonck
in [Verdonck96], but color images from cryosections in high resolution were not available until 1995.
Spiral CT-imaging allows to scan thick sections 2 of the thorax for local exploration of the air-
ways, in vivo. The main limitation is the maximum allowed dosis of X-ray exposition for non-clinical
studies, and the short apnea lapses, all of which reduce the amount of CT-scans for 3D reconstruc-
tion analysis. Thus, with actual technology, a large structure as the vascular trees of the lungs or the
bronchial tree is only accessible for high resolution 3D reconstruction through post-mortem analysis,
either by CT imaging of the fresh cadaver (first generations of the airways), or from histological
cross sections from prepared specimens, as those provided by the VHP (blood vessels, mainly).
For the particular 3D segmentation of color images from anatomical slices of the whole vascular
trees, there is no current reported literature on automatic methods. However, general segmentations
approaches as those applied on CT and IRM imaging can be employed. Using the VHP database
Imielinska et al. [Imielinska96] extracted the bronchial tree by hand segmentation by an expert, for
pedagogic purposes, as illustrated in Figure 4.13.
Figure 4.13: Hand segmentation and 3D-rendering with color texture mapping of the bronchial tree of the
lungs (same VHP database). Extracted from [Imielinska96b].
4.2.2 Detection Methods

Very thin vessel structure has been successfully detected in 2D images by probabilistic approaches,
using Markov random fields [Descombes95]. The extension of this method to 3D and large databases
2
Thick sections of about 1-1.5cm in a set of 20 images, after Dr. J. Frija, from the Hôpital Saint-Louis, Paris.
is very difficult and costly. For example, it relies on the use of look-up-tables of pixel configurations
to be penalized or enhanced during relaxation, in order to preserve those corresponding to fine struc-
tures. In 2D images, 28 configurations are required (eight nearest neighbors) while in 3D up to 2 26
configurations would be needed to be somehow coded, even if only a fraction is needed. Even if
memory is not the main concern, the energy calculations would require a huge amount of terms to be
pre-calculated.
Many other approaches exist for small-vessel detection in 3D, but we describe in the following
those we have tested and finally adopted:
✦ A two dimensional approach, slice-by-slice. In this approach a 2D segmentation is done on

each slice of the ROI. Slices can be organized (reformatted or “resampled”) in three orthog-
onal directions for 2D-image processing. We tried to use the output of three slice-by-slice
segmentations of the same volume. Segmentation itself was tested using:
– Local thresholding in small ball neighborhoods.

– Refinement by filtering from average noisy pixels. This was accomplished by using the
Sigma-filter.
– Further refinement could be done with hysteresis thresholding; but at this step, we passed
to a 3D approach, and hysteresis was employed for a progressive segmentation method.
✦ A three dimensional approach by progressive segmentation, using first a given segmentation

result (2D or 3D) and then the hysteresis approach of adding more information while scanning
the boundary representation extracted from the segmentation output. This step was combined
with a full 3D segmentation method of region growing, which gave the best result.
4.2.3 Fusion of Cross-Sectional Segmentation

We started our tests with a 2D segmentation of blood vessels in individual images, slice by slice, and
then combining information from the three segmented volumes (orthogonal slices in directions X Y
and Z of the same ROI), which are described in this Subsection. In Chapter 3 we used the original
f g ;
sets of serial slices (images) in the Z axis as a set I n n = 0 : : : (Nslices 1), with Nslices =
160. The first image I 0 corresponds to original color slice number 1320 in the VHP database. To
simplify notation, we have droped the subindex indicating gamma correction, homogeneization, or
binarization, and we assume to work with a radiometric-corrected set.
V
The ROI can be represented as sets of other orthogonal planes by resampling, or reslicing, that
is, reorganizing 3D information into stacked 2D images (recall Figure 3.2, page 147). To distinguish
each set (the ROI itself, expressed in three different ways), we use the following notation, where is
2V
the color or gray-level label of the voxel v at point (x y z ) :
V = 0 N ; 1] 0 N ; 1] 0 N ; 1]

cols rows slices (4.3a)
z
IXY = f((x y) ) j v(x y z) 2 Vg (4.3b)
IYx Z = f((y z) ) j v(x y z) 2 Vg (4.3c)
y
IZX = f((z x) ) j v(x y z) 2 Vg (4.3d)
IXY = fIXY
z j z 2 0 N ; 1]g the Axial set
slices (4.3e)
IY Z = fIYx Z j x 2 0 N ; 1]g the Coronal set
cols (4.3f)
IZX = y j y 2 0 N ; 1]g the Saggital set
fIZX rows (4.3g)
I I
where Nslices = 160 Nrows = 832 and Ncols = 640. Note that Y Z , and ZX are extracted from
IXY , by reading either the rows, or the columns in the X and Y directions (respectively) of XY to I
form coronal or saggital images. To differentiate between rows (columns) from one set and another,
we denote them in an absolute frame of reference as Z -runs of voxels (fixed coordinates x y and
varying z ), X -runs and Y -runs. Figure 4.14 describes orthogonal planes and orthogonal runs of
voxels.
Y
(d)
z x
I XY I YZ
Z X
(e)
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I (b)
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Figure 4.14: Orthogonal planes and runs. (a) A volume I can be processed as a set of image slices fIxXY
z g
in the plane XY (axial representation, axis Z ). Similarly for the axis X (saggital representation, set fI Y Z g)
and Y (coronal representation, set fIZX
y g). (b-e) Given a point in the volume (x y z) 2 I, the linear runs of
voxels parallel to the main axes are univocally identified as X -runs, with fixed (y z) and varying x, and Y -
runs which form respectively the rows (c) and columns (d) of each image IXY . The Z -runs are the transverse
runs of voxels (e), that form the intersections of plane images IY Z and IZX .
We consider now the information extracted by a segmentation operator (local thresholding,S

I I I
for example) from each set XY Y Z ZX and combine it with the following criteria, to obtain a
J \
new set that we denote generically as XY , plus a superindex “ ”, “ ”, or both, to indicate which
combination criterion was applied:
Conjunctive combination XY J
S
If is chosen or adjusted to segment only “well-defined” structures (possibly causing under-
segmentation, because of a “severe” policy), we define:
JXY = S (IXY ) S (IY Z ) S (IZX )

Disjunctive combination \ XY J
S
If is chosen or adjusted to segment also “not-well defined” structures (possibly causing over-
segmentation under an “indulgent” policy), we define:
J\XY = S (IXY ) \ S (IY Z ) \ S (IZX ):

Associative combination \XYJ

S I
If segmentation is for example indulgent with the axial set XY , and severe with the sagittal
and coronal images, then we define:
J\
XY = S (IXY ) \ (S (IY Z ) S (IZX )):
S
we may equivalently have two segmentation procedures, a severe one under , and an indulgent
S
one over , then:
J\
XY = Sover (IXY ) \ (Sunder (IY Z ) Sunder (IZX )):
I I
In both cases, information not present in the segmentation results over Y Z ZX may serve to
SI
“trim-out” the oversegmented set ( XY ):
Note that intersection and union of data are the same as boolean AND and OR operations between
voxels, with binary labels 0 1.
Combination of different segmentation sets depends thus on confidence on the extracted infor-
mation. Our data volume is not istropic, since voxels sides are (L x Ly Lz ) = (0:33 0:33 1:0) in
mm, thus information extracted from each individual image IZY k or image I k is less reliable than
ZX
k
that extracted from IXY which possesses the highest resolution with square pixels.
The combination criteria depends also on data anisotropy and position in space, even if sampling
k , they may be con-
is isotropic. If fine blood vessels are perfectly perpendicular to each plane I XY
founded with texture or noise. Coherence from slice to slice would allow to overcome this drawback.
k , they may be detected by a linear-
If fine blood vessels are more or less parallel to each plane IXY
structure detector. As they are on average slanted, we may restrict the segmentation operator to S
detect elliptical shapes only, because most noise and artifacts won’t exhibit this particular shape, on
average. Thus some vessels will be better detected in one set of image planes than another, and an
overall conjunctive combination is expected to give the best results.
000
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Figure 4.15: Intersections of orthogonal planes with a ramified object.
In the following section we discuss a particular choice of a segmentation operator S compatible

with the cross-sectional approach and with a 3D, boundary-oriented approach.
4.2.4 Local Thresholding with Hysteresis

S S
The segmentation method to obtain over and under was an adaptive-local thresholding to which
we incorporated the hysteresis linking feature introduced by J. Canny in his PhD thesis about seg-
mentation [Canny83]. We first explain the local thresholding, then a sigma-averaging enhancement,
and finally recall the hysteresis concept.
Local Average. The local behaviour of our approach consisted in selecting a 2D segmentation
B
threshold in function of the local average per image, on ball-neighborhoods r (p) of each p , with 2V
radius r. This segmentation consists in finding first a threshold by visual examination of some ROI
samples, as described in Section 4.1.2, and then by using the background/foreground proportion for a
different region where background is darker or lighter (as clearly illustrated in Figure 4.6, page 167).
To this end, an accelerated local thresholding is achieved using the rolling buffer technique presented
in Section 3.3.3, page 156. A typical result with some oversegmentation is presented in Figure 4.19.
Sigma Averaging. We later refined this first step by using the Sigma-average filter, introduced
by J. Lee in [Lee83]3 . Sigma-averaging consists in enhancing the average estimation in r (p) by B
discarding from averaging those pixels too different from the central pixel p 0 . If pk , with k 2
B;
1 : : : KN ], are the neighboring gray level values around p0, with KN = card r 1 (the central
pixel is excluded), we first define the list of selected pixels in the neighborhood r (p0): B
M& = fk j p ; & pk p
0 0 + &g
with & an empirical parameter used to select the pixels to be averaged. Then, the sigma-estimate p^ of
the mean is obtained as [Lee83]:
X
p^ = card1 M pk (4.4)
& k2M&
B
When the list M & coincides with r , then p^ is the usual average.
We tested neighborhood sizes of r = 3 5 7, in order to detect the smallest vessels. Following the
suggestion by Hancock in [Hancock91] from the estimation of hysteresis thresholds, the sigma range
& for the gray-level window was selected as half the standard deviation of gray-levels in r (p). From B
Section 4.1.2 we had, inside small blood-vessels the color values ~ in = (11:5 6 8:5), and using the
red channel (thus, passing to gray-levels), we obtain & = 1=2 inR = 5:75.
Hysteresis. Let two threshold levels T low < Thigh . When using a single threshold T such that
Tlow < T < Thigh (no hysteresis), the output of the detection operator fluctuates above and below
T along the edges, breaking their continuity. Canny called this the “streaking problem” [Canny83]
and introduced a conditional connectivity constraint: in a second pass on the “half-thresholded”
image (gray levels > Thigh are labeled with value 255), thresholded voxels with gray level above
Tlow are further selected or discarded if they are connected to well-detected zones (those thresholded
with Thigh > T ). Gerig et al. applied this criterion for cerebral vessel tree extraction, for global
thresholding [Gerig93b].
Since voxels to be added or deleted first are boundary voxels, this technique was thus suitable
for implementation with our boundary-based methods in a growing-region-like approach. We
3
Here the term “sigma” used by Lee has nothing to do with the local standard deviation or other. For the sigma-
average parameter we use the Greek symbol & .
Figure 4.16: Sigma-filter applied to gray-level image of slice 1437. Note that blood-vessel borders are sharp
(not changed by smoothing) and low-contrasted texture is smoothed.
Figure 4.17: Local thresholding applied to gray-level image of slice 1437 after sigma-filtering (from Fig-
ure 4.16), using a window of radius 7. Blood-vessel borders are sharp (not altered by smoothing) and low-
contrasted texture is smoothed.
Figure 4.18: Local thresholding . Undersegmentation arises from considering contrasts proportions, rather
than absolute differences, thus the texture of parenchyma is mistaken as vessel components. However, there
appears a lot of fragmentation.
further added a gradual lowering of threshold T low in a second and third passage of the linking
process, that is, while traversing the boundary extracted so far, neighborhoods were examinated to
segment and label new vessel components, and then repeat the boundary tracking operation.
Gerig et al. and Verdonck et al. concluded that hysteresis thresholding, without overfiltering
image data in angiographic studies, do not allow acceptable segmentations [Gerig93a, Verdonck96].
The VHP color images are not of the same nature, thus the conclusions of these authors are not
necessarily appliable to color images from anatomical slices. Gerig et al. used moreover global
thresholding under the assumption that angiographic images are homogeneous, but we have already
seen that partial volume and background texture depend on the structure of the vessels itself which
is not homogeneous in the lung’s ROI. Both authors chose to enhance blood vessel structures by ap-
plying other dedicated filtering techniques, Gerig et al. working on the whole volume, and Verdonck
et al. locally, using star-contours in a plane perpendicular to the vessels and dynamic-programming
to link each detected contour.
The latter techniques are suitable for single-vessel tracking on smooth-gradient images, as those
available from spiral CT imaging. However, vessels should be relatively large to have a meaningful
contour diameter, for which Verdonck reported a much better extraction.
In a 3D approach we continue to use local-thresholding with a relative value T low but without
including yet the costly sigma-filtering, which proved very useful slice-by-slice, as it can be seen
comparing Figure 4.19 (just local threshold) and Figure 4.17.
The algorithm of progressive segmentation is described as follows (see Figure 4.22). There are
remarkable similitudes with a conditionnal MM dilation.
Figure 4.19: Local thresholding with a window radius of 7 pixels. Oversegmentation arises from consid-
ering contrasts proportions, rather than absolute differences, thus the texture of parenchyma is mistaken as
vessel components (though texture does includes sub-sampled small vessels). As in Figure 4.18, there is high
fragmentation, too.
P ROGRESSIVE S EGMENTATION A LGORITHM .
1 2D local threshold at T high , with Sigma-averaging, slice by slice, in all the volume.
2 3D boundary extraction of connected components @ k . V

V
3 Scan (traverse) all boundaries @ k and examine the main-front voxels of each facet (that is,
the front-voxel boundary + k ). V
4 For each v 2 V
+ , examine a 3D 5x5 neighborhood; do a local-segmentation of the original
k
;
volume with a lowered threshold T low = p p, with p the local average read from the original
volume, and p = 3 (the “lowering” that would produce oversegmentation, if applied to the
whole volume).
5 Segmented voxels are automatically connected to the boundaries (since they are 6-adjacent,
V
belonging to all + k ) and may produce new inter-connections when considering the first-
segmented volume, reducing the number of connected components k. Segmented voxels are
labeled as foreground.
6 Repeat as in step 2 the boundary extraction of the hysteresis-thresholded volume.
7 Extract all boundaries on the whole volume. If there are many connected components (more
than 10, for example4 ) then repeat step 3-6, lowering threshold T low by 1 gray-level to pro-
4
10 is an arbitrary number to allow easy identification with different colors; fragments may initially be just too many
(thousands).
Figure 4.20: Local thresholding applied to gray-level image of slice 1437 with Sigma-filtering (from Fig-
ure 4.16). Note that vessels are detected at all regions and the interior of large constrasted structures is well
respected.
Figure 4.21: Segmentation, surface extraction and 3D-rendering of the bronchial vessel tree of the lungs.
S \S
Method: associative combination over (IXY ) ( under (IY Z ) S S
under (IZX )), where under is a Sigma-
S
average local threshold, and over are local thresholds. The arrow indicates an artifact from the left oblique
fissure (see Figure 4.3).
mote inter-connection voxels. Else, stop and analyse the biggest components (the extracted
tree and some large branches).
(b)
(a)
(c)
(d)
++
>> Sunder(V)
Sunder (V) Sover (V)
real object
"well" under-segmented branches S k under (V)
over-segmentation S over (V)
Figure 4.22: Progressive segmentation. Solid contours represent the real object and light shaded areas rep-
resent large vessel fragments k = 1 2::: detected by a coarse but restrictive (or severe) segmentation (left),
Sunder. This operator can be for example a local sigma-thresholding with T as in our implementation.
Missing detected connected components (a) may be detected by “relaxing” Sunder , while retaining connec-
high
tivity (as with hysteresis thresholding, with threshold T ). In a dual approach, dark shaded areas represent
oversegmentation by a coarse but permissive (or “indulgent”) operator (right), Sover and progressive seg-
low
mentation consists in eliminating spurious areas (b). S over may be still unable to extract some areas (c) and
create topological artifacts (d) (see for example the artifact in Figure 4.21). The connected components of the
extracted regions are the starting dataset for a more “indulgent” (left) or “restrictive” (right) operator, un-
SV
der connectivity constraints. Note that either conditionned growth (dilation, merging) or contionned pruning
(erosion, splitting) may proceed by voxel layers, on ( ).
This progressive method is suitable for a complementary operation (as if exchanging background
V
and foreground), eliminating voxels from the inner boundary voxels ( k or even ; k ), if they V
are oversegmented voxels. In this case, the first threshold is “permissive” (or indulgent) instead of
“constrictive” (or severe), and the second threshold is higher than the first one. In such approach
the advantage is to begin with very few connected components (ideally one), and elimination is
nothing else than an adaptive erosion. The connectivity constraint is then similar to that of simple-
point elimination (but using a gray-level threshold criterion), and the progressive segmentation is
rather similar to a 3D thinning. However homotopy is not necessarily preserved if threshold analysis
imposes to unselect a too low-valued voxel.
A third technique was implemented and tested: it consisted in replacing step 1 with a 3D region
growing segmentation. It is explained in the following subsection.
4.2.5 Region Growing Segmentation

A widely used method for segmentation of blood vessels is region growing (RG). It has been already
tested for the extraction of the blood-vessel tree of the lungs from MRA and contrasted CT images:
Pommert et al. [Pommert93], Pisupati et al. [Pisupati95], and Wood et al. [Wood95] report more
or less satisfactory results of this approach. RG complements an edge-detection approach where
interior regions are not detected by gradient methods, while RG allows to better identify interior
points where statistics is robust but detection is less reliable at boundaries (where growing stops).
There are two attractive features of RG:
✦ It can be combined and implemented with the local-threshold method, in order to get robust
statistics, since well-segmented vessels establish a confident reference for the mean value used
during RG.
✦ It can also be combined with a boundary based approach, since the growing front is itself a
boundary.
Furthermore, the change in cardinality of connected components of this boundary is an indicative of

branching events, or converging/fusing events, depending on the growing direction and the number
of seeds. When considering locally “fast” growing regions, such as blood-vessel branches, a large
volume is traversed (because of the branching nature of the lungs), and only a very small part of the
ROI is processed for the segmentation by RG (because of the diameter of vessels), which is thus very
economical. If the RG region becomes too compact, then the growing criterion is not applicable (a
sudden increase in volume or “volume explosion”, indicates a large oversegmentation, including too
many background voxels). This sensitivity regarding traversed volume versus grown volume allows
to adjust region growing parameters to maximize voxel-merging in the region, just before attaining
oversegmention.
RG is usually accomplished by seeding and growing several regions, which are merged if they
are connected and sufficiently similar. The bronchial-vessel tree of the pulmonar artery is a single
object, so we worked on the basis of a single voxel-seed for RG, located at the center of one of the
main branches of the lower generations. The seed v0 is considered to belong to the object but initial
B
statistics (average and standard deviation) are measured on a ball-neighborhood r (v 0), with r = 5.
After 5 branching generations the vessel diameter is smaller than r.
We further take advantage of facet information of each voxel that is a candidate for growth, in
order to implement a fast version of traditional 3D RG as described in the following paragraph,
using a queue data structure Q for the new voxels and a second queue Q stat for the local statistics.
Figure 4.23 illustrates how voxels are incorporated from the starting seed, examinating the next-front
voxels for each facet (oriented boundary face). We call this implementation a facet-driven region
growing .
R EGION G ROWING S EGMENTATION A LGORITHM .
1 v0 ! Q Queue the seed voxel,

v ∋ fk ∋ Vgrow
Vgrow
fk ∋ v f k+ ∋ +V
grow
f k+ ∋ +v
^
u
(a) k (b)
f
f+
(c) (d)
(e)
Figure 4.23: Facet-driven region growing in 3D. Neighboring voxels of a seed-voxel are examinated follow-
ing the 6 faces of the seed (a). For each one satisfying the growing criteria the process is repeated, except for
the initial face (b). All visited voxels are labeled to avoid multiple tests. Shape boundaries are formed where
growing stops (c), and the number of connected components of the front increases after bifurcations (d). The
spherical fronts of the figure are approximative (e); at advanced front generations, their shape become irreg-
2 V 2 V
ular. 6-connected neighbors are automatically visited by the facet-representation offsets (LUT of coordinates
for each facet fk @ grow , and frontal facet neighbor f k+ @ + grow ).
2 label(v0 )=Lab growth label the seed.

Calculate the statistics(v 0) of r (v 0). B
!
statistics(v 0) Qstat queue the statistics
3 6
While( Q = ∅)
4 f Q ! v Unqueue a voxel,
5 Qstat ! statistics(v ) un-queue statistics.
Update statistics(v ) of Br (v).
6 8 w i 2 N i = 1 : : : 6 :

6
7 if( label(wi )=Lab growth AND Growth(statistics(w i ))=YES)

8 f wi ! Q Queue the grown voxel.
4.3 Conclusions and Perspectives. 187
statistics(wi ) ! Qstat Queue its statistics.

label(wi ) =Lab growth Label the voxel.
g
9 g End of growing. Voxels labeled as Lab growth form a region connected with seed v 0 .
In steps 2 and 5 average and standard deviation are calculated for the given candidate w i . This
operation can be omitted or done from time to time: statistics are thus calculated for each point (very
coslty in time ressources), or just for regions far from the seed, or during first thousand grown voxels
in order to have several new seeds well distributed in several places. One possibility we did not tested
is to partition the ROI into large blocks, pre-calculate statistics for each block and use this value.

In step 7 a decision Growth( ) in function of local (or global) statistics is count (we used a
threshold criterion equal to the last local average minus half the standard deviation). The final results
from RG segmentation with the progressive segmentation enhancement (with two iterations) are
visualized in Figures 4.24 to 4.27 for two different points of view.
Even if no local statistics are obtained, RG performs still better than simple thresholding, since a
small part of the total ROI is analyzed. When boundary extraction is later used, RG allows to isolate
single connected objects, while thresholding and local thresholding leave thousands of ”particles”,
noise artifacts or fragments of other organs. Several connected sub-branches extracted by RG re-
main to be merged into one single tree, if appartaining to the Pulmonary Artery. At the same time,
Pulmonary Vein components are also to be identified and separated, as well as the heart components.
4.3 Conclusions and Perspectives.

We presented in this chapter some of our experiences with the 3D extraction and visualization of the
bronchial blood-vessel tree of the lungs in man, from serial images of cryosections from the VHP
database. Original data presented a number of problems, such as:
(i) color camera callibration and radiometric discontinuous inhomogeneities (for which Chap-
ter 3 is specifically devoted),
(ii) a branching fractal structure that makes difficult the separation of background from fore-
ground, and
(iii) the presence of several other objects and noise which makes difficult the boundary extrac-
tion from segmentation results, since thousands of complex objects remain in the ROI. Local
thresholding was useful by selecting pixels for the average to be classified as background or
foreground. Selection is based on similarity to the central pixel to be examinated (such slec-
tion constitutes the Sigma filter). Combination of results from sets of orthogonal sections gave
some preliminar results, but a full 3D approach gave much better results. The 3D method
consisted in a preliminar segmentation by region growing, boundary extraction and further
refinement by hysteresis thresholding on voxel neighborhoods of the voxel-based boundary.
Further tests must be performed to obtain a satisfying validation of the methods and a later
anatomical validation by an expert morphologist would also be valuable.
Besides the reported work, we explored several ideas for designing and implementing tubular
extraction methods; some of them using our boundary-based approach, as well as rolling buffers and
other concepts described in the precedent chapters. Time limitations did not allow us to present here
Figure 4.24: Best obtained segmentation, surface extraction and 3D-rendering of the bronchial blood-vessel
tree of the lungs (region growing and merging of connected voxels). Observe some correspondences with the
diagram in Figure 4.4.
in detail all these methods and the preliminar results. However, we give a draft of the main ideas in
Appendix B, page 239.
4.3 Conclusions and Perspectives. 189
Figure 4.25: Same segmentation result as in Figure 4.24. Visualization of the depth buffer (gray-levels code
distance to the point of view).
Figure 4.26: Same segmentation result as in Figure 4.24; another point of view.
Figure 4.27: Same as in Figure 4.26; visualization of the depth buffer.

Chapter 5
Analysis and Visualization of Computer

Simulations of Amorphous
Photo-Deposition
Abstract
As an aid to understand models and experimental data of ultraviolet induced chemical vapor
photo-deposition (UV CVD), this chapter explores the use of quantitative and qualitative tools
and methods to analyze numerical volumes from computer simulations of UV CVD produced at the
CNET-Bagneux laboratories. We give an account of different discrete-geometry techniques oriented
to extract morphological characteristics of bulk (mainly porosity and atom-species mixture), and
surface (mainly roughness) of discrete volume data corresponding to computer-simulated deposits.
Emphasis is given on measures and features that can be obtained or estimated through experimental
validation, which allows evaluation of the simulator and the physical model. A choice of methods
and specific measures is proposed and some of them were implemented. We finally present some
results from our collaboration with the CNET-Bagneux. The proposed and tested techniques can be
applied in a great variety of microstructural analysis in material sciences and other fields.
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192

5.2 Objectives of the Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
5.3 Monte-Carlo Simulation of Amorphous Deposition . . . . . . . . . . . . . . . 194
5.3.1 Model and Simulation Parameters . . . . . . . . . . . . . . . . . . . . . 195
5.3.2 Morphological and Topological Dynamics . . . . . . . . . . . . . . . . . 196
5.4 Characterization of Deposition Morphology . . . . . . . . . . . . . . . . . . . 197
5.4.1 Surface Features and Bulk Features . . . . . . . . . . . . . . . . . . . . 197
5.4.2 Complex Internal Features . . . . . . . . . . . . . . . . . . . . . . . . . 199
5.5 3D Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
5.6 Analysis methods and feature extraction . . . . . . . . . . . . . . . . . . . . 203
5.6.1 Other Possible Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 212
5.6.2 Visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
192 Analysis and Visualization of Computer Simulations of Amorphous Photo-Deposition
5.7 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213

5.7.1 Porosity, Roughness, Connectivity, and Anisotropy . . . . . . . . . . . . 213
5.7.2 Surface Density, Interfaces Surface . . . . . . . . . . . . . . . . . . . . 213
5.7.3 Interpenetration Quality and Segregation of a Three-Species Deposit . . . 215
5.7.4 Experimental Validation . . . . . . . . . . . . . . . . . . . . . . . . . . 217
5.8 Conclusion and Perspectives . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
5.1 Introduction
This chapter is based on a draft proposal for a collaboration between the Groupe Modélisation et
Simulation de Procédés pour l’Optoélectronique (GMSPO) of the Centre National d’Etudes en Télé-
communications (CNET)1 , at Bagneux, and the Traitement du Signal et des Images (TSI) Department
of the Ecole Nationale Supérieure de Télécommunications 2 (ENST) at Paris.
The GMSPO group has developed models and computer simulations of cold, ultraviolet-induced,
”UV CVD” I chemical vapor photo-deposition mechanisms (UV CVD ) in three-dimensional discrete space.
Laboratory experiments are very expensive and complex, with a high number of parameters to test.
Hence, computer simulation of amorphous or crystalline deposition becomes a valuable method to
help understanding optoelectronic devices, their modelling and fabrication, and for the morphologi-
cal study of surface phenomena (reflectivity, conductivity, layer interfaces, etc.), required in applied
research of thin films, semiconductor interfaces and the design of photonic devices.
Understanding and evaluating models of physical phenomena, as well as their computer simula-
tions, require in general to study the effect of model parameter variations on the numerical outcome of
the simulation. In the case of UV induced photo-deposition, simulations produce three-dimensional
discrete samples, in a face-centered cubic (fcc) grid, where each site (voxel) information may be
binary or includes a gray-level label, for instance. A binary value indicates a vacant or occupied
site, while a gray-level value encodes information about one or more parameters, such as the type of
atom species, or the elapsed time in relaxation cycles units. In this document, the term species refer
to single atoms, ions, molecules, atom clusters, or the substrate chemical composition. The term
adatoms refers to adsorbed3 atoms or ions.
Complexity of per-site information depends on what is recorded during simulations (i.e., the in
situ conditions). In our collaboration with the CNET, each site corresponds to the particular discrete
position in space where calculations were done for a single atom or molecule, and microstructure
is studied at the nanometer scale. Other deposition or aggregation phenomena may consider big-
ger entities (atomic clusters, molecules or particles), and structural features span on many scales
[Armin96].
This chapter is organized as follows.
✦ In Section 5.2 we mention the original objectives of our collaboration with the CNET-Bagneux
laboratories and the expected results.
✦ In Section 5.3 we describe the computer simulation of deposition phenomena, in order to

understand the origin of structural features of the data to be analyzed.
1
http://www.cnet.fr
2
http://www.tsi.enst.fr
3
Not “absorbed”, but accumulated on a surface (cf. Webster dictionary).
5.2 Objectives of the Study 193
✦ Section 5.4 presents a summary of physical characteristics such as roughness and porosity,
which can be generalized to other kinds of complex volume data.
✦ The 3D methods to represent and quantify the physical features of simulated deposits are ex-
plained in Section 5.5 and Section 5.6; we also show in these sections how we took advantage
of the boundary-based approach to 3D-analysis, as presented in Chapter 2.
✦ In Subsection 5.6.2 we discuss the utility of the 3D visualization of the boundary representation
of the volume data, and particular details concerning the present application.
✦ Results so far obtained are presented and discussed in Subsection 5.7.
✦ Some validation issues are commented in Section 5.7.4.
✦ After the conclusions and perspectives, we present in Appendix C an implementation of a

Diffusion Limited Aggregation process, capable of generating complex structures useful as
phantoms for the development and validation of analytical tools.
5.2 Objectives of the Study

The aim of our collaboration is to develop and test quantitative and qualitative tools and methods
to analyze numerical volumes obtained by computer simulation of amorphous photo-deposition of
Nitride-Silicium. These simulations are obtained at the CNET-Bagneux. Details of the model and
the specific Monte-Carlo simulator of the CNET may be found elsewhere [Flicstein97a, Pata97,
Flicstein97b].
Our contribution (ENST) focuses on analyzing the morphology of computer simulated deposits
and extracting morphological parameters which will be interpreted and related by the CNET re-
searchers to simulation parameters and experimental observations. This kind of correlations have
already been performed, as for example the theoretical, experimental and model/simulation curves
of bulk features (v.g. porosity) and deposition surface features (v.g. RMS roughness) versus temper-
ature [Armin91, Flicstein97a].
The specific goals comprise the following:
1. Extraction of morphometric data for each simulation to characterize parameter dependence,

mainly porosity and roughness versus temperature, luminance, or incidence rate.
2. Characterization of species mixture quality versus diverse deposition conditions.
3. Visualization (surface renderings) of 3D reconstructions of the simulation data, for different

experimental conditions. The objective of this visualization is a qualitative display of data,
with colors and gray-levels representing data features (e.g., species, connected components,
etc.). A selective display of information should provide a quick overview of particular data
and their structural organization.
The CNET will independently validate these correlations and compare them with experimental
estimations on real deposits.
5.3 Monte-Carlo Simulation of Amorphous Deposition

We present in this section a summary of the amorphous deposition models and relevant details of the
Monte-Carlo simulation of UV CVD.
The Monte-Carlo character of numerical simulations consists in the computer “throwing” of
randomized events: random displacement of particles represented by memory locations, particle
interactions, substrate absorption and other. The asignment of event probabilities is based on theoret-
ical considerations (more precisely, from statistical-mechanics and physico-chemical models) which
enhance the approximation. After some number of simulated events (or cycles), the outcome ap-
pears as a complex distribution of occupied sites in computer memory. The structural characteristics
of this distribution reflects physical features of the model: shape, texture, roughness, anisotropies,
clustering, and so for.
The models of amorphous deposition are elaborated cases of a Diffusion Limited Aggregation
”DLA” I (DLA) process, as described in Chapter 1, Section 1.4.3. There are however several physico-
chemical constraints in the interaction of aggregated particles (adsorbed atoms or adatoms in the
atom-by-atom vapor deposition). An important stage is relaxation after particle aggregation (atom
adsorption). In this stage further interaction occurs along the deposit surface. We are not concerned
with energetic-bond calculations and experimental realization, and limit our attention to the origin of
structural features, having in mind their quantitative characterization.
Several simple models of deposition exist, giving rise to different aggregation phenomena. The
main models, in increasing order of sophistication are: random deposition, random deposition with
surface diffusion, ballistic deposition, restricted solid-on-solid deposition and spatially correlated
deposition. In random deposition particles fall down at random positions to form a deposit which
exhibits some bulk and surface features, but no lateral movement or interactions are allowed (see
Figure 5.1a-b). Particles stick to the cluster when they touch the top of the last deposited layer or by
touching the side of a particle.
More elaborated Physics-based models exist. A first improvement is lateral displacements mod-
eled by brownian-motion. Vulgarization literature often compares this improved model to the computer-
game “Tetris” when variously-shaped particles are considered, and refers to such deposition modality
as “ à la Tetris”. Further improvements to the models consist in introducing particle (ion or atom)
interaction and surface dynamics in function of the several external and internal parameters, such as
temperature, luminance, adatom species and substrate, as described later. This interaction is simply
called “surface diffusion” or relaxation. With all these model characteristics, real physical deposits
have been accurately modeled and simulated, but analytical tools as those presented in this chapter
have not been reported.
The deposition process simulated by the CNET is illustrated in Figure 5.1, in terms of discrete
sites (voxels). Following the color labels (a-j) in the figure, we explain the stages and events during
deposition. In the random deposition and the ballistic deposition models the particles fall vertically
(a) into a substrate (b) where other particles already form a deposition cluster (c). In the extended
models, each particle (d) arrives at growth sites (e), by random walks. Then the particle interacts
with the top layer (g), sticking or migrating to an equilibrium position. The final local configuration
creates new growth sites (h), and forbids the access to other sites. Further interactions with next-
nearest neighbors fill gaps (i), but there remain inaccessible, stabilized voids as for example those in
(j), forming pores and meanders (see Figure 5.4h and Section 5.6-5d).
In Figure 5.2 a step-by-step description of the computer simulation of vapor deposition process
is presented. It corresponds to different simulators mentioned in literature [Eden60, LAFEM92,
Merriman98] and to that designed by the CNET. Physical formulations and other details, includ-
5.3 Monte-Carlo Simulation of Amorphous Deposition 195
1111111111111111111
0000000000000000000
(a) (e)
01 (b) (f) (i)
(c) (g) x (j)
(d) (h)
Figure 5.1: Cross section of a deposition model (each cube represents a site). A Physics-based real-
istic model comprises lateral displacements, particle interactions and surface dynamics. In random
deposition and the ballistic deposition models, the particles fall vertically (a) towards a substrate (b)
where other particles already form a deposit (c). In the extended models, each particle (d) arrives at
growth sites (e), by random walks (f), interacts with the upper layer (g) and creates new growth sites
(h). Further dynamics fills gaps (i), but there remain inaccessible, stabilized voids as for example (j),
forming pores and meanders.
ing the particular implementation of the CNET are given in [Pata97, Flicstein97a, Flicstein97b,
Armin91]. The parameters listed in Figure 5.2 control the deposition process; they are briefly de-
scribed in the following paragraph.
5.3.1 Model and Simulation Parameters

Regarding UV vapor photo-deposition, we consider model parameters, and simulation parameters.
The model parameters comprise: atom species a, substrate species s, temperature T , UV irradiation
luminance L, and incidence rate of atoms Ir . The simulation parameters include: adatom-adatom
dissociation energy E aa , adatom-substratum dissociation energy E as , total precursor rate Pr , de-
posit efficacy Deff and the neighborhood characteristics for atomic interactions [Pata97, Flicstein97b].
In the data-set provided by the CNET-Bagneux, up to three deposited species are being studied: sili-
con (Si), nitrogen (N) and hydrogen (H), and there are three substrate species: Indium phosphate (In
P), Si, and silene or silicium oxyde Si O2 . The participating species determine the dissociation ener-
gies, the temporal evolution of photonucleation (the early substrate coverage) and photodeposition.
Monte-Carlo Simulation
Amorphous Photo-Deposition
(a) fcc (face centered cubic) grid

Initial conditions (a, s, T, L, Ir , E aa , Eas , Pr , Deff , neighborhood)
(b) Nucleation center creation (precursors -defects)

Random deposition on the substratum
(c)
Random adsorption in function of sticking coefficients
(d) Relaxation (diffusion or surface dynamics)
(e) Migration, stability or random desorption of adatoms

probabilites in function of energy barriers
(f)
Crystalline or amorphous structure
Repeat for N relaxations

(g)
Repeat for M cycles

Figure 5.2: Standard model of amorphous deposition with relaxation by Monte-Carlo simulation.
Initial conditions (a) consist in: atom species a, substrate species s, temperature T , UV luminance
L, incidence rate of atoms I r , adatom-adatom dissociation energy E aa , adatom-substratum dissoci-
ation energy Eas , total precursor rate P r , deposit efficacy Deff and the neighborhood characteristics
for atomic interactions. See text for details.
5.3.2 Morphological and Topological Dynamics

The effect of the aforementioned parameters on the simulation outcome includes morphological and
topological changes in the deposition bulk and its top-layer surface. Morphological changes include
shape, size, texture, and spatial distribution of features. Topological changes refer to number of
components, connectivity relationships, neighborhood configuration, and holes 4. All these features
characterize physical or chemical properties in laboratory experiments, and relate to mechanical,
optoelectronic and surface phenomena in general.
The terms topology and morphology bear a different meaning in surface Physics. The first refers
to the geometric shape of the substratum, and the second to surface shape and roughness. Internal
shape is named microstructure, nanostructure, or ultrastructure when fine details are considered. In
4
these features are related to formal definitions of topology properties as those “invariant under continuous transforma-
tions”, and are also related to homotopy.
5.4 Characterization of Deposition Morphology 197
this document, morphology and topology of the numerical deposit will preserve their mathematical
usage: morphology will refer to shape and structure of one or more objects and their boundaries in 2
or 3 dimensions, and topology will refer to cardinality, connectivity and neighborhood configurations.
The terms substratum geometry and microstructure or nanostructure, will be used with their surface
Physics meanings. We use the term surface with two connotations: (1) as in surface Physics, it is the
three-dimensional top boundary of the deposit (Figure 5.11) which may be sometimes represented
by a level-set, that is, a single-valued function of 2D coordinates, z = f (x y ), and (2), as surface
area, referring to the bidimensional metric quantity, expressed in squared-length units. The context
should clarify which meaning, (1) or (2), is intended.
Since morphology and topology features change in function of simulated or real experimental
conditions (sets of parameters), there exists an evolution or dynamics associated to time-varying
conditions. The interest in knowing their characteristics is the possibility of controlling such struc-
tural features, with some particular goal. This includes the design of solid-state or opto-electronic
devices, or the control of particular physical properties of interfaces, from mechanical stability to
dielectric and refraction coefficients. As in any dynamical system, researchers of the CNET expect
to identify phase-transitions, and extremal numerical values (e.g., minimal porosity, maximal mix-
ture of components), corresponding to particular parameter-settings. Figure 5.20 in page 220 shows
a graphical example of transitions in the distribution characteristics of pore shape and size.
In the following sections we describe in more detail the main structural features and their discrete
representation, in order to make clearer how a quantitative analysis can be done.
5.4 Characterization of Deposition Morphology

We examine first the most relevant and global characteristics of microstructure in amorphous deposits
and then the more complex features arising from connectivity inside the bulk. The latter are closer
to three-dimensional textural features and our analysis applies to other kind of complex sets (particle
clusters, sponge-like and networked structures).
5.4.1 Surface Features and Bulk Features

Morphology features of a deposit are broadly classified in “external” or surface features and “inter-
nal” or bulk features.
External or surface features are often represented by roughness of the external surface (the last
deposited monolayer). In Image Processing, intensity may be interpreted as height, and con-
versely. Thus, the surface texture may be viewed as the projection to infinity of each top-layer
site height (see below Equation 5.6), giving a one-to-one function of coordinates x,y, which
may be subject to wave or periodicity characterization, that is, by frequency domain analysis,
in particular by examining the power density autocorrelation function.
Internal or bulk features are exemplified by porosity of the material, which may include not only
the volume densities of material/void, but also the size distribution, or other features of inter-
stices and cavities.
Surface roughness and bulk porosity have been the most common studied features, mainly be-
cause theoretical models and experimental validation enable their estimation on real data. For ex-
ample, roughness relates to surface refraction index, measurable by ellipsometry techniques [Guenther84],
or by laser speckle metrology [Briers93]. Porosity is in turn estimated by backscattering analysis,

or X-ray density measurement. In amorphous deposition models by the CNET, roughness is simply
represented by the root mean squared (RMS) deviation from the mean height < h > of the last
deposited layer (see Figure 5.3):
hRMS = N N
2 1 NX
x ;1 NX
y ;1
(h ; < h >) 2
ij (5.1)
x y i=0 j =0
NX
x ;1 NX
y ;1
where < h >= N 1N hij (5.2)
x y i=0 j =0
where hij is the top-surface height at growth site (x y ) = (i j ), N x = Ny = 50 Nz = 100 are

the deposit space dimensions, and N x Ny = 50 50 is the number of substrate growth sites in a
square grid. In the simulations of the CNET, energy calculations restricted simulations to very low
resolutions in the three axes, but mean height (direction Z ) was allowed to attain up to 90 monolayers
in some simulations. Due to discretization and scale, this low resolution makes very imprecise the
Fourier, multiresolution and scaling-behavior analysis of surface characteristics, which are more
meaningful for resolutions starting from 128 128.
j hij
i x
Figure 5.3: Top-surface heigth z = h ij at growth site with coordinates (x y ) = (i j ). Mean height

< h > is the average of all h ij in a deposit of 50 50 growth sites. Root-mean-square height
deviation from < h > defines the RMS roughness (see also Figure 5.13). Simulation data provided
by the CNET, visualization by the author.
5.4 Characterization of Deposition Morphology 199
An example of a theoretical model to predict hRMS evolution (sometimes named RMS rough-
ness), is the KPZ nonlinear equation (Equation C.1 in Appendix C, page 250), where parameters are
estimated from the deposition model (random deposition with relaxation, etc). A short exposition is
given in Appendix C.
In a broader sense, roughness is a much more complex notion, closely related to surface texture.
Concerning porosity, the CNET uses in its experimental protocols the standard definition: porosity
is the ratio of vacant-sites volume to total deposit volume. As for roughness, “porosity” also encom-
passes more complex structural features of bulk, as explained in the following paragraphs. With
the simple definitions of RMS-roughness value and void/material volume ratios, dependence on op-
erating conditions of surface roughness and bulk porosity can be predicted [Flicstein97b]. To our
knowledge, more complex morphological characteristics have not been studied until now in amor-
phous deposition simulations and similar volume data.
5.4.2 Complex Internal Features

Complex relations of internal features arise when connectivity is taken into account. Connectiv-
ity may be ’weak’ or ’strong’, giving rise to ’closed’ pores or ’open’ pores, respectively (see Fig-
ure 5.4). Closed pores or bubbles, are more or less round in shape (’compact’), while open pores
may have more complex shapes, may contact the space around the deposit, or even may form an
intrincate network through the deposit. Open pores are sometimes considered as interconnected bub-
bles [Armin91], and the size of the connection neck determines a degree of ’openness’5.
z
(a) (b) (c) (d)
(e)
(f) (g) (h) (f)
Figure 5.4: Cross section of amorphous photo-deposit bulk of a single atom species: growing axis
Z (a) in monolayer units; closed pore or bubble (b); external wavy surface (c); surface overhangs
(d), substrate (e); ”open” pores (f) and (h) with a connection neck (g); surface meanders (h) (also
”open” pores). Notice that meanders and overhangs imply one another.
More complex features may become meaningful when considering several atom species (or site
labels in general) in order to characterize species segregation and inter-species mixture quality (Fig-
ure 5.5). Such complex features include the contact surface between different bulk components, the
mean local neighborhood composition of a site, size or shape of homogeneous bulk components,
5
A formal treatment is possible using Mathematical Morphology (MM), if we identify the minimum detectable size of
the neck with the structuring element size of MM operators.
etc. Other global attributes can be induced by simulation conditions, for example: the anisotropy
of shape characteristics, and three-dimensional “textures”. Many features of the deposition models
are similar to random-field model realizations, which may produce coherent structures, as for exam-
ple: filamentary, trabecular or column structures, granular, flake or layered structures (see Chapter 1,
Section 1.2.5 and Section 1.6).
A practical consequence of all these structural relations and features is that even if rough esti-
mations of porosity and roughness can be made by simple volume scans, there are new structural
characteristics that must be taken into account, such as connectivity relations 6. Thus, connected
components need to be extracted, and this is where we have participated using the discrete geometry
approach described in Chapter 2.
Bulk internal properties are very difficult to study or to isolate by simple slice-by-slice analysis
or sampling tools. However, three-dimensional reconstruction makes available a set of methods to
directly measure some of those 3D internal features, and to estimate or just make evident (i.e. visible)
other characteristics. These methods include volume processing, three-dimensional visualization,
shape morphometry and Mathematical Morphology (MM) filtering (“shape filtering”).
Quantitative analysis frequently requires a processing stage, which may include some filtering,
using for example MM operations. An example is the decomposition of the bulk species or the
porous phase into ’weak’ connected components, whose number and shape distribution can then
be analyzed. Another example of MM analysis is Granulometry, as detailed in Section 5.6. Thus,
MM-based processing can be applied to simplify (by separating, or regrouping), select or discard
specific shape components, before analysis. Some shape modifications may also be performed (shape
smoothing, for example).
species 1
(a) species 2
(b)
Figure 5.5: Amorphous photo-deposition of two atom species: low-quality mixture (a) is charac-
terized by species segregation, small simple interfaces and large volume clusters of each species;
high-quality mixture (b) is characterized by high species inter-penetration, large complex interfaces
and small volume clusters of each species.
We explain in the next section the application of our boundary-based approach to analyze mor-
phologic characteristics of amorphous depositions resulting from computer simulations.
6
In percolation aggregates connectivity is the most important feature.
5.5 3D Methodology 201
5.5 3D Methodology
Besides traditional 3D analysis, we use a discrete-geometry approach for surface extraction, 3D
image processing, morphometry and visualization of volume data with any degree of complexity. In
Chapter 2 we have described how external surfaces or boundaries of detected objects are represented
by lists of facets (voxel faces). An important step of the 3D image processing consists in analyzing
and modifying these lists and their associated data structures, by examination of neighboring facets
and voxels in order to perform the desired operation or measurement.
Let us consider foreground and background boundaries in amorphous deposits. The first bound-
aries comprise particle clusters and the second all voids or pore structures. With our methods, these
boundaries are extracted by traversal of a directed graph associated with the discrete surface of each
object, and a voxel representation is replaced and simplified to a face representation, which preserves
all connectivity relations, since all connected components are identified. Neighborhood relationships
are taken into account by coordinate offsets from each facet, combining the 6-, 18- and 26-adjacent
voxel neighbors (see Subsection 2.3.5). These neighbors correspond to the first, second and third
next-neighbors or also the nearest, next-nearest and next-to-next nearest neighbors in the terminol-
ogy of Crystallography, solid and surface Physics (see Figure 5.6).
Figure 5.6: First-order, K -adjacent voxel neighborhoods, with (a) K = 4 8 in 2D, and (b) K = 6 18 26 in
3D (same as Figure 2.7). (a) Voxels of E6 are named the nearest neighbors of the central site, while (b)-(a),
n
i.e., E18 E6 are the next-nearest neighbors and (c)-(b)-(a) (i.e., those sharing a vertex) are the next-to-next
nearest neghbors.
The three following examples illustrate the interest of our approach:

1) Filtering: a morphological conditional erosion (or background dilation) becomes a selective
elimination of voxels only at the object’s boundary @ ; V
2) Morphometric calculations: the volume (or any higher-order moment) of an objet is calculated
from its boundary, using the discrete Gauss Theorem (or Divergence Theorem), given in Equa-
tion 2.12. In general, instead of a single object, we may also consider a particle distribution,
and study its bounding volume, centroid, of other morphometric features.
3) Local analysis: Neighborhood analysis or processing operations can be done exclusively on
the object boundaries. See Figure 5.7.
4) Visualization: to render realistic shadings the local normal is estimated from the facet neigh-
borhood configuration, and only the external surface components are displayed.
Interactive visualization allows to perform complex analysis tasks by proper chaining of body
selection criteria (size, shape):
✦ regrouping,
✦ shape-filtering by MM operators,
✦ boundary traversals for labeling of specific configurations,
✦ other boundary-based morphometry or processing.
As noted in Chapter 2, our software includes some standard volume processing and volume mor-
phometry tools. The format of volumic data is also compatible with the software package TIVOLI
(Traitement d’Images VOLumIques) of the TSI departement, at the ENST [Geraud98].
V
(a) 0
1
0
10
1
01
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1
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0
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0
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v ∋
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E 6 (v)
1
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...
0
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01
101
00
10
1 (c) discrete sphere:
01
0
10
1 ∋ 3
B r (v) = { w N | round( || w-v || ) < r }
Figure 5.7: Neighborhood operations on geodesic discrete boundaries. (a) Local analysis or processing (e.g.
MM operations) follow the voxel-based boundary V(only a 2D profile is shown). Euclidean neighborhoods
include from (b) single voxels, to K -adjacent voxel neighborhoods EK , with K = 6 18 26, and even r-balls
B
(discrete spheres) r (v) withv 2 V .
Quantitative analysis of species segregation (mixture or inter-penetration quality) is a good exam-

ple for which our boundary-based approach has useful properties. In Section 2.3.6 we have described
voxel and face neighborhoods to explore on the boundary interfaces of each species, in order to mea-
sure the local composition of atom species (See Figure 2.8). Figure 5.8 illustrates in a 2D slice
various shape and structure configurations: top-surface boundary, pore boundaries and interfaces be-
tween al least two species A B . Two (or more) species give rise to sets of deposition clusters A BV V
constituting the bulk. Inter-species boundary characteristics in 3D are shown in Figure 5.9.
Notice in Figure 5.9 that the internal intersection (e) B V \V C is the interface (d) between both
species. Also note that in voxel representation ( B V \ V 6 V
C ) @ , and in a face representation
V \V V \ V
( B C) @ B @ C.
Given for example 3 species, 100% of background neighbors correspond to no mixture at all, and
a 25% of each other species labels per voxel ideally corresponds to perfect mixture. Other kind of
5.6 Analysis methods and feature extraction 203
(a) (b) (f)

last
01101010 01010110
01 01 0100
11 010100
Layers z
11
00
1
0 1
011
00
11
00
1
0 11
00 1
0 1101
0000000000000000000
1111111111111111111
01010101 00
11 00
11
0101 0100
11
00 11 0100
11
0000000000000000000
1111111111111111111 01
0000000000000000000
1111111111111111111
zero 1111111111111111111
0000000000000000000
(c) (g) (h)
(d) VA (f) V c
01 (e) VB
Figure 5.8: Top-surface-boundary topology and pore-boundary topology. Upper layer of the deposit
Vj
as a 3D face-boundary @ c zlast (a), where meanders and overhangs (b) are taken into account.
Last-layer voxels (solid boundary) are in a lighter shade. The entire boundary of the deposition
V
bulk includes the closed pores (c). In this case, the background c in (f) (i.e., the complement of
V V
the foreground ) is said to have several connected components, with N @ c boundaries @ k c k =
1 ::: N@ c. Also, two or more atom species a (labels A (d), and labels B (e)) give rise to a partition
V
of the bulk (the foreground) into several connected components ( = A V V V B ). This partition
V \ V
creates boundary interfaces (g), constituted by all intersection components of (@ A ) (@ B ). Shape
of the substrate (h) (”geometry” in surface Physics) can also be taken into account as an additional
Vj
boundary, the boundary of the ”zero” or null layer @ z=0 , which constitutes part of the initial
conditions.
local information is obtained from geodesic neighborhoods which are calculated in a system of ori-
ented faces, as described also in Section 2.3.6 (See Figure 2.9 in page 107 which shows first, second
and third order geodesic-neighborhoods). Table 2.1 and Table 1.4.1 from Section 2.5.1 summarizes
some morphometric measures and operations obtained with our boundary-based approach.
5.6 Analysis methods and feature extraction

In the next paragraphs we list the simplest and most representative features that may be studied to
characterize bulk and surface morphology of a discrete scene (volume), once the connected com-
ponents extraction and representation has been performed. All features assume ’closed’ pores, but
’openness’ may be taken into account. The main items describe the general feature to be character-
ized, and their following sub-items the specific measure or analytic method to be employed. A short
discussion is given for some of them.
1. Bulk porosity in a deposit with one or several species.

(a) (b) (c)
A
1111
0000
0000
1111
0000
1111 0000
1111 B
0000
1111
(d)
000111
111
000000
111111
0000
1111 000
0000
1111 C
000
111
0000
1111
000
1110
1
000000
111111
111
000000
111
000
111
0000
1111
000
111
0000
1111
0000
1111
000
1110
1
000
111
000000
111111 0000000 1111
000
111
1111111
000
111
0000
1111 0000
0000
1111
U
B C
0000
1111
000
1110
1
000
111
000000
111111
0000
1111000
111
0000000
1111111
000
111
00
11
0000
1111
000
111
0000
1111
0000
1111 00
11 0000000
1111111
000
111
0000
1111
000
111
0000
1111
0000
1111 00
11
0000
1111
0000
1111 00
11
0000
1111
(e)
0000
1111 000
111
0000
1111
0000
1111 000
111
0000
1111
0000
1111 000
111
000
111
0000
1111
0000
1111
0000
1111 000
111
0000
1111
0000
1111
Figure 5.9: Discrete inter-species boundaries (interfaces). Surface (a) with labels corresponding to
3 species A, B, and C. The boundary (b) of the B/C inter-species boundary B V \V C (or interface)
V \V
is constituted by polygonal contours @ ( A B ) @ ( V \V
A C ) and @ ( V \V
B C ) . A voxel (or site)
can have only one associated label (c), but interfaces are implicitly defined by two voxels with two
different labels sharing the same face (e) (a single site may thus share up to six different interfaces).
V
(1.a) Let a denote the atom-species aggregates, with a 2f g
1 2 3 corresponding to atom
species Si, N, and H. We proposed and implemented the following measures:
Npores number of pores,
NVa number of aggregates,
Vpores volume of pores,
Va volume of aggregates of atom species a,
S V
surface area of @ a and
S=V surface/volume ratios of pores or species aggregates a V
We further proposed to compute histograms and observe the correlation factor as function
of a simulation parameter (T , L, etc.; we actually did it for T ). Other studies may be
designed, such as a histogram analysis of the maximum diameter of balls contained in
the bulk, or the porous phase, and so for.
(1.b) The same as above, taking into account the “openness” of the pores. A differential com-
parison may help to evaluate validity of the “closed pore” approximation.
2. Morphometry of species aggregates and pores.
(2.a) Surface density per volume unit and volume density. These measures can be calcu-
lated for pores, or clusters of one species in relation to another (species density). The
V
”surface” for surface density here refers to the N@ a boundary components @j a , with
j = 1 : : : N@a and a 2 f1 2 3g. Inter-species boundaries (interfaces) are defined as

the intersection sets: @ V 1 \ @ V2 @ V2 \ @ V3, and @ V1 \ @ V3, in face representation,
S
where @ Va = 8j @j Va. When the objects are the pores themselves (a 2 = f1 2 3g),
we use N@ c to denote the number of background components (the complement of fore-
ground, the bulk V = V 1 V2 V3). Pore boundaries are thus denoted by @k V c , with
k = 1 : : : N@c , where inter-species boundaries are not included, since the foreground
V
is all the bulk . Pores boundaries and inter-species interfaces are illustrated in 2D slices
in Figure 5.8 and 3D interfaces in 3D are shown in Figure 5.9.
(2.b) Voxel-based boundaries give rise to similar measures (e.g., V\ V
2 ), which is a closed
V\ V
1
surface, from the point of view of facet boundaries, while @ 1 @ 2 is a boundary patch.
V
Furthermore, what is measured as “solid surface” (card j ) has a different meaning,
which can not be directly validated by physical experiments (these are internal surfaces
making up the bulk porous structures). What turns out to be more meaningful, is to
analyze some average internal surface density V , interpreted as site density using Eu-
clidean neighborhoods of v 2 V
, Equation 2.9:
V =< card(Er (v)) = card(Nr (v) > (5.3)
(2.c) Local topology (number of components, neighborhood connectivity). These measures

should provide information about two opposite qualities: granularity and percolation,
that is, to which extend the bulk aggregates are structured as a network.
(2.d) Granulometry for a fixed parameter set [Coster89]. The MM operation of “opening”7
is applied several times, and the size and number of residual objects is recorded after
each opening. The curve of size distribution should be characteristic of the aggregation
process (small or high population of big, medium and small sized components). A similar
analysis can be done with the complementary MM operation of “closing”.
(2.e) Vertical distribution of pores. The growth axis of the deposit is a privileged direction,
and distribution of pores in this axis can be expected to be non-uniform, in function
of the number of cycles, T , and other parameters. The z component of the Center of
Mass (CM z ) of each pore should provide a simple, meaningful measure of pore spatial
distribution.
(2.f) Pore anisotropy. Orientation of pores is expected to be isotropic at least in the X and
Y directions. Vertical-elongated or flat- horizontal pores may be important if anisotropic
trends are present in the Z axis. Simple measures of pore anisotropy can be obtained from
the eigenvalues of each pore’s tensor of inertia; for example the ratio: max1=(min2 +
min3), or those introduced in Section 1.2.1. The corresponding eigenvectors are the
object’s principal axes.
3. Mixture quality estimation with several species.

An “inter-penetration” measure of two or more species may be estimated in several ways:
(3.a) By contact area or area of the inter-species boundaries (i.e., the area of the interfaces
between different-species components): a high contact area corresponds to high inter-
penetration and low segregation.
7
An erosion operation thins objects, shrinking them into points, filaments or membranes, while dilation thicks objects
and fills gaps. Topology changes usually arise after combination of these operations. For example, erosion-then-dilation
(or opening) splits weak connected objects, widens concavities and filter small particles, while the dilation-then-erosion
(or closing) connects close objects, and remove small holes.
(3.b) By local inter-species topology characterization; for example, the average number of
neighbors < NN > of different species. With 3 species and a fcc grid (6 faces), an
optimum value of < NN > would be close to 2 (in average), which corresponds to
“perfect” inter-penetration through the bulk. These measures may be taken only at the
species interfaces, or through the whole bulk volume.
(3.c) By granulometry analysis per species, followed by comparison of residual size distri-
butions for different sets of parameters: very sparse and small residuals (or none) corre-
spond to low segregation and high mixture quality; big residuals indicate high segregation
and poor mixing of the species.
4. Deposit characteristics evolution, as a function of one specific parameter.

Deposit simulation of a single species may include a label per site, as noted in the Introduc-
tion. This label can be an integer value in the interval 0 255] for each site, representing
an in situ variation of some varying parameter recorded during one single simulation, or for
many accumulated simulations with the same initial conditions. An input look-up-table would
f g
map the integer values 0 : : : 255 to the real physical model values for a later correlation
analysis. In this particular kind of labeling, each isovalued bulk layer is analyzed and visual-
ized separately, allowing to make a sequence of “level sets”, in function of the time-varying
parameter (see Figures 5.10 and C.1). While studying the effect on bulk features of particu-
lar time-dependent variations (of temperature, precursor rate, or any order parameter), phase
transitions and critical states, if present, may be detected and further studied.
Lz1 Lz2
Figure 5.10: Deposit evolution (one species), as a function of the changing parameter L (e.g., lumi-
nance). In this example, gray-level labels encode at each site a parameter value from L z1 to Lz2 , with
z1 z2 as functions of height, in monolayer units. Early nucleation dynamics is expected to shape
bulk and surface characteristics (compare early (light) and advanced (dark) profiles after growth).
5. Top-surface roughness of the deposit.

There are two posible definitions for the external or top surface of a deposit: the last-layer top
surface , and the projected top surface .
The last-layer top surface takes into account the meanders and overhangs and is constituted
by the last deposited layer of adatoms. It is denoted as:
@ Vjz last
(5.4)
and is an open surface (see Figure 5.11). For a precise definition, we consider the background,
constituted by a closed surface including the scene boundaries in contact with the deposit, and
Vj U
including the last-layer top surface; we denote it as @ c zlast (see Figure 5.8a). Let @ be the
box bounding volume of the scene (a N x Ny Nz parallelepiped). The last-layer top surface
is then defined by:
@ Vjz = opface(@ V cjz

last last
n @U ) (5.5)

where the opface( ) is the opposite face operator, which swaps the face orientation interpreta-
tion from u+ to u; , and u; to u+ , with u 2f g
x y z .
The projected top surface of the deposit V is the set of surface points seen from infinity, and
simply denoted by height z = f (x y ) (or alternatively, the intensity image z = I (x y ))), and
in discrete coordinates, x = i = 0 : : : (Nx ; 1); y = j = 0 : : : (Ny ; 1). In a formal
definition of f (x y ), let ]a b denote the open set from a to b, then:
f (x y) = fz j (x y z) 2 @ V and ]z 1 V c g (5.6)
In practice, projected top surfaces are easily calculated from projecting a vertical line from
the upper bounding plane z = N z down to the deposition volume, for each pair x y , and
V f g f g
reading the first intersection with @ to build an array f (i j ) = h ij (see Figures 5.3,
Vj
and 5.11). We also denote @ z=+1 the face-based representation of the projected top surface.
Vj Vj
Notice that in general card(@ z=+1 ) card(@ zlast ), and if meanders are important, @ zlast Vj
1
occludes itself and parts of it are invisible from z = + . Using these definitions, we propose
the following roughness measurements, which include the simplest measurements that can be
obtained using our 3D boundary-based approach:
(5.a) Surface roughness analyzed as image-intensity texture,

(5.b) surface density,
(5.c) average extrema width at mean height,
(5.d) mean width-to-height ratio and
(5.e) density of line intersections.
These measurements are examinated in the following paragraphs.
(a) (b)
z = f(x,y) z = f(x,y)
x x
Figure 5.11: Three-dimensional renderings of the z = f (x y ) projected top surface of a deposit. (a)
discrete surface rendering (facets of the fcc-lattice); (b) triangulated surface rendering. Simulation
data provided by the CNET; same simulation as in Figures 5.3, and 5.12.
(5.a) Surface Roughness Analyzed as Image-Intensity Texture

Interpretation of height z = h ij as gray-level intensity values for pixel (i j ) leads to
image representations of the projected top surface of deposits (see Figure 5.12). In order
to use frequency domain analysis tools (power density autocorrelation), a higher sub-

stratum size is desirable (at least 128 128 sites) to obtain more meaningful results
and reduce low-resolution artifacts (e.g., the Gibbs effect at the borders). Neverthe-
less, the roughness of low-resolution substratums may be studied with features other
than the RMS value of the deposit thickness (Figure 5.13). The most simple “texture-
from-roughness” features in classic image processing include: edgeness, obtained from
the image Laplacian, thus depicting slope properties, density surface per unit of vol-
ume, relative extrema density (see Figure 5.14) [Haralick92]. Gray-level co-occurrence
matrix (GLCM) features may also prove useful, as they depict second order statistics
of spatial correlations between pairs of separated pixel values (with height interpreted
as intensity). Two-dimensional extrema characteristics can also be estimated from one-
dimensional profile statistics through Integral Geometry tools (also known as Stereolog-
ical quantification [Weibel79a]). Some of these tools, applied widely in texture analysis
[Jain89, Chu90], include run-length statistics, density of line intersections, average ex-
trema width at mean height, and mean width-to-height ratio [Corkidi98].
Figure 5.12: Two-dimensional image display of the z = f (x y ) projected top surface of a deposit,
as visible from axis Z . Gray-level intensity represents height, and roughness details turn into texture
and shape features. Data provided by the CNET; same simulation as in Figure 5.3.
(5.b) Surface Density

In our discrete-boundary approach, several estimates of discrete surface are available,
with different accuracy/performance ratios. For comparison purposes, we are concerned
with relative measures. The simplest local surface-area measure is the number of bound-
N N
ary faces Nbf (p ) in a 3D neighborhood (p), for each point p 2 Vj
@ zlast , with
p = (i j hij) lying on the last-layer top surface (see Figure 5.3, at page 198). It is
thus defined as:
Nbf (p N ) = card( @ Vjz last

\ N (p)) (5.7)

As the deposit is small (50 50 sites), we have considered the 26-connected neighbor-
N

hood (p) = E26 consisting of 3 3 3 voxels. The average surface density is
2 Vj
the ratio < Nbf > =V (E26) = 1=27 < Nbf >, calculated on all p @ zlast . Other
possible first-order neighborhoods are shown in Figure 5.6, where each voxel represents
N
a site from the fcc-grid. By varying the size of neighborhood , a fractal dimension
describing roughness could be estimated from the log-log correlation between size and
surface density. We only estimated surface densities of the last-layer top surfaces with a
N
fixed .
(5.c) Average Extrema Width at Mean Height
(b) (c)
(d)
(a)
(e)
Figure 5.13: (a-d) Some profile measures related to surface roughness (any cross section through
axis Z ). (a) mean height < h > in monolayer units; (b) peak width at mean height; (c) valley width
at mean height; (d) RMS height-deviations from < h >; (e) mean free path at height h. Similar
measures can be obtained by exchanging the roles of deposit and pores as foreground/background.
(5.d) Mean width-to-height ratio of extrema. Corkidi, Marquez et al. recently introduced a
roughness quantification measure in surface-intensity images, the mean depth-width ra-
tio of extrema (MDWRE) based on a stereological approach [Corkidi98]. This parameter J ”MDWRE”
proved to be very useful as textural feature for the classification of metaphase images of
limphocytes in optical microscopy images. In the present work we changed the notation
and name convention of MDWRE, since we deal with physical heights, instead of inten-
sities, and also adopt the notation used in surface Physics. We thus introduce it as the
Mean Height-to-Width Ratio of Extrema (MHWRE). J ”MHWRE”
Haralick and Shapiro [Haralick92] have analyzed a simple and effective texture feature
proposed by Rosenfeld and Troy [RosenfeldVTA70]: the number of extrema per unit
area in row scans for a texture measure (Relative Extrema Density (RED)). We studied a
more robust feature sensitive to differences in the spatial distribution of specific extrema,
adapted for noisy and very low-resolution images, which appear as sub-sampled textures.
This feature is well adapted to very low-resolution surfaces from deposition simulations

(50 50 50 sites), where Fourier analysis is poorly suited, due to quantization artifacts.
Let us consider one-dimensional scans or profiles from an image; that is, 1D signals.
A single rough or wrinkle feature on a profile can be characterised by depth or height
(grey-level intensity) and width (separation between extrema). Instead of counting se-
lected peaks as the RED-like feature, we considered height-to-width ratios of all valleys
in all scans. Heights weighted by the inverse width of each valley permits selective fil-
tering of specific ratios, making MHWRE tunable to structural-induced texture at very
low resolutions [Corkidi98]. These lengths are also known in surface Physics as char-
acteristic width k and characteristic height ? . Thus, we measured the horizontal (for
width) and vertical (for height) projections of vectors and at each valley of the profile
(Figure 5.14), and summed their ratios in all scans. Notice that peak (or valley) height
;
i i = 0 : : : N% 1 is the average (? i + ? i )=2, and the peak (or valley) width i is
the sum k i + k i , with N% the total number of one-dimensional extrema (roughs) of the
object (either valleys or peaks).
The height selection ”window” consisted in testing the following conditions: a) the ratio
between the min/max vertical peak projections should be greater than 0.5 (approximate
value where the human eye distinguishes a roughness feature or wrinkle in textural im-
ages) and, b) the peak height (the average of the two vertical projections) should be
greater than a preestablished threshold of noise (smallest wrinkles):
X
N%
MHWRE = 1=N% wi %i
i=1
where
%i = ( ? i ++? i )=2
k i k i
and 8
> min(? i ? i )
max(? i ? i ) > 0:5
<1
> if
wi = > and (? i + ? i )=2 >
>
:0 otherwise
The window wi allows to measure only certain peaks (or valleys): those which are narrow
and depth enough.
(b)
ξ || ζ ||
(a)
(c)
ξT
ξ ζ ζ ξ
Figure 5.14: Characterization of roughness by relative extrema in cross sections through axis Z .
Valley left-side height (a), and Valley left-side width (b) are also the coordinates of vectors (left
arrow) and (right arrow) joining minima and maxima in scanline profiles. (c) Similar vectors
defining peaks. Simple features of roughness are derived from properly combining these measures.
(5.e) Meander Analysis. Traditionally, pores are more likely to be treated as internal cavities
or bubbles separated from the exterior of the bulk. In a closer look, many open pores usu-
ally contact the external surface, and all “true” surface features and pore features should
take into account interconnections that may tunnel deeply inside the bulk, the meanders
of the external surface are not visible in a vertical projection of the deposit (Figure 5.15b),
and are then often mistaken as pores. A meander is accompanied by a corresponding
overhang, the bulk portion above (Figure 5.15c). A complete, unbiased, morphological
characterization is possible by analyzing a true, “internal-and-external” surface, which
1
includes the projected top surface (the one visible from z = + ) and the non-visible
meander surface (which we called the last-layer top surface). Both approaches provide
two sets of measurements of porosity and roughness. Differential comparisons between
both sets should provide a measure of “meander-ness”, indicating how important are
interconnections between open pores and external surface.
z (c)
(a)
(e) (b) (d)

(f)
Figure 5.15: Dashed contour (a) represents a section profile of the projected top surface f (x y ),
1
as visible from z = + ; open pores (b) form surface meanders under overhangs (c) that may be
misinterpreted as closed pores (d) when the projected top surface (a) is extracted. When using a

f (x y ) representation, the observed deposit (e) (f) has neither meanders nor overhands (f), which
can lead to a misunderstanding of the underlying physics.
Table 5.1 summarizes a choice of:
Column 1: The physical properties to study.

Column 2: The simulation methods or protocols such as required samples or sequences in function of T ,
L, simulation parameters, etc.;
Column 3: The main features and measures to characterize them (there may be others).
All tests were done on a basis of data sequences in function of one parameter (T ) of about 8 volume
samples. Results were returned in sorted tables, and color GIF images. Analysis, interpretation and
presentation of morphometric and visualization results, in terms of the Monte-Carlo simulation and
the physico-chemical models, were performed by the CNET, with participation of the ENST. De-
sign of complex analysis, as granulometry, meander-ness, and percolation shall be further discussed.
Mixture quality analysis includes measures of species segregation and interpenetration. Custom or
in-detail studies such as specific visualization settings, granulometric sequences, or feature evolution
for in-situ variations, may be considered, after careful design of the simulation/analysis protocol.
Table 5.1: Table of microstructural features, method, morphometrical parameters and calculation
time. Bold names indicate those features actually measured on deposition simulations from the
CNET, in function of temperature T.
Physical feature Method/Protocol Parameters
Porosity(T) sequence 1 V , S , Number
Open porosity (T) idem V , S , Number
Pore distrib. Z (T) idem CM Z
Pore anisotropy (T) idem max1=(min2 + min3 )
Granularity(T) idem Histograms
Open granul.(T) idem Histograms
Percolation samples Local topology
Open percolation samples Local topology
Roughness(T) sequence 1 surf. dens.: 1=27 < Nbf >
Open roughness(T) idem surf. dens., MHWRE
Meanders(T) idem differences with/without TS
Granulometry samples Hist. openings
1 species visualiz. sequence 1 pore distrib.
Mixt.Qual.2 sp.(T) sequence 2 bulk distrib.
Mix.Qual.3 sp.(T) sequence 3 bulk distrib.
3 species visualiz. sequence 3 bulk distrib.
5.6.1 Other Possible Analysis

Scale invariance properties, described by fractal dimensions and critical exponents, have found
much recent attention in porous media and surface-Physics literature [Armin91, Armin94, Wong86,
Jacquin87, Ruffet91]. A pertinent example is a structure with a large surface-to-volume ratio, pro-
duced by intricate foldings found in networked pores or interfaces between different species. Owing
to the space-filling properties of fractals, a high fractional dimension of contact surfaces between
species phases imply high species interpenetration, hence, a high mixture quality. A second applica-
tion of fractals is the scaling behavior analysis of in pore structures, and features such as lacunarity,
defined in Section 1.7.1 would be employed. Nevertheless, the same as with frequency domain
(Fourier) analysis, in order to estimate fractal dimensions, self-similarity properties and other mul-

tiresolution features, a larger volume simulation is required, say 256 256 100 voxels. There are
many other measures useful in microstructural characterization, and some of them may eventually be
considered in our collaboration, but previous experience must be acquired before exploring further
possibilities. It has been noticed by the researchers of the CNET that, no matter how descriptive are
these morphological and structural features, interest in some of them depends on feasibility of their
experimental validation. This concern would require the development of stereological techniques for
5.7 Results 213
parameter estimation on slice samples, when it is not possible to obtain full experimental equivalents
of computer simulations of volumic data.
5.6.2 Visualization
Three-dimensional color renderings of internal structures allow to assess at once many of the afore-
mentioned features and their spatial distribution, and help to better choose which measures shall prop-
erly characterize the observed features. Visualization with the programs we developed may be highly
selective, allowing to render visible only certain specific components or slanted slices (stereotomies)
or sub-volumes, to make evident anisotropic trends or internal relations. With a sensible design of
the display settings, assigning color maps and intensity cues may quantitatively represent numerical
values (a local size density, for example) to convey information in a way that no table of numerical
measures or correlation curves may be able to do. In the long term, a simple visualization sequence
(animated, or in a mosaic display) may replace the trial of a high number of combinations of morpho-
logical/model parameter correlations. For example, a phase transition may be more easily detected
by visualizing in sequence the bulk simulations for different luminance sets: transition of one deposi-
tion mode to another may be gradual or discontinuous, being characterized by specific trends in pore
distribution, even if porosity remains more or less constant. In this example, simple rendering of the
pores themselves, in a set of simulations with a progressive luminance scale may allow to visually
detect at what value a transition occurs and what kind of morphological features it characterizes.
5.7 Results
We present in this section some preliminar results representative from our current collaboration with
the CNET. These include 3D renderings and data correlations with temperature variations. Some
simulation runs have been very time-demanding, and some features of the simulator of the CNET are
still in the development stage. At present, we have tested a small subset of the proposed measures to
evaluate bulk porosity (Figure 5.16), surface roughness (Figure 5.16), and inter-penetration quality
(mixture) of multiple-species simulations (Figure 5.16b).
Detailed reports of results concerning visualization, porosity distribution, roughness and their
interpretation in terms of the simulator can be found in [Pata97, Flicstein97, Guillonneau98].
5.7.1 Porosity, Roughness, Connectivity, and Anisotropy
5.7.2 Surface Density, Interfaces Surface

Note the lost of meaning of the classical RMS roughness measure in the last-layer surface of Fig-
ure 5.18a. Surface density describes better meanderness, but experimental validation works on a
top-projected-surface interpretation as in Figure 5.19b and c, presenting a ’visibility’ effect, if pho-
tons or electrons strike the surface perpendicularily to its plane. Note other characteristics of pore
distribution.
Figure 5.16: 3D-reconstruction of selected pores. Empty space and pores are rendered
in opaque colors, and the bulk (the deposition material) is transparent in the figure.
a b Color labels identify each pore. (a) All pores present in the amorphous photo-deposition
c d of a single species, at T = 450 K , and 20 monolayers. (b) Same as (a), with selection
of pores smaller than 5 atomic sites. (c) Rendering of the 20 biggest pores. (d) Idem,
from another point of view.
Numerical simulations from the CNET were obtained for varying temperatures Tn 2 f375400
450 500550 600650K g, with n = 1 : : : 7. A transition or critical temperature TC from high to
low porosity is easily located at the minimum of the distribution of porosity against temperature:
TC = argmin
T
( porosity (Tn) )
n

It is shown in Figure 5.20c, that is, at T C = 550K 25, at a resolution of 7 samples on a 275K
temperature interval (only four samples are shown).
There is also a “structural” transition between T = 400 K and T = 450K (See Figures 5.20a
and b); located at the temperature which maximizes the mean volume (or other size measurement)
of pores:
Tvol = argmax
T
( V olk (Tn ) ) with k = 1 : : : Npores:
n
5.7 Results 215
150 600
µm 3
*
Pore number (volume < 20 sites)
125 * 500
Porosity without meanders

100 400
75 300 *
50 * 200
*
25 100
* * * *
*
0 * 0
*
400 450 500 550 600 650 700 o K 400 450 500 550 600 650 700 o K
Temperature T Temperature T
600
µ m -1
µm 3
0.20
500
*
Surface density roughness

0.10
Porosity with meanders
400
*
0.08
* *
300
0.06
200
* 0.04
*
*
100 *
0.02
*
* *
0 * 0
400 450 500 550 600 650 700 o K 400 450 500 550 600 650 700 o K
Temperature T Temperature T
Figure 5.17: Porosity and roughness measures obtained from deposition simulations for
a b temperatures from T = 400 K to T = 675K . (a) Number of pores having a volume of
c d more than 20 sites; (b) global porosity, without meanders; (c) global porosity, including
meanders; (d) surface-density roughness in function of temperature.
Other state transitions could be analyzed in a similar fashion for other morphological or structural
parameters, and different simulation conditions. It is in particular interesting the rough to smooth
transition, which can be observed also experimentally by atomic force microscopy and refraction
index ellipsometry.
5.7.3 Interpenetration Quality and Segregation of a Three-Species Deposit

The mixture of three absorbed species in amorphous photo-deposition presented interesting features
during simulations, difficult to assess without a three-dimensional discrete representation. Once seg-
mented with one color label per species, each connected network of deposit material (one species)
can be visualized in isolation or together with the other species cluster. The results illustrate our
work with mixed species to show interpenetration and interface between different labels. Visualiza-
Figure 5.18: Top rough surface of amorphous deposition data. (a) Projected surface
at T = 400K , with several holes corresponding to meanders and overhangs. Some
a pores are shown. (b) Projected surface at T = 500 K , with holes blocked out to form
b a solid boundary. Empty space and pores are rendered in opaque colors, and the bulk
(the deposition material) is transparent in the figure. (Simulation data provided by the
CNET).
5.8 Conclusion and Perspectives 217
tions consist in cross sections of 3D segmented volumes and 3D renderings of them (bulk with any
combination of labels ”on” or ”off”). These results are summarized in Figure 5.21, for a 20-layer
photo-deposit and Figure 5.22. Porosity is rendered as voids, whose cardinality and morphology is
now relative to each species or combination of species, and is thus ”multiple-defined”, since 0-voxels
(voids) share neighboring sites with labels from different species.
5.7.4 Experimental Validation

There are two aspects concerning validation, the analytical methods per se, independent of data, and
the morphometrical data themselves (simulator and modelling).
Validation of the analytical methods on numerical data has already been done for many morpho-
metrical parameters extracted by our 3D software, using synthetic shapes or phantoms in discrete
grids. More sophisticated computer phantoms, for texture and complex growth modeling, have been
recently tested for binary or multi-valued labels given by Monte-Carlo simulations of Diffusion Lim-
ited Aggregation (DLA) with relaxation [Witten81, Armin91, Armin94]. A brief exposition is given
in Appendix C. Even with very simple particle interactions, they can emulate some features of
complex morphology similar to many real aggregation processes (Figure C.1). Their morphological
characteristics per se have been controlled to a certain degree, first without reference to a particu-
lar physical phenomenon. With a proper integration of physico-chemical constraints, they may be
eventually be related to the amorphous deposition models and simulations from the CNET. We have
also noticed that aggregation and deposition process, 3D texture simulations and DLA model char-
acteristics relate very closely and could be modeled with those of random Markov fields, at least
qualitatively. It remains to investigate more closely this relationship.
For the data series, experimental validation techniques exist in some cases. In particular, RMS-
roughness and porosity can be measured from ellipsometric analysis and other techniques during
a real deposition. This provided recent validation of the simulator and the theoretical model behind,
for both characteristics [Guillonneau98, Flicstein99]. In order to apply all other analytic methods to
real, experimental data (mainly to validate the physico-chemical models and their simulation imple-
mentation), three-dimensional digital samples should be extracted. For example, a per-slice image
acquisition should be first implemented from X-ray diffraction, Rutherford Back-Scattering (RBS) or
TEM/SEM techniques [LAFEM92], then a 3D alignment of image slices and a 3D-image segmenta-
tion process should all be performed, in order to attain the same starting condition as with computer
simulation data (ie. digital volumes in a fcc grid). Otherwise, if no direct comparison of simula-
tion and real experimental results is possible, some real-deposition features can still be estimated by
stereological analysis of slice samples, or other indirect measurements.
5.8 Conclusion and Perspectives

Quantification performed on simulation results of amorphous or crystal photo-deposition will al-
low researchers of the GMSPO-CNET or similar groups to assess, on a selective basis, the size
and shape of pores and deposition clusters, the porosity and feature distribution in function of tem-
perature or other parameters, and the inter-penetration quality of multi-atom species simulations.
Visualization of bulk and parameter distribution in space should also provide efficient, global qual-
itative evaluations of complex structures and phase transition phenomena, in response to different
parameter settings of simulations. On an interactive basis, visual cues may guide the selection of the
morphological analysis to be applied, help as a feedback of the simulation conditions, or assist in
computer implementations of new improvements to the deposition models. In short, the final goals
of 3D quantification of computer simulations are: (1) to reduce the time and cost of experiments,
(2) to help understanding of simulation process and their parameter dependences and (3) to provide
numerical means for testing, through simulations and experiments, the theoretical models.

Figure 5.19: True rough surface and complement of the bulk of a 50 50 90 deposit at
a b T = 375K . (a) Last-layer surface, with meanders and overhangs. No pores are shown.
(b) Projected surface without meander voids (similar to Figure 5.18b). (c) Pores and
c d meander voids interpreted as “open” pores. Subfigures (b) and (c) constitute together
the complement of the bulk. (d) First 100 biggest pores, when identifying and separating
large meanders (not shown). (Simulation data provided by the CNET).
Figure 5.20: 3D reconstructions of amorphous deposition in function of temperature.

(a) Surface and pore distribution at T = 400 K , with several connected components
a b and 100 Kcycles (about 100 monolayers). (b) Surface shape and pores formed at T =
c d 450K , (c) at T = 550K , and (d) at T = 650K . Empty space and pores are rendered
in opaque colors, and the bulk (the deposition material) is transparent in the figure.
(Simulation data provided by the CNET).
Figure 5.21: Mixed species. Axial sections of a photo-deposit at heights (a) z = 2, (b)
a b z = 10, (c) z = 20 and (d) z = 24. Contours of level-set (regions in black) account for
c d surface waviness. Color represents each species: Si in yellow, N in red and H in blue.
See also Figure 5.22. (Simulation data provided by the CNET).
Figure 5.22: Mixed species. (a) Clusters of amorphous photo-deposition of three species (Si in
yellow, N in red and H in blue.), and one single connected component by each species. Occupied
sites (the bulk) are now rendered in opaque colors and empty space and pores are transparent. See
also Figure 5.21. (Simulation data provided by the CNET).
Conclusions and Perspectives
The present work comprise an exploration of complex-shapes and complex-structure character-

istics in 3D, and a development of several methods of representation, processing, visualization and
morphometric analysis based mainly on discrete boundaries. These methods can take into account the
potentially arbitrary nature of complex shapes. We have further applied some of them in two specific
applications, one in Biomedicine and another in surface Physics where complex-structure features
are present: the extraction of the blood-vessels of the lungs from serial slices at high resolution, and
the analysis of 3D data from simulations of amorphous photo-deposition.
Previous personal experience in other applications, mainly biomedical, guided some of the topics
presented in chapter 1 and 2. Since literature abounds in multiple meanings of “complexity”, and nu-
merous shape features exist, it was difficult to choose or to build a guiding thread from the beginning.
Boundary representations themselves (the “main thread”) may not be well-defined for fractal objects
and R3. We noted that several definitions or calculations must be adapted or radically changed when
passing to discrete spaces (e.g., connectivity, solid interior, normals, surface area, etc.).
From the conclusions already drawn in each chapter, we summarize here our most relevant con-
tributions:
✦ To our knowledge, very few works have tried an exhaustive exploration of the concepts charac-
terizing structural complexity. Chapter 1 constitutes an overview of literature from many fields
where we identified common properties of complex features, without attempting any indepth
description (which can be found in the cited references). Number of components, features,
local coherence, dimensions and lenght of descriptions are key characteristics, together with
the relative absence of one or many of several invariances (scale, topologic, geometric, etc.).
We linked several of these concepts with our boundary-based approach (Chapter 2) and the
solution of specific problems in Chapters 3, 4 and 5.
✦ Boundary-based descriptions (or b-reps) constitute another key concept in our work, and sev-
eral features can be defined or mesured from boundary information. We implemented some
processing and analytic methods based on b-reps, and made use of both, the face-based bound-
O O
ary @ of an object and its voxel-based boundary O. Facets allow to define and obtain
estimations of the local normal, which was used for visualization, and has a high potential for
analysis in the normal directions of the local surface boundary. In the other hand, voxel-based
boundaries allow for example to define and perform mathematical-morphology operations.
✦ Regional-based descriptions were not explored enough by us to make a useful comparison

with b-reps, but we used a hybrid approach in the segmentation of the vascular (blood-vessel)
pulmonary tree, by applying region growing and boundary extraction, from which a refined
segmentation was obtained.
✦ A tool related to regional analysis is the moving-discrete neighborhood known as rolling buffer
or sliding window. We used a 2D-implementation of this tool to scan adjacent images for local
226 Conclusions and Perspectives
color-histogram analysis. A 3D-version was employed in a preliminar implementation for a

Central-Axis detector in tubular structures.
✦ We were the first group reporting the radiometric inhomogeneities of the Visible Human
Project database, and proposed an original method of correction, by analysis of locally differ-
ential images. The method itself exploites a feature examined in Chapter 1, that of structural
coherence. We also deviced several color visualization methods to make evident the inhomo-
geneities in the serial images.
✦ We were also the first group to obtain automatic extraction of a substantial part of the vas-
cular pulmonary tree of the VHP. There are several reasons for the lack of bibliography: (i)
the radiometric inhomogeneities that make the use of global and local segmentation methods
unadapted, and (ii) the size of the volume and the nature of the data which are only avail-
able since 1995. Our results remain to be validated, since no measurements and comparable
segmentations of the same dataset exist until now in literature.
✦ The amorphous-deposition application in collaboration with the CNET gave us the opportunity
to demonstrate the pertinence of some features and means to quantify them; these include
boundary-interfaces, and the taking into account of meanders and overhangs, which are not
traditionally studied, due to lack of analytical tools (existing literature in this kind of analysis
do not report comparable methods). We exploited local connectivity properties at the atomic
-site level to extract large-scale, topological features of voids (pores). We proposed several
ways to characterize porosity and roughness, and tested some of them with success. Finnaly,
3D-visualizations of labelled volumes further allowed to make evident critical transitions with
temperature variations in the bulk morphology and the pore distribution of several simulation
runs.
To mention further perspectives of our work, we require an understanding of our failures and the
recognition of the weak points of the present work:
✦ Since a great quantity of topics were treated or approached at the same time, some lack of
deph and organization resulted. A more natural strategy for such a general subject would be
the constitution of a line of research in 3D analysis and visualization of complex objects. This
was, as stated in the Preface, our personal objective, but the lack of an effective collaboration
in various fields and the difficult in obtaining numerical data reflects how ambitious the task
was.
✦ The Geometry of Digital Spaces (as termed by Herman et al., [Herman98]) is a very recent
field of developpement in which discrete Mathematics play a fundamental role. We did not
presented nor used some important concepts (e.g. Jordan paths and graph representations), and
did not give enough emphasis to topological notions in N 3 (e.g., simple point remotion), which
are timely notions in complex shape modeling and manipulation. Further work is required in
this direction to fully exploit b-reps, processing, analysis and visualization using them. Some
other concepts were only drafted or used scarcely (e.g. geodesic neighborhoods and the run-
lenght compression nature of the face-based boundaries).
✦ We presented only few quantitative results (data tables and graphics), and chose rather to have
first a qualitative evaluation of various algorithms, through 3D renderings and other visualiza-
tion modes. Other numerical tests and performance were indeed done to validate and evaluate
boundary extraction, processing and morphometrical methods, but not presented here due to
time limitations.
Conclusions and Perspectives 227
✦ We did not exploit all the color information present in the VHP images, and we did not demon-
strated that the red channel indeed is the only useful information in this case. Principal Com-
ponent Analysis and adapted Color Space representations could be employed for this set of
data. A 3D morphological approach is feasible, extracting and examinating the structures in
color space of the clouds of color points.
✦ Some quantitative work remains also to be done, such as comparing time processing of a whole
scene against processing of only the boundaries of the objects of interest (the superiority of the
latter seems evident but overheads in boundary traversal have to be carefully estimated, for
example).
✦ Computer implementation of the user interface in particular requires improvements and some
work remains for a full exploitation of our software and their integration within the ressources
of the TSI Department.
Topics that represent other interesting tracks to explore in future works include the following:
✦ Many of the concepts characterizing complex shapes, such as fractals, shape factors, Kol-
mogorov Complexity and other constitute an unexplored field of potential morphological fea-
tures in which analytical methods based on discrete boundaries may prove very valuable.
✦ Strong relationships between object structure and texture were indicated at several points of
this thesis, e.g. the coherence principle used for radiometric homogenization, the components
of the bronchial blood-vessels that become “background” texture at a given resolution, and the
pore distribution in amorphous photo-deposits. It would be valuable to explore the transition
between one and another, and study the relations between textural features and shape features
in rough surfaces, for example.
✦ Various ideas for tubular-structure detection and Central-Axis-Tree extraction were proposed
and preliminar implementations are on course. These should allow a throughout exploration
of branching structures in the lungs and their morphometrical analysis (diameters, lenghts
and bifurcation laws). Some of the presented methods (see Appendix B) are complementary
approaches to contour tracking and snake approaches, and interesting comparisons could be
done.
✦ Local neighborhoods combined with either regional representations (Central Axis Tree, or Me-
dial Axis Transform in the case of a tubular branching structure), or boundary representations
constitute a subject with high potential, in view of geometry-driven analysis and scale-space
representations which were not treated in the present work.
✦ Due to the lack of experimental data we explored very briefly the synthesis of complex objects
by Monte Carlo methods (such as those produced by Diffusion-Limited Aggregation simula-
tions in 2D and 3D), in order to obtain various complex-structure situations in which analytical
tools may be tested (see Appendix C). In such a case, b-reps serve not only for analysis of data
but for simulation purposes. This research track is however a subject belonging to model-
ing objectives, in which physical information has to be included, in order to obtain realistic
models.
Along this manuscript we saw how discrete boundary representations are present and timely
in several fields in science and engineering, and we believe that our contributions can be further
extended and exploited in the characterization, analysis and visualization of complex data.
228 Conclusions and Perspectives
Appendix A
Further Definitions of Object Subsets

and Boundary-Related Subsets
In this section we introduce further concepts and definitions concerning interiors, sub-boundaries,
cavities and their organization. Some of them are used to describe complex features, specially in
Chapter 1. We propose also some equivalent concepts in discrete spaces, in Chapter 2. As with with
the preliminar notions of Section 1.1, general references are [Weisstein98, Kiyosi96a, Kiyosi96b,
Iyanaga68, Koenderink90, Coster89, Barnsley88, Herman98, Klette98]. We examine first the notion
O
of Solid Interior of an object .
Solid Interior of an Object

In this work we are in particular interested in boundary representations and other definitions that use
them. Some difficulties arise when trying to define what is the interior of an object O Rn, ex-
pressed in terms of its boundary, even when it has one-single connected component (no cavities). We
choose to avoid altogether a formal definition of Solid Interior in the continuous case, assuming that
O
it is equivalent to the object itself, as a set of points which define it, given only the information of
O
its boundary @ , when such representation is possible. In the discrete case, several “filling” methods
O
exist to find points inside @ , and we give Definition 2.15, page 96. When cavities are present, but
the largest boundary is considered, then the solid interior is the object plus its “filled” cavities, includ-
ing thus all voids bounded by sub-boundaries geometrically bounded by some connected component
O
of @ . Figure A.1 illustrates solid interiors, cavities, fragments and nested boundaries, introduced
later.
O
We denote such a representation of , its “solid interior”, and use the following notation:
interior(@ O) (A.1)
To be more precise, and firmly set the foundations of some concepts later introduced, we would
require an operational definition, which does not exist, to our knowledge, for the general case of any
object O O
Rn. If has one single boundary, we may try to express such a solid interior as:
interior(@ O) = fp 2 O j 8 p 9 T : Rn ! Rn 9 q 2 @ O such that p = T (q) g

(A.2)
230 APPENDIX A. Further Definitions of O Subsets
T
This presuposes the existence of a method or function which describes (and allows to find) an
infinite set of points p2O 2 O
, given some q @ . This makes better sense as a limit-process of a
discrete representation, but also has several problems.
T
An example of such in 2D is the classical test of a point p as belonging or not to the interior
O
of , by considering the integral of all subtended angles bewteen p and all contour points q @ . 2 O
If this sum is 0, then p2O , and such test may take into account voids and nested boundaries, if
oriented contours are defined.
Definitions in terms of Cauchy sequences, accumulation points and other entities would be also
possible, but several discontinuous, fractal objects pose an operational-definition problem which is
to-date an open issue, not treated here. To be strictly formal, we may restrict our study for objects
T
where such a can be found even in implicit form (v.g. most smooth objects, deterministic fractals
and other sets), and take equation A.2 as an operational definition of solid interior.
O
For an object with several boundary components @ , the latter definition is extended to include
points p 2O O O
c , inside the cavities of , and inside the main, largest boundary component of (see
Figure A.1). This solid interior blocks out the cavities and gives a set of points spatially containing,
O O
but different from itself, if we take only one connected component of @ , containing all other.
This will be precised later with “nested boundaries” and the “outermost boundary”.
(a) O (b)
kO
interior( kO
)
O O
Figure A.1: (a) An object with cavities; its boundary has several components, such as @k . (b) Solid
O
interior of @ k ; cavities are “filled”. See also Figure A.2.
O
Even if no cavities are present (one-boundary component), a distintion between and its solid
interior arises in discrete representations where discrete boundaries are sets of facets or voxels, etc.,
which have a finite extension. A useful operational definition is given in Chapter 2 (see Defini-
tion 2.15), in terms of local discrete orientations, and will allow to extract the solid interior of an
O O
object , given only its boundary representation @ . This definitions can be extended for a multiply-
defined boundary and negative boundaries.
T O
We finnaly note that, for feature extraction, something equivalent to an operator (@ ) do exists
in differential geometry: boundaries that can be described by analytic functions may be used to
extract some morphometric features of an object, using for example the Green Theorem in 2D and
Gauss theorem in 3D (which expresses a volume integral in terms of a surface integral defined by
boundary of the region in question). Thus, information from the solid interior of such may beO
obtained from its boundary specification.
APPENDIX A. Further Definitions of O Subsets 231
Nested sets, Cavities and Solids

We introduce in this section nesting relationships, which allow to describe several ways in which
boundary sets may be organized to form cavities and unconnected components, and other elements
of a solid.
D EFINITION A.1 (Sub-Boundary)

O
Let be an object whose boundary is composed by N @ connected components that we denote as
S
O 2 O O
@j , with j 1 N@]: Thus, @ = Nj=1@ @j . The subsets @j are called a boundary O
component or sub-boundary of @ iff O
(8i j 2 1 N@ ] i 6= j ) ((@i O \ @j O ) = ∅ ) ^ (@j O is a closed surface):
O
Note that not any subset of @ is a sub-boundary. We also express N @ as the cardinality of the
O O
boundary, that is, N@ = card(@ ). The solid interior of @ is then defined also as:

N@
interior(@ O) = interior(@j O ) (A.3)
j =1
We will describe in Section 2.4.4 an explicit method to find the discrete solid interior of a given
boundary, using horizontal run-lengths. The method is also equivalent to discrete volume traversal,
volume filling, or 3D flood of region boundary. Such a boundary may be that of an object , or any O
of its fragments or cavities, as defined later.
Let @ = N
S
D EFINITION A.2 (Nested Boundary)
O O
j =1 @j , a boundary consisting of multiple-connected, closed components. A bound-
@
O
ary component @i is a nested boundary of @j Oiff interior(@i )O O
interior(@j ), for some
2 6
i j 1 N@], with i = j .
We also say that @i O is embedded or nested within @j O (for some i j with i 6= j ), or that @i O is a
child of @j O and @j O is the parent of @i O. Figure A.2a and Figure A.3b show an example of nested
boundaries.
N OTATION A.1 (Symbol “is nested within”) We introduce the symbol “b” to represent the ex-
O O
pression “@i is nested within @j ”:
(@i O b @j O) = (interior(@i O) interior(@j O) )

Remarks. All the properties of the relation symbol “ ” are inherited by “b”. The symbol b means 6
“not nested within” or “not a child of”, etc. Symbol “c” applies in reverse order, meaning the relation
“is parent of”.
D EFINITION A.3 (Direct Child)

O
Let an object with N@ boundary components @ i , with i O 2 1 N@]. Let @iO b @j O . We say that
O O
a @i is a direct child of @j iff
( 6 9 k 2 1 N@ ] ) (@i O b @k O b @j O) (A.4)
otherwise, @i O is called an indirect child of @j O, and @k O is an intermediary child between @i O

and @j O. Similarily we define direct and indirect parent.
In the example for 2D boundaries of Figure A.3b-f boundaries 20,24 and 26 are indirect children of
O
@1 , while the 32,33,34 and 35 are direct children of @19 . O
D EFINITION A.4 (Negative Boundary)
A boundary component @ k O O
@ is a negative boundary if it has no solid interior, i.e, (interior(@ k O)n
O
@k ) ∅.
Remarks. An analytic formulation of oriented boundaries could also be employed for defining
signed boundaries, if certain regularity conditions are satisfied (e.g., to be a regular and continuous-
O
differentiable mapping). In that case we could define @ as “negative” if a certain surface integral
satisfies: ZZ
V (O) = ~f (s) ~n ds < 0
@ O
n the outer surface normal vector at each p 2 @ O, with k~nk = 1; ds is the surface differential
with ~
element, and ~f (s) a vector function such that jV (O)j is the volume of O.
A non-empty and closed boundary @ k O @ O is called a positive boundary iff it is not a
negative boundary (i.e., (interior(@ O) n @ O) = 6 ∅). We also call the solid interior of a positive
boundary its positive interior, and use notation: interior @ O = interior @ O. Important remark:
+
we reserve notation @ and @ for other purposes. To indicate that a subset @ k O is a positive (+) or
+ ;
a negative (-) boundary, we use the notation “@k O ” and “@k O ”, respectively, which is consistent
+ ;
with the following definitions.
D EFINITION A.5 (Fragment of an Object)

O O
Let @k + @ be a positive boundary, with k = 0 : : : N @ indexing all boundary components of
O O O
@ . The set k+ = interior @k + is called a fragment of . O
O
Remarks. Fragments of an object are connected components of the foreground , and if frag- O
ments have no nested boundaries, = N @ +O O
k=0 k . Otherwise, we need to account for the cavities to
be defined in the following paragraphs. For negative boundaries we denote first their negative solid
O
interior, which allows to define cavities of . We again define it here as the set of points, found
O
from the boundary information @k ; . An operational definition, as with solid interior, is possible in
discrete sets.
N OTATION A.2 (Negative Solid Interior)

O O O
Let @k ; b @ be a negative boundary component nested within @ . The negative solid interior
O
of @k ; is denoted by:
interior; (@k O; ) (A.5)
O
Note that it is different from the positive solid interior of ; , which may correspond to all
p 2O O
c if @ has a single connected component. Together with the boundary componenet itself,
O
the negative solid interior of @ k ; constitutes a cavity of : O
D EFINITION A.6 (Cavity)
O O O interior (@k O ) @k O is called a cavity of O.

Let @k ; b @ . The set k; = ; ; ;
Cavities of an object O are connected components of the background O c (not necessarily all of
them) including negative boundaries of the object. We also define the solid exterior of @ O as the
complement of its solid interior 1:
1
Recall that no formal definition was given for solid interior for continuous sets.
(a) (b)
1O 2O 13 O 2
O out
19 O
O
12
O
5 5 O out
6O [ O1 ] = interior( O )
1 out
(c) (d) (e) (f)

p q q
q q’
p
p q’
+ = interior+(
O19 19 O
)
p’
+=
O19 interior+( 19 O
)
p’
- c
O 6 = interior - ( 6O
) O6 = exterior( 6O
)
Figure A.2: Nested boundaries and interior sets in 2D. (a) Object O
with multiple-connected, closed bound-
O SN@
O O
aries: @ = k @k , where N@ = card(@ ) = 43. Shaded area represents the solid interior of @ ; O
O O O
boundary @19 is nested within @ 6 , which is in turn nested within @ 1 . Boundaries 6, 12, 13 are examples
O Oj
of negative boundaries, and boundaries 1,2,5 and 19 are examples of positive ones. Their solid interiors form
respectively some cavities and fragments of . (b) Outmost boundary @ out , composed of five connected
components, which are non-nested within other boundaries. (c) Solid interior of @ 19 , (d) Interior of bound- O
O O O
ary @1 9 . (e) Solid exterior of boundary @6 . (f) Note that 6c = exterior(@6 ). Notice the intersection O
properties of points s (pq 2 \O 2 O
), for some p q @19 , for example. These intersections may characterize
O O
smooth interiors, but may not hold for irregular objects. (f) Note that an “exterior” of a sub-boundary may be
the complement of its interior, such as 6c = exterior(@6 ).
N OTATION A.3 (Solid Exterior)

O
Let @ be a 3D boundary composed by one connected component. The solid exterior of @ O is
denoted by:
exterior(@ O) (A.6)
D EFINITION A.7 (Absolute Solid Interior)

O O
Let @k b @ be a boundary nested within @ , with k O 2 1 N@]. The absolute solid interior of
O
@k is the set:
jO j jinterior j(@k O ) = ;

(A.7)
fs j s 2 pq \ interior ;
(@k O )
interior +
( @k O ) g
8 pq2@k O
p6=q
1O 2O 13 O 30 O
(b)
O
32
O
+
(c) O1 2 3 4 5
19 O
(d) 6 7 8 9 10 11 12 13 14 15 16 17 18
6O O 12
O
23
5
O
O (e) 19 20 21 22 23 24 25 26 27 28 29 30 31
38
(f) 32 33 34 35 36 37 38 39 40 41
(a)
(g) 42 43
Figure A.3: Tree structure representation of nested boundaries in 2D. (a) Object with multiple-connected O
O
closed boundaries: @ = N
S @
O O
k @k , where N@ = card(@ ) = 43. (b) Subset organization as a containment
O
tree structure; nodes represent each boundary (or component ); for clarity only indexes are shown. (c)
First branching level corresponds to outmost boundaries 1-5; levels (c),(e) and (g) contain positive boundaries
(fragments) and levels (d) and (f) contain negative boundaries (cavities).
O
Remark 1. The exterior of @ excludes the boundary itself, and it is the complement of the solid
interior. For boundaries without cavities, interior(@ ) O O
and exterior(@ ) c. O O
Remark 2. In union-set operations, the solid interior of a negative boundary is to be subtracted.
These definitions allow to treat in a consistent fashion objects with nested cavities and non-connected
components. A consistent connectivity remains to be included for the discrete case.
Remark 3. Operational definitions of discrete volume and discrete surface are given in Chapter 2.
We only note here that we define the volume of a negative solid interior to be a negative quantity
O jj
V ( k; ) < 0, where V is the volume contents of the absolute solid interior k; . jO j
A boundary consisting of N @ multiple-connected and closed components can be partitioned into
N@+ positive and N@; negative boundaries, with N@+ + N@; = N@ :

N@
N@
@O = @i O @j O (A.8)
i=1 ^ j =1 ^
(interior(@i O)n @i O)=∅ (interior(@j O)n @j O)6=∅
or using notation with superindexes (N @+ N@; O O

+ ; ):
+
N@; N
@
@O = @i O ;
@j O+ (A.9)
i=1 j =1
O O
When considering the corresponding solid interiors i j (positive or negative) of nested bound-
O O
aries, that is, fragments or cavities of , we have also nested objects and say that “ i is nested within
O O O
j ”, and represent this property by the expression i b j , which is a slightly stronger condition
O O
than i j if we consider cavities and fragments as belonging or not to each object. In practice
we consider negative boundaries nested within a positive boundary (nested cavities), or conversely
O
(which define solids within cavities). That is, i b j . O
Remarks. We formulate remaining definitions using condition “ i O Oj ”, rather than “Oi b Oj ”,
which needs further study.
D EFINITION A.8 (Empty Fragment and Empty Cavity) A fragment (or cavity) i = interior (@i O O ),
with @iO O @ is called empty fragment (or empty cavity) if it has no children (no nested subsets).
82 6
That is, ( j 1 N@ ] j = i) j
O 6 O
i.
Remarks. In R2 and R3 a containment tree structure representation of @i i = 1 : : : N@ , fO g
empty fragments (cavities) are leaves (terminal nodes).
We define also the external or outmost boundary as the union of connected boundary components
in whose solid interior lay all other nested boundaries; i.e, those boundaries which have no parents
(see Figure A.2b and Figure A.3c):
Let @O S O S
D EFINITION A.9 (Outmost Boundary)
+
= ( Ni=1@ @i + ) ( Nj =1
;
O
@ @ ; ) be a boundary consisting of multiple-connected closed
j
components (fragments and cavities which may be nested). The outmost boundary of is the set: O
@ Ojout = f@k O+ @ O j k 2 1 N@+] ^ (A.10)
(8 j 2 1 N@ ] j 6= k) @k O 6 interior (@j O)g
Oj
That is, @ out is the set of all boundary components that are not children of (i.e., not nested within)
other boundary components (we restricted the definition positive outmost boundaries). The outmost
boundary is also defined as the boundary of the union of all solid interiors, excluding the cavities
(which possess negative interior):
N@+ N
@
;

@ Ojout = @
interior+ (@i O )
+
n interior; (@j O; ) (A.11)
i=1 j =1
D EFINITION A.10 (Filled Interior)
O
The filled interior of is the set: O] = interior( @ Oj out ).
D EFINITION A.11 (Principal Background)
The principal background, or principal exterior of O (or principal component of Oc ) is the set
O Oj
]c = (exterior( @ out )).
O Oj
Shaded areas of Figure A.2b represent ] = interior( @ out ). Note that ] describes an object O
O
with all its cavities “filled” or blocked out; that is, ] c is a connected set (one connected-component
object). Porosity of an object can be characterized by studying the filled interior and the solid interior
of its boundary. We can define for example a porosity measure as the ratio:
porosity = volume(interior(@ O))

volume(interior( @ Ojout ))
(A.12)
In Chapter 5.1 we have done some work with discrete open boundaries (interfaces), but we just
give a provisional and intuitive definition for the continuous case:
D EFINITION A.12 (Open Surface)

Let Q O C Q
@ , and let @ = @ be the set of border points of Q. The set Q is a connected open
surface or a boundary patch of O C6
iff @ = ∅.
C
In physical objects, basically in region transitions, @ consists usually of closed contours. Surface
C
phenomena, textures and surface patterns may produce @ consisting also of clouds of points, fila-
ments or paths on a surface boundary.
From the notion of open surfaces, we are able to give a definition for interface boundaries,
through the notion of restricted boundary, but first introduce some notation conventions.
N OTATION A.4 (Set Restricted to “Condition”)

j
Let A any set. The set A condition A is called set A restricted to “condition”, where “condition”
2
is a mnemonic for a rule to select P A elements p A or PA sets Ak
A, with k 1 MA], for 2
some PA MA N. 2
j
Remarks. For example, R3 z=z0 can denote the set of points in the plane z = z 0 , for some z0 2 R.
N OTATION A.5 (Restricted Cardinality)

Let A be a finite set; let NA = card(A), its cardinality. The number N A condition j
NA is called
cardinality NA restricted to “condition”, where “condition” is a mnemonic for a rule to select P A S
2 2 j
subsets Ak A, with k 1 MA ], for some PA MA N, such that NA condition = card( Pk=1 A Ak ).
j
Remarks. Depending on how is it formulated, the “condition”, finite sets A A condition, and the
j j
numbers NA = card(A), and NA condition in general satisfy NA condition = card(A condition). For j
j j
example, let A = 0 5], and A k>3 , then NA = 6, and NA k>3k2A = card(A k>3 ) = 2. j
Oj
N OTATION A.6 (Restricted Boundary) The set @ condition O
@ is called boundary @ re- O
stricted to “condition”, where “condition” is a mnemonic for a rule to select p @ or boundary 2 O
O 2
components @k , with k 1 N@ ].
Oj
When @ condition is an open surface, we call it a boundary patch. The outmost boundary @ out is Oj
an example of restricted boundary that remains closed. Empty cavities and fragments are restrictions
to a “no-children” condition. Examples of open-restricted boundaries (boundary patches) are the
O O
boundary interface components between foreground regions A and B from Definition 1.7:
@ OAj B @ OB j A = @ OA B
O O \ (A.13)
O
To identify the case of two labels A B on a single object, we shall use notation @ A\B . For inter-
VW Vj
faces between two objects , we use either @ W , or @ V .Wj
From the above definitions it is clear that multiple objectsSO P Q, etc., or different labels
A B C etc., affecting several regions of a single body O = k ABC::: Ok , give rise to much
=
more complex combinations of sub-boundaries, nesting, interior and exterior relations. Other con-
cepts in Nn (solid or voxel boundary, face boundary, internal and external boundaries, etc.) are
introduced in Chapter 2.
O
For a static physical object with one of its sub-boundaries @ 1 nested within another sub-
O
boundary @2 , we have @1 O O
2 , which express that cavities can only contain fragments as
their direct children (and conversely).
We may however consider nested boundaries of the same sign when comparing two objects, or
when comparing the same object and its boundaries before and after successive transformations. To
that end we define:
D EFINITION A.13 (Evolving Objects, Evolving Boundaries, Evolution sets)

O P P O
Let (t) be two objects, and let @ (t) , where (t) and @ (t) depend of a parameter t N (i.e., 2
O 6 O P6 P 6 O O
(t1 ) = (t2 ) , and @ (t1 ) = @ (t2 ) , for some t = t ). In either case, (t), @ (t) and @ (t) are P
2
1 2
said to be evolving in function of t. Let t0 : : : tn n N. The sequence
E n (@ P ) = f@ t0 P : : : @ tn Pg
0
( ) ( )
is called an evolution set of boundary @ P from t to tn . The sequences f@ O t0 : : : @ O tn g and

( ) ( )
fO t0 : : : O tn g also form evolution sets.

0
( ) ( )
Note that the object O t itself can be the result of a transformation: O t = T (O t ), for some
() () ( ;1)
T : R ! R . For an evolving boundary @ t P , its evolution comes from the way the boundary (or
3 3 ()
boundaries) of P is (are) extracted; for example, as isodensity surfaces when P is a scalar field. In
this case the parameter t is a scalar threshold for density values. Note that E n (@ P ) is an example of
0
level set functions [Sethian96].
D EFINITION A.14 (Shrinking and Expanding Boundary)

P E P
Let an object, and 0n (@ ) an evolution set of its boundary. Let t 2 0 n ; 1] n 2 N,
✦ @ P is called a shrinking boundary iff @ t P interior(@ t P ), 8 t 2 0 n ; 1].
( +1) ()
✦ @ P is called a expanding boundary iff @ t P interior(@ t P ), 8 t 2 0 n ; 1].

() ( +1)
✦ Strict subset in the above definitions, instead of “” correspond to monotonically or strictly
shrinking boundaries and strictly expanding boundaries. Similar definitions apply for the
boundaries of an evolving object O t . ()
We introduce a notion of weak and non-local homotopy under boundary transformations.
D EFINITION A.15 (Boundary Homotopy of Order 1)

P E P
Let an object and an evolution set 0n (@ ). Let Ttk : R3 !
R3, for some k N be a transfor- 2
t P t P t P
mation such that @ k+1 = Ttk (@ k ). Let card(@ k ) = 1 be a one-component boundary. We
( ) ( ) ( )
say that:
✦ Ttk is boundary-homotopic of order 1 iff card(@ (tk+1)P ) = card(@ (tk ) P ) = 1.
✦ Otherwise, we say that there has been a global change of topology of order 1 under T tk .
✦ E n (@ P ) is boundary-homotopic of order 1 iff
0 8 k 2 1 n] card(@(tk+1)P ) = card(@ (tk)P ) =
1.
Other notions of topology require to consider local transformations and topological spaces. We deal
here with very coarse properties of boundary transformations.
Symbolic notation and most definitions used along this work are summarized in page 11.
Appendix B
Tubular Extraction Methods and

Branching Analysis
The extraction problem of the blood-vessels of the lungs from color cryo-sections of the VHP
database (Chapter 4) prompted us to device and test several methods for tubular-structure detec-
tion. Some of them take advantage of our boundary-based approach, as well as rolling buffers, and
other concepts described in the precedent chapters. One of the objectives is to guide the segmentation
process presented in Section 4.2.5 by a preliminar central axis-based description. We give in these
pages a draft of the main ideas, introducing first a local characterization of tubular structures and
then some notes about a classical region representation, using the Medial Axis Transform.
From Boundary to Regional Representations

Boundary representations (b-reps) use a set of elements derived or equal to the set of boundary
elements or features of an object. In principle, there is no explicit reference to internal information
in the b-rep. We discussed some characteristics of tubular structures using b-reps in Section 1.6.1,
page 64.
The dual paradigm of b-reps are regional representations, where feature elements (used to de-
O

scribe shape) are now internal (i.e., in ) and derived from other features in the object, including
O
@ itself. These internal features are most often geometric loci, that is, sets of points satisfying a
geometric relationship with boundary points. 1
The duality with b-reps appears for example in the importance and complementarity of charac-
teristics of the normal behaviour. Let (~n ~t? ~tk ) be a local orthogonal coordinate system on a 3D
surface; this set is for example the Darboux trihedron , where basis vectors are the normal, binormal
O
and tangent, and ~t? = ~tk ~n (see Figure B.1b). Consider a 3D object possessing a smooth surface
O 2 O
boundary @ . In such a case a well-defined normal vector ~n exists for each p @ and a slowly
“varying” tangent plane with directions t~k ~t? can be assigned to each point p.
O
A skeleton or Medial Axis Transform (MAT) of the same object will be in general constituted
by 2D interfaces for which no stable ~n can be assigned, nor a single tangent plane exists. At the
same time, a dominant tangent plane with directions t~k ~t? do exists for this regional representation,
following the orientation of the linear elements.
1
See for example the operational Definition A.2 of “solid interior”, page 229.
240 APPENDIX B. Tubular Extraction Methods
n (a) (c) (d) (e)
Φ=
8
n?
(b) nk
n t || t ||
t ||
t
Φ
T
Φ >>0 t T ?
Φ= 0
Figure B.1: Behavior of a local reference system for a tubular structure according the size of its
mean radius . (a) On a plane the normal ~n is constant, and no tangent directions ~tk , ~t? are
predominant ( 1 ). (b) For smooth curved surfaces or (c) “fat” cylinders, ~n varies slowly and
~tk, ~t? correspond to the direction of the principal curvatures of the surface (0 < < ). (d) 1
In a tubular object a coherent direction ~tk appears when ~n ~t? change fast in small neighborhoods
on the surface (0 < 1 ). (e) In a thin filament only vector ~tk characterizes the object ( 0).
Discrete Tubular Structures (II) and the MAT
O
The most common regional representation of an objet is its skeleton denoted by MAT( ). As- O
suming a voxel connectivity choice in a othogonal discrete representation, the MAT( ) of is con- O O
stituted by a one-voxel-wide tree or graph, in its simplest implementation. Let us consider boundary
2 O 2
points p @ and their nearest points q MAT( ), that is, O
q = 0arg min kp ; q 0 k
q 2 MAT(O)
and let us define the average distance d@ MAT ( O) = < kp ; qk >, and the standard deviation
X
@ MAT (O) = 4
(p ; d@ (O)) MAT
2
p2@ O
These two parameters offer several morphological possibilities, but we just mention the following:
✦ d@ MAT(O) = 0 and @ MAT(O) = 0. The object is identical to its skeleton. Furthermore,
@ O = MAT(O) and the object is constituted only by thin or filamentary structures.
✦ 0 < d@ MAT (O) < , @ MAT (O) < for some small integers . In general, the object may
be a thin membrane or convoluted surface, a tubular structure, or a branching one; the size
determine the “bulkyness” of the object, and its roughness.
✦ @ MAT(O) = 0, and d@ MAT(O) = is a constant. If the MAT(O) is a one-voxel-wide tree
or graph, then O is generalized cylinder, or a cylindrical ramified structure.
APPENDIX B. Tubular Extraction Methods 241
Thus, tubular ramified objects such as botanic trees and blood-vessel trees are well characterized
as being very similar2 to their own regional representation, constituted by a one-voxel-wide tree or
f g O
graph. A local slow varying set of orientations t~k along MAT( ) is also a more representative
fg
feature than the distribution of their surface normals ~n , which is rather perturbated or even un-
defined for thin filaments. This behavior is illustrated in Figure B.1, where the predominance of a
particular direction vector changes when passing from a smooth surface to a filament. Let p @ , 2 O
N
and @ (r p) a geodesic neigborhood of p, as in Definition 1.8. with a number N geo of points q i ,
with i = 0 : : : Ngeo. Note that smooth tubular surfaces present local directional coherence (we
avoid the term “linear”); recalling Definition 1.17, page 42: the average vector ~tk =< ~tk i >, with
4
i = 1 : : : Ngeo is constant over small and medium-sized neighborhoods, and its standard deviation
v =4 < kv~i ; ~v k2 > remains small (all tangents point to the same direction at each p).
Tubular structures and generalized cylinders can be thus represented by a central axis and a set
of radial functions. In many cases, just a constant radius may be specified for each branch. It may
be specified as a function of the branching order according to flux conservation laws [Kalda93]. The
relevant features are coded along the central axis and the most successful models of complex ramified
objects are represented by L-systems, as described in Section 1.6.2
A similar observation can be made about thin convoluted surfaces and sheets, where a regional
representation is close to the object itself, and the behaviour of ~n can be locally described by planar
coherence. Figure 1.16, in page 69, shows an example of a convoluted surface.
Extraction of the Central Axis Tree by Local Centroid Tracking

A first problem to deal with the extraction of the MAT of complex objects is the simple-point identi-
fication and the conversion of the resulting set of voxels into a list of vertices that should be traversed
in a determined exhaustive way. A second problem is the noise sensibility of a MAT, which has been
solved by regularization, and hierarchical approaches [Ogniewicz94].
There are several methods in the litterature for simple-point identification, but most of them
rely on some kind of assumption, such as the unimportance of the two-dimensional character of the
extracted skeleton, from the fact that the analyzed object (e.g. the brain cortex) is two-dimensional in
nature [Mangin95]. Graph representations require the reduction of the 3D skeleton to linear chains
of single voxels, and to record only the most important branches.
Tubular structures should ideally produce robust unidimensional skeletons, but they present the
same problems that any bulky object. The final set of MAT points may be almost as difficult to ma-
nipulate as the initial object itself. Less precise, but more robust representations have been proposed,
specially for branching objects and tubular structures. Time limitations do not allow us to review
these definitions and the rich bibliography on the MAT and the more general concept of medial-
ness or centerlines and cores (see for example [Morgenthaler81, Lee82, Matheron88a, Schmitt94]
for the MAT definitions and [Niblack90, BurbeckPizer94b, Fritsch94, Fritsch95] for medialness and
cores). Moreover, scalespace representations allow for example to account for the roughest features
[Morse94]. We mention those issues related to our work.
Since average operations are robust to small deviations, the local Center of Mass (CM) or Cen-
troid is also used in some approaches. This is the case of the Central Axis Tree (CAT), which is
defined as a simplified graph representing a branching tree structure, where nodes are found at the
center of branching regions or curvature points in such a way that polygonal arcs always lay inside
2
Close to MAT (O), up to a characteristic radius .
Br BR
U
BR
---2r--- 11111111
00000000
00000000
11111111
00000000
11111111
00000000
11111111
r 00000000
11111111
Br
00000000
11111111
R .r 00000000
11111111
.
00000000
11111111
00000000 T
11111111
T 00000000
11111111
00000000
11111111
00000000
11111111
00000000
11111111
Tc 00000000
11111111
1/2
R=2 r
Vol (BR\ Br ) = π r 3 4/3 (23/2-1)

111
000 1/2 2
(B R \ B r )) = π r 3 (2/3 (2 -1) (8 +1) +1 )
U 1/2
000
111
111 Vol (T
000
c U U
Vol (T BR \ Br ) = Vol (B R \ Br ) Vol (T (B R \ B r))
Figure B.2: Minimal and maximal radii and intersected volume relationships for the coupled balls (see text)
the branches. A local CM is obtained by moving average calculations, given a neighborhood of a

test-point inside the tubular structure.
The region growing (RG) segmentation described in Section 4.2.5 provides the means to track the
center point of sliding neighborhoods required for a moving average calculation, in order to update
region statistics during growth. The 3D-extension of the rolling buffer described in Section 3.3.3
accounts for an incremental approach. In [Pisupati95], Pisupati et al. took advantage of a simi-
lar process preserving the voxel coordinates of the RG process (usually these coordinates are just
popped-out from a queue), and they calculate a local centroid of the extracted tree, when the neigh-
borhood under analysis is not fragmented (that is, the RG-wave has passed a branching point, as
illustrated below, in Figure B.4-c). Pisupati et al. do not describe how they are able to know how
many components of the queue are or not connected; these components are not generally found at
adjacent locations in memory and tracking them requires a more sofisticated data structure than a
parallel buffer.
However, the idea of Pisupati et al. prompted us to device a similar approach, keeping track of the
local centroid, in order to be able to detect a medial-axis approximation by using coupled spheroidal
B
sensors, which are a dynamic extension of local annular-neighborhoods (r R p) = R (p) r (p), B nB
where p is a moving point, tracking the centerline of a vessel, in function of gray-level statistics
B B
of r (p) and R (p). The main problem we encountered, in a feasability study, was the quantity
of parameters to control, such as R=r ratios, and size in function of vessel diameter and the many
p
cases to deal during detection. Figure B.2 shows details of annular neighborhoods inside a tubular
segment T in the case of a centered point p and a radius R=2 = 2. Figure B.3 illustrates several
situations to be analyzed and resolved by the annular detector, in which complex decisions depend
on combinations of the values R r R=r p and the foreground and background proportions inside
B B B
regions r (p) R(p) and (r R p).
(c) (f)
(b) . . 111
000
(e) . 000
111
000
111
(a) . 000
111
000
111
. 000
111
. 000
111
. (d)
111111
000000 .
000000
111111
000000
111111
000000
111111
000000
111111
000000
111111
000000
111111 . (h)
000000
111111 .
000000
111111
000000
111111
000000
111111 Br BR
U
. (i)
(g) . (j)
111111
000000
000000
111111 111111
000000
000000
111111 000000
111111
000000
111111
000000
111111 000000
111111
000000
111111 000000
111111
.
000000
111111 000000
111111
000000
111111 000000
111111
000000
111111 000000
111111
(k)111111
000000
000000
111111
000000
111111
000000
111111
000000
111111
000000
111111
000000
111111
000000
111111
Figure B.3: Some of the problematic cases to be analyzed by a tubular detector based on coupled balls.
Detection of Branching Points.

2
Large ball-neighborhoods of a test-point p T could also be analyzed in terms of their intersections
with a tubular structure T , a branching point being characterised by the number of intersections
between the ball and the tubular boundaries (see Figure B.6).
Separation of branch components.

In a region-based approach, the MAT provides a graph representation of a branching structure, in
which morphology analysis and measurement can be done to extract, for example, the branch lengths,
average diameters (or the radii distribution itself). A boundary-based approach can be devised by an-
alyzing information from boundary representations. Figure B.7 illustrates this approach by extracting
a local depth map using the estimated normal of the facets of @T . Gray-level labels are then assigned
to boundary points (facets) and branches separated in terms of length and diameter transitions. Error
due to normal estimation, vessel deformation, and natural variations do not warranty that separation
will occur exactly at branching points (see Figure B.7f).
Detection of Tubular Components by Local Tensor of Inertia Analysis

We have already mentioned the importance of local coherence in complex structures. The bronchial-
vessel tree provides an example, since vessels follow relatively straight paths for short distances 3.
Even some tortuous vessels preserve a global orientation in the sense of having a global principal
axis in neighborhoods not much larger than the largest diameter. An ellipsoid of inertia can be
assigned to each point in space, as illustrated in Figure B.8. Hence, Principal Component Analysis
3
The neighborhood of the branching nodes poses some problems.
(e)
(a) (d)
(b)
(c)
(f)
Figure B.4: Central-axis tracking by growing-ball intersection. (a) The intersection between the tubular
structure T and a sequence of R discrete balls Br of radius r = 1 2 : : : R (with R 2 N) is tested to
determine the number of connected components kc of its boundary (k c = card(Y ), where Y := @Br T ). \
After the first step (a), subsequent ball sequences produce one new intersection at branch segments (b), and
\
two or more after bifurcations (c). The green dot (a) is a recalculated Center of Mass of the tubular segment
defined by BR T , and is saved for later use. At each sequence (R steps) the CM of each intersection Ykc is
calculated and a new sequence is initiated (b,c). At the left (d) the approximated cross sections of T are shown,
\
corresponding to contours defined by @(@BR T). Inset (e) shows the corrresponding graph tree formed by
the CM at each intersection step nR k = 1 2 : : : False intersections (f) constitute one of problems to deal
with.
(PCA) may provide information of the presence of a tubular structure as well as a particular case of
orientation trends and anisotropy, as presented in Section 1.2.1.
The remaining figures further illustrate these and other ideas for tubular structure detection.
(b)
(a) rmax > (T)
U
rmin < ( Brmax T)
(b)
Figure B.5: Initial and final radius r min rmax for ball growing determine the tracking step (the approximate
distance between CM nodes). The smallest ball (a) before restarting (or maximum growing ball), B rmax ,
shoud not be smaller than the average local diameter of the tubular structure, (T ). The largest minimal ball
(b) should not exceed the average diameter of the intersection of the last ball B rmax with T .
(a) (b) (d)
T
p1 p
2
Br (p)
p3
p (c)
p
T 4
T
U
card { Br (p) T}=3 T
Br’(q) p5
q
p
6,7,8...
U
card { Br’(q) T }=2
Figure B.6: Branching points are characterized in several ways. (a) Their ball-neighborhoods ideally have
a defined number of intersection with the tubular components. Analysis is done at interior points p q T , 2
ideally near the medial axis. The number of connected-component intersections define the branching degree
equal to card(intersections)-2, with 0 indicating no branching, and -1 indicating a terminal point. (b-d)
2
Saddle zones also locate branching points in a boundary-based analysis where p i @T . Terminal points are
less evident to characterize.
(a) (d) 11
00
00
11
11111
00000 00
11
00000
11111 00
11
00
11
00000
11111 000
111
000
11100
11
000
111
d
(b) p
n (e)
(f)
r
(c)
1
0
order
0
1
0
1
Figure B.7: Local thickness (or depth) analysis, applied to branching structures T . (a) a normal is estimated
at each p 2 @T , and distance to the opposite site is measured and used for (c) a depth label on p which
codes local diameter. (d) Rough branch-components segmentation of the depth-labeled boundary, using an
average-diameter criterion.
(b) (d)
(a)
(c)
Test points (e)

Object
Principal local axes
Artifacts
Figure B.8: Local tensor of inertia analysis (or PCA of the local scatter matrix) for geometry-driven detection
of oriented fine structures. (a) A proper local neighborhood (dotted circle) allows to detect tubular regions.
(b) At isotropic regions, interior and exterior points present uniform eigenvalues (much larger than zero for
foreground and very small or zero for background) in small neighborhoods. (c) Boundary or tubular-near
points define anisotropic regions. (d) elongated artifacts are also detected. (e) “missing” segments may be
completed by directional filtering (e.g. oriented closennigs).
Appendix C
Synthesis of 3-D Phantoms of Complex

Porous Structures by Diffusion-Limited
Aggregation with Relaxation
We discuss in this appendix some considerations of simulated data using the Diffusion-Limited Ag-
gregation (DLA) model. During the collaboration with the CNET we recognized the richness of the
DLA growth and random deposition models as versatile generators of complex structures, having
fractal (scaling) features and various morphological behaviours (evolution) in function of simula-
tion parameters. Data generation to develop and test our methods posed one particular problem:
physico-chemical calculations are very expensive for computer simulations of real phenomena, lim-
iting resolution and parameter ranges. In consequence, only some short ranges of parameters were
studied on a this first approach.
In order to understand and characterize morphological configurations of 3D data, from a more
abstract point of view, we found ourselves concerned with the per-se study of complex structure
generation, and considered the DLA model incorporating relaxation (thus, “DLA+R”) in a similar
way that deposition models, but reducing physical interactions to random controled behavior. Sim-
ilar paradigms for complex structure generation (phantoms) are Markov Random Field realizations
for texture synthesis, auto-regressive models, and fractal recursive generators with randomization
(fractional brownian motion and Fourier synthesis are common examples).
A second goal is to simulate data for the development and test of morpho-analytic tools for three
dimensional data. In order to analyze different complex configurations and 3D-textures (branching,
multiple connectedness, porosity, mixed and convoluted surfaces), we developed a DLA+R process
simulator in 2D and 3D, incorporating many features to allow for semi-controlled structure variation.
The simulator’s features include initial geometry configuration, topology constraining, displacement
through potential fields and barriers, neighborhood interaction (which allows to emulate relaxation
and surface dynamics after cluster coalescence), anisotropic flux of the clustering particles, sticking
probabilities, temperature-like and reaction behaviour, configuration-specific penalization or favour-
ing, and other emulating real phenomena. Instead of calculating precise energy balances to favor a
specific event, random decisions are taken on the basis of pre-calculated probabilities corresponding
to particular neighborhood configurations.
Interest in diffusion process relies in the possibility of mathematical modeling of important fea-
tures that may be verified by experiments. In surface growth, DLA process takes place on a substrate
layer (for example, a plane). The expected roughness of the projected top surface, defined as the
250 APPENDIX C. Synthesis of 3-D Phantoms by DLA+R
RMS deviation from a mean height h can be predicted by the diffusion (Kardar-Parisi-Zheng) KPZ-
equation [Vicsek92], which is a non-linear version of the Langevin equation used in brownian motion
models:
@hRMS (~x t) = F + r2h (~x t) + (rh (~x t))2 + (~x t)

@t RMS RMS (C.1)
where hRMS = h ; hhi
and:
✦ hRMS is the RMS roughness of the projected top surface, h the continuous height as function
of ~x, the vector position in the substrate, and t, the particle diffusion cycles. The discrete
definition of hRMS was given in Equation 5.2.
✦ F is a “drift” offset.
✦ is the coefficient associated to surface tension (or viscosity), and the Laplacian term is
known as the relaxation, or diffusion term.
✦ is the coefficient for the lateral growth contribution, which accounts for neighborhood
reaction interactions. It is also known as bias term.
✦ is the “input signal”, which usually is constituted by gaussian noise.
(a)
(b)
Figure C.1: 2D deposition emulated by Diffusion-Limited Aggregation process with relaxation

(DLA+R). (a) Deposit with complex porous structures (porosity is higher than 25%); the arrow
points at a single layer, in light gray. (b) Column-like structuring with deep vertical meanders and
a very rough surface (RMS-value: z > 75%). Gray-levels correspond to time, in 10K deposition
cycles per level. Instance (a) is qualitatively similar to a real physical phenomenon: surface growing
in microgravity conditions. Simulation program developed at ENST.
APPENDIX C. Synthesis of 3-D Phantoms by DLA+R 251
The terms in this equation code the steps of several growth and deposition process. When =
0 6= 0, the KPZ equation corresponds to random deposition with surface diffusion, as described
in Figure 5.2. Using this and other parameter-evolution equations, the CNET has predicted some of
the observed results for roughness and porosity, in computer simulation as well as in experimental
validations.
At the same time, the KPZ equation codes the main components of the 2D DLA+R simulator we
developed for complex micro-structure generation. Some examples are presented in Figure C.1 and
in Chapter 1, in Figure 1.12, page 58. The instance of Figure C.1a is similar to a real physical phe-
nomenon: surface growing in microgravity conditions (remark made by Dr. Flicstein, of the CNET).
The instance of Figure C.1b is qualitatively similar to viscous fingering phenomena. A 3D imple-
mentation of the DLA+R generator of complex structures is in work at present. This generator could
provide 3D phantoms to test and develop new analytical methods as those presented in Chapter 5.1.
Résumé long
Ce résumé présente brièvement les différentes parties successives de la thèse, les idées principales,
nos contributions et les résultats les plus importants.
Objectifs et organisation de la thèse

Le but général de ce travail est le développement de méthodes de segmentation, morphométrie et
visualisation de structures complexes en trois dimensions, en particulier des microstructures poreuses
et des vaisseaux sanguins qui présentent des ramifications compliquées.
Dans la première partie de la thèse nous avons étudié les différents problèmes posés par l’analyse
de ce type de données volumiques, comprenant les définitions des attributs de complexité structurale
examinées dans le chapitre 1, et les représentations par frontières discrètes, décrites au chapitre 2.
Nous proposons aussi quelques outils exploitant ces représentations.
La deuxième partie concerne des applications sur deux ensembles de données volumiques cor-
respondant à deux problématiques différentes respectivement en biomédecine (chapitre 3 et 4) et en
physique (chapitre 5). La généralité et la souplesse du modèle de représentation par frontières nous
a permis d’utiliser les mêmes outils informatiques pour les deux applications. La notation utilisée
dans cette thèse est présentée en détail à la page 11.
Caractérisation des structures complexes dans R3

Nous avons d’abord identifié et caractérisé les attributs morphologiques intrinsèques et extrinsèques
des différentes structures complexes, tels que : les axes principaux, la compacité, la cohérence lo-
cale et globale, les caractéristiques des structures tubulaires et le comportement de la normale (si
elle existe), la représentation des ramifications, convexités et cavités, les interfaces et membranes,
la porosité, la rugosité et d’autres. Pour ce faire, nous avons d’abord fait une revue des concepts de
géométrie dans R3, tels que : voisinage, voisinage géodésique, boule euclidienne, frontière (contour
3D), intérieur, cavités et d’autres, qui permettent une description géométrique des diverses propriétés
des formes irrégulières et complexes. Le sujet de la complexité a été aussi abordé brièvement, et
nous avons constaté qu’il y a peu des cadres théoriques pour sa description ; ces cadres consistent
principalement en : (1) la complexité algorithmique de Kolmogorov et (2) les dimensions fractales et
les systèmes dynamiques non linéaires. Le premier cadre théorique permet de mesurer la complexité
par la longueur de la description la plus courte possible. Le deuxième cadre prend compte des répé-
titivités sur plusieurs échelles, mais s’avère peu générale, lorsque les irrégularités ne présentent pas
254 Résumé long
la propriété d’auto-similarité. D’ailleurs, des objets fractals soi-disant complexes, dont l’ensemble
de Mandelbrot, peuvent avoir une description mathématique très courte, en termes des systèmes dy-
namiques, mais ils peuvent présenter des détails géométriques très irréguliers et à tous les niveaux
de l’analyse. Nous faisons dans ce chapitre une exploration systématique des définitions existantes
et les liens particuliers entre plusieurs attributs morphologiques et les applications dont nous avons
connaissance ou une expérience personnelle. Un objet s’avère complexe lorsque sa description est
très longue et présente des régularités très spécifiques, mais aussi lorsqu’elle fait appel à une cardi-
nalité élevé d’éléments structuraux ou de relations internes.
Les modèles dans N3 : une approche fondée sur les frontières

Pour l’étude des objets de structure complexe, nous avons choisi une approche en géométrie discrète
pour l’extraction des surfaces, le traitement et la visualisation des données volumiques. Dans cette
approche, les surfaces extérieures ou frontières des objets détectés sont représentées par des listes de
facettes. Dans le chapitre 2 nous étudions des éléments dans N 3 qui permettent la formulation d’une
représentation complète, et la possibilité d’étendre les définitions du cas continu au cas discret, pour
un objet ou sous-ensemble V N 3. Ces éléments comprennent : une maille discrète, des voxels
et leurs faces ordonnées, une affectation cohérente des orientations des faces, et finalement deux
ensembles d’éléments : l’ensemble des faces orientées de la frontière (facettes) donnant lieu à une
V
frontière par facettes @ , et l’ensemble des voxels correspondant à une frontière par voxels V. Avec
un choix spécifique d’orientation de la surface, et des connexités compatibles (parmi les cas 6-,18-,
ou 26-connexes), cette double représentation comporte des avantages pour l’analyse et le traitement
V
des ensembles de voxels : la première représentation (@ ) est liée au parcours et l’extraction des
surfaces par suivi de contour 3D, et les paramètres volumiques que l’on en peut déduire ; la deuxième
V
( ) est liée aux notions de morphologie mathématique classique dans N 3. Nous formulons aussi le
passage d’une représentation à l’autre.
Une partie importante des traitements 3D avec ces représentations consiste à analyser et modifier
V
les listes des facettes qui constituent @ et les structures de données associées, en examinant les
facettes et les voxels voisins pour effectuer les opérations ou mesures nécessaires. L’extraction de
telles frontières se fonde sur une méthode (existante dans la littérature) de parcours du graphe dirigé
associé à la surface de chaque objet (en fait, de chaque composante connexe). Diverses structures
et outils sont alors introduits, tels que : les voisinages des facettes, ceux des voxels et des frontières
V V V
(@ ; @ + , + , ...), les voisinages géodésiques, et des implantations de filtres de morphologie
mathématique fondées sur la représentation de frontière par voxels. Certaines opérations sont acti-
vées durant le parcours du graphe dirigé, dont par exemple l’estimation de la normale à la surface
pour chaque facette, et l’élément d’aire surfacique par facette, à partir de la configuration locale des
V
facettes voisines. La méthode de parcours de @ et un choix d’orientation permettent aussi d’utiliser
V

V
une méthode novatrice de parcours de l’intérieur géométrique d’un objet discret , étant donnée
V
seulement sa représentation @ structurée comme une liste de couples de facettes opposées. Cette
méthode est liée aussi à une compression par plages de voxels (run-length coding).
Les trois exemples suivants permettent d’illustrer l’intérêt de notre approche :
(1) Filtrage : une érosion morphologique conditionnée revient à une élimination sélective des
voxels situés sur la frontière V
de l’objet ;
Résumé long 255
V
(2) calcul morphométrique : le volume d’un objet est calculé à partir de sa frontière @ , en utilisant
V
le théorème de Gauss discret, et notre méthode de parcours de l’intérieur géométrique “ ” de

l’objet ;
(3) visualisation : pour calculer l’ombrage d’une facette à afficher, la normale locale est estimée à
partir des configurations des facettes voisines.
Nous montrons aussi quelques attributs morphométriques dérivés ou formulés en termes des élé-
ments introduits, notamment à partir de : @ , V V V
, la méthode de parcours de et les voisinages de
voxels et des frontières. Ces attributs, introduits déjà au chapitre 1 pour le cas continu, permettent
l’étude quantitative de formes très complexes dans le cas de données volumiques discrètes. Quelques
exemples de segmentation des composantes faiblement connexes et de visualisation réaliste illustrent
les possibilités de notre démarche. D’autres exemples sont présentés dans les chapitres suivants.
Homogénéisation radiométrique des images des cryo-sections

en couleur du VHP
La première application a été développée sur des données biomédicales correspondant aux poumons
et provenant de la base de données du Visible Human Project (VHP) de la National Library of Medi-
cine et du National Institutes of Health (Bethesda, EU). Les coupes anatomiques en couleur du VHP
posent des problèmes particuliers pour la segmentation et la visualisation des structures internes et
nous avons ainsi développé une technique novatrice pour la correction d’hétérogénéités radiomé-
triques régionales. Notre démarche a consisté à exploiter le principe de cohérence locale structurale
(introduit au chapitre 1) pour chaque pixel, dans des images de différence entre deux coupes adja-
centes. Plusieurs techniques de visualisation des hétérogénéités ont été proposées, en particulier les
images entrelacées en échiquier et les histogrammes couleur empilées (stacked color histograms),
qui mettent en évidence le caractère régional et irrégulier des discontinuités qui gênent l’analyse
en 3D. Notre technique, utilisant un modèle auto-régressif de première ordre, consiste à décaler à
chaque pixel le profil de l’histogramme local pour les images différentielles, de sorte que les maxima
de deux histogrammes de coupes consécutives soient alignés. Cette correction est propagée au long
du volume dans les deux sens, une seule fois. Une telle correction n’introduit pas de bruit, ni de
flou, car elle dépend des discontinuités radiométriques locales et ne se fait pas si les pics des his-
togrammes sont alignés. Les techniques de visualisation en échiquier des coupes adjacentes et les
coupes ré-échantillonnées axiales et sagittales ont démontré l’efficacité de cette correction.
La description de notre technique et les résultats obtenus ont fait l’objet de deux travaux présen-
tés en congrès internationaux, et une publication internationale avec comité de lecture. Les images
corrigées ont été utilisées pour l’extraction des structures vasculaires, présentée au chapitre suivant.
Extraction des vaisseaux sanguins à partir des cryo-sections

en couleur du VHP
Dans ce chapitre nous examinons les données du VHP en vue d’une segmentation de l’arbre vas-
culaire des poumons, ainsi que les techniques que nous avons testées ou proposées et les résultats
obtenus.
256 Résumé long
Les sections des vaisseaux plus fins forment une “texture” dans les images des coupes coronales.
La nature fractale de cette texture rend difficile et inefficace l’utilisation des approches classiques de
segmentation, car les données (la forme) et le fond (le tissu plus des vaisseaux sous-échantillonnés)
se trouvent fortement mélangés. Nous avons néanmoins proposé une méthode hybride, qui com-
bine le seuillage par hystéresis et le filtrage par moyenne “Sigma”. Cette combinaison compense
partiellement le problème de discrimination entre fond et forme. Nous avons combiné aussi ces
deux approches avec une approche de segmentation par croissance de régions pour une segmenta-
V
tion préalable, et la segmentation par hystéresis est effectuée à l’aide des frontières voisines ( + ,
V
++ ) de la frontière principale, définie par la croissance de régions. Cette dernière exploite aussi
la représentation par facettes et leurs voxels voisins.

A partir des résultats de segmentation, nous avons fait des visualisations réalistes de l’arbre vas-
culaire pulmonaire obtenu à la suite des différentes étapes de la segmentation et du traitement 3D,
toujours en utilisant la représentation par frontières. La qualité des rendus surfaciques est suffisam-
ment bonne pour permettre d’apprécier la complexité des structures extraites, leurs interrelations
spatiales, et l’effet sur ces structures de tout traitement spécifique.
D’autres méthodes possibles pour l’extraction des structures tubulaires sont décrites très briève-
ment, mais en raison des limitations de temps, notre étude sur ces méthodes est restée préliminaire.
Analyse et visualisation des simulations numériques

de photo-dépôt amorphe
La deuxième application, en physique, a pu être abordée dans le cadre d’une collaboration avec le
laboratoire de Physique des Surfaces du Centre Nationale d’Etudes en Télécommunications (CNET),
à Bagneux. Le problème a consisté à mesurer les propriétés de porosité, rugosité, connexité et dis-
tribution des paramètres morphométriques extraits des résultats obtenus par simulation numérique
d’un photo-dépôt amorphe de Nitride-Silicium. Nous présentons d’abord les caractéristiques mor-
phologiques de ces simulations, et leur dépendance des paramètres de température, pression, champ
électromagnétique et les conditions initiales.
Les structures poreuses des dépôts amorphes et la nature de la ségrégation du dépôt avec deux
ou trois espèces d’atome (Si, N, et H), nous ont amenés à considérer les définitions de connexité, les
interfaces discrètes et la pertinence des outils introduits dans la première partie du travail de thèse.
La collaboration avec le CNET a permis de proposer et tester des outils d’analyse supplémentaires
aux outils traditionnels (porosité volumique globale et rugosité RMS, correspondant à l’écart-type de
la hauteur moyenne), qui sont mal adaptés au cas des surfaces qui présentent des “méandres” (pour
la rugosité), et lorsque les pores présentent une distribution de tailles et de formes très diverses (pour
la porosité). Nous faisons la distinction entre une surface projetée à l’infini (qui peut être étudiée
V
comme une image d’intensité ou de hauteur z = f (x y ) ), et la surface réelle @ du dépôt, qui inclut
des composantes surfaciques à l’intérieur des amas. De telles composantes constituent les méandres
et repliements cachés dans une simple projection dans l’axe Z .
Nous proposons aussi différentes techniques et paramètres pour étudier la rugosité d’une telle
surface complexe, dont la densité de surface locale, et les densités relatives à chaque espèce ato-
mique. Une hauteur et une largeur caractéristiques permettent aussi d’étudier la densité moyenne
des rapports entre la profondeur et la largeur des extrema locaux. Ces mesures sont aussi liées aux
notions des textures surfaciques et de rugosité revues au chapitre 1.
Résumé long 257
Nous avons effectué des reconstructions 3D des données de simulations, l’identification des com-
posantes connexes pour les pores ou les amas d’espèces différentes, et l’extraction des paramètres
morphométriques. Les visualisations et les mesures obtenues ont permis aux chercheurs du CNET
de connaı̂tre : la taille et la forme des pores, la taille et la forme des amas du dépôt, la distribution
de la porosité par rapport à la température ainsi que la qualité d’interpénétration de plusieurs espèces
atomiques. En outre, les rendus 3D permettront de repérer des transitions critiques de la morphologie
des amas (ou de la distribution de pores), identifiés clairement par des étiquettes en couleur.
Vers la fin de cette collaboration, une validation expérimentale a pu confirmer les mesures de po-
rosité fournies au groupe du CNET-Bangeux, en mesurant la porosité par des méthodes d’ellipsométrie
in situ, correspondant aux paramètres de simulations étudiées par ordinateur. Ces résultats et un
aperçu de notre contribution ont fait récemment l’objet de deux publications supplémentaires ac-
ceptés en revue avec comité de lecture, ce qui complète les travaux de deux étudiants de DEA du
CNET-Bangeux pendant 1997 et 1998, et deux travaux présentés en congrès (mêmes dates).
Conclusions et perspectives
Nous avons identifié et étudié plusieurs concepts relatifs à la complexité structurale des objets typi-
quement présents en biologie, médecine et en physique de surfaces. Cette exploration est loin d’être
achevée totalement, et constitue désormais une partie importante de nos axes de recherche.
La méthode de parcours de surface, existant déjà dans la littérature, a été exploitée systéma-
tiquement et enrichie avec notre démarche et les différents éléments pour l’analyse 3D que nous
avons apportés, en utilisant des frontières par facettes et par voxels. Il nous reste encore à raffiner
ces méthodes, et par exemple tenir compte du théorème de Jordan qui permet de résoudre certains
problèmes de topologie discrète, et à les mettre en valeur dans des publications à venir.
Notre groupe a été le premier à signaler les hétérogénéités présentes au niveau des poumons
dans les coupes anatomiques de la base des données du VHP, et nous avons proposé une méthode de
correction efficace que nous a permis d’extraire une partie considérable de l’arbre vasculaire pulmo-
naire. Les méthodes d’analyse et segmentation de structures tubulaires que nous avons commencé à
explorer sont aussi une voie intéressante à suivre dans le futur.
Dans la collaboration avec le CNET-Bagneux nous avons tenu compte des caractéristiques réelles
de la surface et de l’intérieur des dépôts. Ces caractéristiques sont normalement ignorées dans les mé-
thodes traditionnelles, faute des moyens pour leur évaluation. D’ailleurs, deux des techniques testées
ont pu être validées de façon expérimentale, ce qui a permis de mettre en valeur notre contribution.
Une voie future de collaboration pourrait consister à mettre en relation des techniques expérimentales
pour pouvoir valider les outils et mesures proposés (densité de surface, quantification des méandres,
granulométrie des pores,...), ainsi que d’autres caractéristiques de la simulation numérique réalisée
par le CNET-Bagneux.
258 Résumé long
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Index
K -adjacency, 97 coronal cross-section, 145

K -connectivity, 97
Darboux trihedron, 239
adaptive homogenization, 150 Diffusion Limited Aggregation, 56, 194
adatom, 192 digraph, 119
airways, 161 dimension
amorphous deposition, 192, 194 capacity, 50
anatomical cryosections, 144 embedding, 48
Euclidian, 48
b-reps, 81, 239 Hausdorff, 49
back-face boundary, 110 information, 50
back-facet, 109 Lyapunov, 51
back-voxel, 109 mathematical-morphology, 51
back-voxel boundary, 110 Minkowski, 51
background, 25 similarity, 49
ballistic deposition, 194 spectral, 51
body-centered cubic, 88 topological, 49
bronchial tree, 161 distance, 98
DLA, see Diffusion Limited Aggregation
cardinality, 27
Central Axis Tree, 241 ellipsoid of inertia, 243
characteristic
height, 45, 210 face-based boundary, 110
length, 34, 44 face-centered cubic, 88, 192
width, 45, 210 facet, 90
checkerboard display, 147 facet boundary, 92
chemical vapor photo-deposition, 192 facet wall, 121
CNET, 192 facet-driven region growing, 185
co-occurrence images, 146 facet-to-voxel operator, 90
coherence fading memory constant, 154
directional, 42 Fat-boundary neighborhood, 112
local, 41, 153 foreground, 25
spatial, 41 front-face boundary, 110
color front-facet, 109
histograms, 146 front-voxel, 109
computer simulation, 192 front-voxel boundary, 110
connected components, 27
connected set, 26 gamma correction, 144
contention wall, 121 geodesic neighborhood, 24, 104
continuous boundary, 92 geodesic path, 98
convoluted surfaces, 68 geometric interior, 93
278 INDEX
Hamiltonian circuits, 119 sagittal cross-section, 145

hysteresis thresholding, 176 Sigma-average filter, 179
solid boundary, 93
immediate K -neighborhood, 103 solid interior, 96
innovations, 150 species, atom, 192
interfaces, 25, 68 Stereology, 63
structuring elements, 103
Kolmogorov Complexity, 58
surface density, 108
laminar structures, 68 surface diffusion, 194
last-layer top surface, 206 surface tracking, 113
lateral directed circuits, 105, 117 surface-intensity images, 209
Lindenmayer formal grammars, 66
tensor of inertia, 29, 248
lung parenchyma, 162
Tetris deposition, 194
maximum intensity projection, 157 top layer, 194
MDWRE, see mean depth-width ratio traversal circuits, 91
mean depth-width ratio, 209 tubular detector, 243
meanders, 194 tubular structure, 36, 64, 241–244
Medial Axis Transform, 239
UV CVD, see chemical vapor photo-deposition
microstructure, 196
MIP, see maximum intensity projection Visible Human Project, 144, 164
Monte-Carlo simulation, 194 volume traversal, 96, 123
morphological boundary, 128
moving average, 242 watershed segmentation, 84, 131
weakly-connected components, 84, 130
neighborhood
annular , 24
discrete, 24
geodesic, 24, 26
spherical, 24
next-front-face boundary, 110
next-front-voxel boundary, 110
PCA, see Principal Component Analysis

Point-Spread-Function, 70, 170
pores, 194
porosity, 193, 197, 199, 213, 217, 235
Principal Component Analysis, 29, 159
projected top surface, 206
PSF, see Point Spread Function
pulmonary artery, 161
pulmonary veins, 161
radiometric inhomogeneities, 144

region growing, 185
regional representation, 239
RMS roughness, 193, 198, 208, 213, 217
ROI or Region Of Interest, 62, 83, 86
rolling buffer, 156

Analysis and Visualization of Complex 3D Structures - JorgeMarquez

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Analysis and Visualization of Complex 3D Structures:

a discrete boundary-based approach

Analyse et visualisation des structures complexes en 3D :

Jorge Alberto Márquez Flores

Soutenu le 6 avril 1999 devante le jury composé de :

Département du Traitement du Signal et des Images

c JORGE A. MÁRQUEZ PARIS , F RANCE , LE 6 AVRIL 1999

L’objectif de ce travail est la segmentation, la morphométrie et la visualisation de structures com-

1 Characterization of sets with complex structures in R3 21

2 From Raw Data to Models in N3: A Boundary-Based Approach 77

4 Extraction of Bronchial Blood-Vessels from Color Cryosections of the VHP 161

5 Analysis and Visualization of Computer Simulations of Amorphous Photo-Deposition 191

A Further Definitions of Object Subsets and Boundary-Related Subsets 229

B Tubular Extraction Methods and Branching Analysis 239

C Synthesis of 3-D Phantoms of Complex Porous Structures by Diffusion-Limited Aggre-

Résumé long 252

Symbol Description First used in page #

X = ”expression” ”X ” is defined as ”expression”. 24

(a b) An ordered pair (or vector) of entities a b. 26

~a = (a1 : : : an) An ordered set (n-tuple or vector) of n entities fa k gn

card(A) Cardinality of set A (number of members). 27

A n B A ; B The set difference between sets A and B . 25

V W Scene domains in R3. 86

@j V The j th connected component of the (face-based) boundary of . V 231

Nfacets = Nbf (V ) = card(@ V ) Number of boundary faces of @ V .

d@ (p q) Geodesic distance between points p q 2 @V V  R3. 26

dK Discrete distance under K -connectivity between grid points p q 2

@ V ; = opface(@ V ) Negative boundary, the reverse-oriented version of @ . V 92

@;V The back-face boundary of .V 110

facettovox(@ V ) = V Facet-to-voxel operator to build V from @V . 110

voxtofacet( V ) = @ V Voxel-to-facet operator to build @ V from V . 94

O = O n @O Geometric interior of continuous set O. 25

V = V n V Discrete Geometric interior of voxelized set V . 93

Nbf (p N ) = card( @ V \ N) Number of boundary faces in a neighborhood N (p). 208

N@ (r p) B@ (r p) Geodesic neighborhood of radius r around a point p 2 @V : 104

@ Vj Boundary @ V restricted to ”condition”.

Projected boundary (top surface) as seen from z 207

Notes about text notes, captions and figure symbols:

✦ Bibliographic references are listed in square bracket format: [LastNamesYY,...].

Problem Definition, Applications, (and what came of it:)

Jorge Márquez, ENST, Paris, February 1999.

Characterization of sets with complex

1.1 Preliminar Notions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

1.4.2 Morphological Features of Fractals . . . . . . . . . . . . . . . . . . . . 54

1.1 Preliminar Notions

An open n-ball or disk is defined by n (r p) = q B

D EFINITION 1.2 (Open Annular Neighborhood in Rn )

1.1.2 Boundaries and Interfaces

@ O = fp 2 O j (8 " > 0) (9 q1 q2 2 B n (" p) such that (q1 2 O) ^ (q2 2 Oc ))g

D EFINITION 1.4 (Open/Closed sets, Closure.)

✦ O is an open set iff (8 p 2 @ O) p 2= O.

D EFINITION 1.6 (Interior and Exterior Points, Boundary Points)

D EFINITION 1.7 (Continuous Interface in Rn )

@ OA B = fp 2 OA OB j 8 " > 0 (9 q q 2 B n (" p) such that (q 2 OA ) ^ (q 2 OB ))g

If (OA B n @ OA B ) = ∅, then @ OA B is called the interface between regions OA and OB (or

(b) (d) (e)

Figure 1.1: Boundary @ O0 of an object O  R2. (a)0 Point pa is a boundary

D EFINITION 1.8 (Geodesic Neighborhood)

Remarks. Strictly speaking, the Euclidean distance kk

1.1.3 Connected Sets and Objects

N OTATION 1.1 (Closed and Open intervals)

Finnaly, if A is not disconnected, it is called connected.

D EFINITION 1.10 (Object)

d@ (p q) Geodesic distance between points p q 2 @V V R3. 26

O = O n @O Geometric interior of continuous set O. 25

V = V n V Discrete Geometric interior of voxelized set V . 93

Figure 1.1: Boundary @ O0 of an object O R2. (a)0 Point pa is a boundary

9 N 2 N 9 fOk R j Ok is a connected set

uu = OR R R dx dy dz v w 2 (fx y zg; fug): (1.7)

✦ if c a and b a, then I1 measures an elongated, prolate uniaxial anisotropy. Equiv-

✦ I3 is the relative intervariance eccentricity; if it is high (case a

fx 1 + (1 ; )x2g 2 O with 2 0 1]: (1.15)

(8 function B ) (9 constant C ) (8 x 2 X y 2 Y ) j KA(xjy ) KB (xjy ) + C

L = frtjrt = pk + t(pk ; ql ) t 2 0 1]g