Lattice-Fringe Fingerprinting Bjorge PDF

Volume 1, Issue 1, 2007
Lattice-Fringe Fingerprinting: Structural Identification of Nanocrystals

Employing High-Resolution Transmission Electron Microscopy
Ruben Bjorge, PhD student, Norwegian University of Science and Technology. Email: ruben.bjorge@ntnu.no
Abstract
Lattice-fringe fingerprinting is a novel method of identifying nanocrystals on the basis of the Fourier trans-
forms of high-resolution transmission electron microscopy (HRTEM) images. The spacings between lattice
fringes and the interfringe angles, measured when nanocrystals show crossed lattice fringes in HRTEM
images, are used to initially “fingerprint” the nanocrystal. The two-dimensional space group symmetry of
the projected electrostatic potential can also be used within the range of the validity of the weak phase-
object approximation (and probably also somewhat beyond) for fingerprinting purposes. For an abundance
of nanocrystals, the theory of lattice-fringe visibility (Fraundorf et al., 2005) makes it possible to compare the
frequency of the observation of any zone axis in a HRTEM image to the theoretical probability of observing
that zone axis, providing additional fingerprinting information.
Lattice-fringe fingerprinting was applied to three different crystal systems: titania, iron oxide and simulated
images of gallium nitride. The titania nanocrystals were found to be rutile in the [111] orientation. For iron
oxide, the results were inconclusive because a solid solution between magnetite and maghemite is likely to
exist. The majority of the iron oxide nanocrystals showing crossed lattice fringes were oriented close to the
[211] orientation.
The analysis of simulated images of gallium nitride demonstrated the prospective possibility of using the
phases of the Fourier coefficients of HRTEM images in identifying a crystal structure. These phases could
in the future be compared directly to calculated structure factor phases for a range of candidate structures in
order to make lattice-fringe fingerprinting more discriminative. In this thesis, only the phase restrictions and
phase relations due to the projected space group symmetry were used as another component of lattice-fringe
fingerprinting.
Lattice-fringe fingerprinting requires a comprehensive database of crystallographic information combined
with search/match algorithms to be employed for the identification of an unknown nanocrystal out of a range
of candidate structures. Such crystallographic information is freely available from the Crystallography Open
Database, its mainly inorganic subset at Portland State University’s research servers, and the emerging
Nano-Crystallography Database.
Lattice-fringe fingerprinting:
Structural identification of nanocrystals employing
high-resolution transmission electron microscopy
by
Ruben Bjorge
A thesis submitted in partial fulfillment of the

requirements for the degree of
Master of Science
in
Physics
Portland State University

2007
Acknowledgments
There are a number of people I would like to acknowledge for their advice and assistance without which this
work would not have been possible.
First of all, I wish to thank my adviser, prof. Peter Moeck, for all his support over the course of my two
years at PSU. It has been invaluable to be able to draw upon his knowledge of electron microscopy and
crystallography in my research.
I would also like to express my gratitude to prof. Bjoern Seipel for his help with the lattice-fringe fingerprinting,
our useful conversations and for his patience with my grading.
I must also thank the rest of my thesis committee, prof. Rolf Koenenkamp and prof. Sherry Cady, for their
valuable suggestions and our discussions concerning my thesis.
I was fortunate to have the opportunity to stay at Technische Universität Chemnitz over the summer of 2006
and to be able to use the transmission electron microscope there. I thank prof. Michael Hietschold for
welcoming me into his group, and Dr. Schulze and Dr. Falke for all their help with using the microscope and
writing scripts.
I thank Modesto Godinez of Portland State University for the images of the titania nanocrystals and Eric
Mandell of the University of Missouri-St. Louis for images of iron oxide nanocrystals. I thank Dr. Klaus
Pecher at Pacific Northwest National Laboratory for providing the iron oxide nanocrystals.
I am grateful for my fellow graduate students in the physics department who have made my stay at PSU so
much more enjoyable and the hard times more bearable.
Finally, I am indebted to Amanda, for her unwavering support, encouragement and love.
iv
Table of Contents
Page
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iv
List of Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
List of Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 Overview of the Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1.2 Review of Standard Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.3 Overview of Experimental Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Chapter 2 High-Resolution Transmission Electron Microscopy . . . . . . . . . . . . . . . . . . . 3
2.1 The Fourier Transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

2.2 Kinematical Scattering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.3 Dynamical Scattering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.4 Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.5 Lattice-Fringe Visibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.6 Fourier Coefficients of the Electrostatic Potential . . . . . . . . . . . . . . . . . . . . . . . . . 9
Chapter 3 Lattice-Fringe Fingerprinting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.1 Lattice-Fringe Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

3.2 Sub-Pixel Interpolation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.3 Lattice-Fringe Visibility and Probability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.4 Phases of the Fourier Coefficients of Images . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.5 Database Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.6 Search/Match Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
v
Page
Chapter 4 Application of Lattice-Fringe Fingerprinting . . . . . . . . . . . . . . . . . . . . . . . . 23
4.1 Computer Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

4.2 Titania . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
4.3 Iron Oxide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
4.4 Fourier Coefficient Phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
4.4.1 Gallium Nitride . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
4.4.2 Titania . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Chapter 5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
5.1 Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Chapter 6 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Appendix Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
vi
List of Tables
Table Page
2.1 Reflection conditions due to cell centering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.1 The effect of lattice parameter distortions on rutile . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.2 Phase relations of the 17 two-dimensional space groups . . . . . . . . . . . . . . . . . . . . . . . 21
4.1 Calculated structure factor phases and measured Fourier coefficient phases for the reflections
present in gallium nitride in the [010] orientation . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
vii
List of Figures
Figure Page
2.1 Lattice-fringe visibility band . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
3.1 Lattice-fringe fingerprinting flowchart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.2 (a) Simulated HRTEM image of silicon in the [100] orientation. (b) Fourier transform of the HRTEM
image. (c) Lattice-fringe fingerprint plot from measurements of the Fourier transform. . . . . . . . 13
3.3 (a) Schematic of an M × N pixel image. (b) Plot of the one-dimensional Hanning window. . . . . 15
3.4 (a) Closeup of a Fourier transform peak. (b) Plot of the intensity of the pixels along the horizontal
line through (k, l) (black dots) and the interpolating intensity curve (solid curve). . . . . . . . . . . 16
3.5 Simulated image showing sinusoidally varying fringes . . . . . . . . . . . . . . . . . . . . . . . . 18
3.6 (a) Fourier transform of a TEM image of amorphous carbon film showing the dependence of
the contrast transfer function on the magnitude of u. (b) Simulated graph of a contrast transfer
function at Scherzer defocus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.1 Theoretical lattice-fringe fingerprint plot of anatase . . . . . . . . . . . . . . . . . . . . . . . . . . 24
4.2 Theoretical lattice-fringe fingerprint plot of brookite . . . . . . . . . . . . . . . . . . . . . . . . . . 25
4.3 Theoretical lattice-fringe fingerprint plot of rutile . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
4.4 (a) HRTEM image of a titania nanocrystal. (b) The Fourier transform of the area inside the white
square. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
4.5 Indexed Fourier transform of the region in figure 4.4 assuming [111] rutile. . . . . . . . . . . . . . 26
4.6 Lattice-fringe fingerprint plot from titania images . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
4.7 Averaged lattice-fringe fingerprint plot from titania images . . . . . . . . . . . . . . . . . . . . . . 27
4.8 Theoretical lattice-fringe fingerprint plot of magnetite . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.9 Theoretical lattice-fringe fingerprint plot of maghemite . . . . . . . . . . . . . . . . . . . . . . . . 30
viii
Figure Page
4.10 (a) HRTEM image of iron oxide nanocrystal. (b) Fourier transform of the nanocrystal. . . . . . . . 31
4.11 Lattice-fringe fingerprint plot from iron oxide nanocrystal . . . . . . . . . . . . . . . . . . . . . . . 32
4.12 Lattice-fringe fingerprint plot of magnetite in the h211i direction . . . . . . . . . . . . . . . . . . . 32
4.13 Indexed Fourier transform of an image of a magnetite nanocrystal . . . . . . . . . . . . . . . . . 33
4.14 (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image. . . . 34
4.16 (a) HRTEM image of iron oxide nanocrystal. (b) The Fourier transform of the image. . . . . . . . 36
4.17 Lattice-fringe fingerprint plot from iron oxide nanocrystal . . . . . . . . . . . . . . . . . . . . . . . 37
4.18 Indexed Fourier transform of the nanocrystal in figure 4.16 . . . . . . . . . . . . . . . . . . . . . . 37
4.19 (a) HRTEM image of iron oxide nanocrystal. (b) The Fourier transform of the image. . . . . . . . 39
4.27 Symmetry elements of the pg two-dimensional space group . . . . . . . . . . . . . . . . . . . . . 47
4.28 (a) Simulated image of GaN, 5 nm thickness oriented along [010]. (b) The indexed Fourier trans-
form of the image. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
4.29 Fourier transform with measured phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
4.30 HRTEM image of a titania nanocrystal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
ix
List of Symbols
Symbol Page
a Diameter of the objective aperture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
aj Parameter for the fit of f e (s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
A(u) Aperture function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
bj Parameter for the fit of f e (s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Cs Spherical aberration of the objective lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
dhkl Lattice-plane spacing of the (hkl) planes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
e Elementary charge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
f (θ) Atomic scattering factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
f e (s) Atomic scattering factor for electrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
fX Atomic scattering factor for x-rays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
F (g) Structure factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
F Fourier transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
F −1 Inverse Fourier transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
g Three-dimensional position vector in reciprocal space . . . . . . . . . . . . . . . . . . . . . . . . 3
g hkl Reciprocal-space vector for the planes with indices hkl . . . . . . . . . . . . . . . . . . . . . . . 5
h Planck’s constant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
hkl Miller indices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
I Intensity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
x
Symbol Page
m Relativistic electron mass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Puvw Probability of seeing a family of zone axes huvwi . . . . . . . . . . . . . . . . . . . . . . . . . . 7
qe (r) Specimen transmission function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
r Three-dimensional position vector in direct space . . . . . . . . . . . . . . . . . . . . . . . . . . 3
s |g|/2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
t Crystal thickness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
t(r) Spread function of the objective lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
T (u) Microscope transfer function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
u Two-dimensional vector in the back focal plane of the objective lens . . . . . . . . . . . . . . . . 6
w Weighting factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Xkl Complex Fourier coefficient of the pixel at (k, l) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
αmax Visibility band half-width . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
χ(u) Phase-distortion function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
δ Dirac delta function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
∆ Difference parameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
∆tot Total difference parameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
∆f Objective lens defocus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
φ Phase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
φobs Observed phase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
φres Phase residual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
φsym Phase determined from symmetry relations and restrictions . . . . . . . . . . . . . . . . . . . . . 19
xi
Symbol Page
ϕ(r) Electrostatic potential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
ϕp (r)Projected electrostatic potential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Φp Fourier transform of the projected electrostatic potential . . . . . . . . . . . . . . . . . . . . . . . 6
Γ Visibility factor in calculating lattice-fringe visibility band half-widths . . . . . . . . . . . . . . . . . 7
λ Wavelength . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Ω Solid angle subtended by the intersection of two visibility bands . . . . . . . . . . . . . . . . . . . 7
ψ0 Wave incident on the specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
ψex Exit-surface wave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
ψim Image plane electron wave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Ψex Fourier transform of ψex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Ψim Fourier transform of ψim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
ρSch Scherzer, or point, resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
σ Interaction constant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
θ Angle between the incident wave vector and the lattice planes . . . . . . . . . . . . . . . . . . . . 4
⊗ Convolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
xii
Chapter 1
Introduction
This thesis deals with a method of identifying nanocrystals using lattice fringes observed in high-resolution
transmission electron microscopy (HRTEM) images. Since these lattice fringes are used to uniquely identify
a nanocrystal, the method is named lattice-fringe fingerprinting.
The interest in nanometer-sized crystals has increased over the last several years. Nanocrystals are ap-
pealing for their novel and improved physical, chemical, and biological properties relative to those of the
materials in their bulk form. New identification methods are needed for ensuring quality and reproducibility
in the production of these particles. Novel methods are particularly desirable for any large-scale commercial
manufacturing process. These new identification methods should preferably require minimal operator skill
and supervision (Saltiel and Giesche, 2000). The goal of lattice-fringe fingerprinting is to meet these needs
using HRTEM.
1.1 Overview of the Method
To identify nanocrystals, lattice-fringe fingerprinting uses the information contained in crossed lattice fringes
that appear in HRTEM images. Lattice fringes are caused by the diffraction of the incident electrons by the
specimen and appear as periodic light and dark bands in the image. Crossed lattice fringes are formed by the
intersection of two or more sets of lattice fringes. Crossed lattice fringes will be visible when the nanocrystal
is oriented close to a zone axis.
The primary information used in lattice-fringe fingerprinting is the spacing of the lattice fringes and the angle
between intersecting lattice fringes (i. e., the interfringe angle). This information is characteristic of the crystal
structure. Instead of working with the actual images, it is more convenient to use the Fourier transform of the
HRTEM image, calculated using the fast Fourier transform (FFT) algorithm.
When the spacings and angles are not sufficient to identify a nanocrystal, and the nanocrystal is suitably thin,
the phase information in the Fourier transform of the image can be used. Determining the phase correctly
requires the determination of the origin of a unit cell in the nanocrystal. For an ensemble of nanocrystals
another way of making use of lattice fringes is to compare the abundance of visible lattice fringes with
calculated probabilities based on the theory of lattice-fringe visibility (Fraundorf et al., 2005).
1.2 Review of Standard Methods
Powder X-ray diffraction is the standard method of identifying crystal structures. This method works best for
micrometer-sized crystals and becomes less useful for crystals in the nanometer range, as demonstrated,
for example, in López Pérez et al. (1997). Powder x-ray diffraction gives the lattice-plane spacings and the
corresponding intensities, but does not provide the interplanar angles as in lattice-fringe fingerprinting. X-rays
are also much less sensitive than electrons to changes in the electrostatic potential.
1
Parallel-illumination electron diffraction is also used to identify crystal structures. This can be done by com-
paring the diffractogram with values calculated from known structures in a database. This process has been
automated by, for example, Hart (2002) using the two smallest reciprocal lattice spacings and the angle
formed by the intersection of these two planes. The information from electron diffraction patterns is often
combined with knowledge of the chemical composition of the material gained using energy-dispersive x-ray
spectroscopy or electron energy-loss spectroscopy. Single crystals down to a size of a few tenths of a mi-
crometer can be identified using parallel-illumination electron diffraction. Smaller crystals, on the order of
tens of nanometers, can be identified using electron powder diffraction, but these ring patterns only give the
lattice-plane spacings.
Convergent-beam electron diffraction (CBED) is also used in studying crystals. The fine structure of the
CBED disks can be used to identify the crystal. However, CBED patterns of nanocrystals are usually devoid
of this fine structure (Williams and Carter, 1996).
1.3 Overview of Experimental Procedures
To study lattice-fringe fingerprinting, HRTEM images of three different materials were examined: titania (tita-
nium dioxide), iron oxide and gallium nitride.
The images of titania were taken using an FEI G2 F20 TEM equipped with a field-emission gun at Portland
State University, with a point resolution of 0.24 nm. Some images of iron oxide nanocrystals were taken at the
University of Missouri-St. Louis using a Philips EM 430ST, with a LaB6 electron source and a point resolution
of 0.19 nm. Other iron oxide images were taken at Technische Universität Chemnitz on a field-emission
Philips CM20 TEM. Theoretical HRTEM images of gallium nitride were simulated using WebEMAPS (Zuo
and Mabon, 2004).
Gatan Digital Micrograph was used to process and analyze HRTEM images. The built-in scripting support of
Digital Micrograph made it possible to automate parts of the lattice-fringe fingerprinting process.
2
Chapter 2
High-Resolution Transmission
Electron Microscopy
The underlying idea of high-resolution transmission microscopy is using both the direct electron wave and
several diffracted electron waves in forming the image. This increases the resolution of the image. The
electron waves interfere with one another due to phase differences, creating an interference pattern in the
image plane of the objective lens. HRTEM is therefore a type of phase-contrast microscopy.
Electron scattering must be treated quantum mechanically. Actually, a 200 keV electron has a speed of
approximately 0.7c, where c is the speed of light in vacuum, and should therefore be treated using relativistic
quantum mechanics. However, in electron microscopy it is normally sufficient to just replace the mass and
wavelength of the electron with corresponding relativistic values (De Graef, 2003, p. 94).
2.1 The Fourier Transform
The Fourier transform plays an important role in HRTEM. It is a convenient tool for analyzing images, but
it also plays a more fundamental role in HRTEM theory. There are a number of different conventions when
using the Fourier transform. Here the convention most common in crystallography will be used. The Fourier
transform of a function f (r) is then defined as
Z∞
F (g) = F [f (r)] ≡ f (r)e2πig·r dr, (2.1)
−∞
where r is a three-dimensional position vector in direct space and g is a three-dimensional position vector in
Fourier transform, or reciprocal, space. The inverse Fourier transform is defined as
Z∞
f (r) = F −1 [F (g)] ≡ F (g)e−2πig·r dg. (2.2)
−∞
When Fourier transforming a set of sampled data, the discrete Fourier transform (DFT) must be used instead
of the continuous Fourier transform above. The most common implementation of the DFT on computers is
the fast Fourier transform (FFT) algorithm.
The convolution is important to understanding HRTEM. The convolution, or folding, of two functions, f (r)
and h(r), is defined as Z
f (r) ⊗ h(r) = f (R)h(r − R) dR. (2.3)
There is a useful theorem relating the convolution in direct space to multiplication in Fourier transform space
called the convolution theorem:
F [f (r) ⊗ h(r)] = F (g) H(g). (2.4)
3
The multiplication theorem relates multiplication in direct space to convolution in Fourier transform space:
F [f (r) h(r)] = F (g) ⊗ H(g). (2.5)
2.2 Kinematical Scattering
In one approach to quantum scattering, the wave equation is converted to integral form using the Green’s
function. This integral equation can then be expanded into the Born series. As a first-order approximation,
only the first term of the Born series is used, the so-called first Born approximation. This is equivalent
to assuming the electron is scattered no more than once when passing through the specimen. This is
called single, or kinematical, scattering. Using only the first term of the Born series also assumes that the
directly transmitted electron wave can be reasonably approximated by the incident wave. In other words, the
amplitude of the diffracted waves is negligible compared to the amplitude of the direct wave.
The first Born approximation is equivalent to the Fraunhofer diffraction approximation, where the diffracting
object is assumed to be much smaller than the distances to the source and the point of observation (Cowley,
1981). From the expression for Fraunhofer diffraction one can derive the phase-object approximation (POA).
The POA gives the specimen transmission function, qe (r), as
qe (r) = e−iσϕp (r) , (2.6)
where σ is the interaction constant and ϕp (r) is the projection of the electrostatic potential of the specimen,
ϕ(r), along the direction of the electron beam. The interaction constant is defined as
2πmeλ
σ= , (2.7)
h2
where m is the relativistic mass of the electron, e is the elementary charge, λ is the electron wavelength and
h is Planck’s constant.
As the name implies, the phase-object approximation assumes that only the phase of the complex electron
wave is affected when moving through the specimen. If the incident wave is ψ0 (r) and the exit-surface wave
is ψex (r) then, in the POA, ψex (r) = qe (r) ψ0 (r). Since ψ0 (r) is assumed to be constant, we can set it
equal to unity. Then, ψex (r) = qe (r).
If we assume that σϕp (r) is much less than unity we can approximate (2.6) using the first-degree Taylor
polynomial of qe (r):
qe (r) ≈ 1 − iσϕp (r). (2.8)
This is called the weak phase-object approximation (WPOA). The assumption that σϕp (r) is small holds for
many thin specimens. However, it fails for an electron passing through the center of even a single uranium
atom (Williams and Carter, 1996, p. 462).
For specimens that are too thick for the WPOA to hold, Li and Tang (1985) proposed the pseudo-weak
phase-object approximation. This approximation takes into account that as the specimen thickness increases
beyond the limits of the validity of the WPOA, the heavy atoms start looking more like lighter atoms and vice
versa. The specimen is therefore replaced by its imaginary isomorph.
The diffraction of electron waves by a crystal can also be understood in terms of Bragg’s law. Electron
waves diffracted by a set of parallel planes with Miller indices hkl will add constructively if the path difference
between waves diffracted by separate planes is a multiple of the wavelength. Hence,
2dhkl sin θ = nλ, (2.9)
where dhkl is the lattice-plane spacing of (hkl), θ is the angle between the incident wave vector and the
lattice planes and n is an integer.
4
A set of parallel lattice planes belongs to a certain zone axis if the planes are parallel to that zone axis. This
is known as the Weiss zone law. A set of parallel lattice planes can be described by a three-dimensional
reciprocal-space vector g hkl = ha∗ + kb∗ + lc∗ , where |g hkl | = 1/dhkl , that is normal to the set of lattice
planes. a∗ , b∗ and c∗ are the basis vectors of reciprocal space. It follows that g must be perpendicular to
the zone axis direction [uvw] = ua + vb + wc, where a, b and c are the basis vector of direct space. Using
a generalized dot product, this gives hu + kv + lw = 0.
2.3 Dynamical Scattering
If the specimen is so thick or massive that electron waves are scattered more than once, the kinematical
approximation no longer holds and we must consider multiple, or dynamical, scattering. The extent of dy-
namical effects depends on the magnitude of ϕ(r). Since a constant term can be added to the electrostatic
potential, it is actually the variation of ϕ(r) that matters. If the crystal is perfectly aligned with the incoming
beam parallel to a zone axis, ϕ(r) will change from a relatively large value at the atomic columns to a much
smaller value between the columns. If the crystal is tilted slightly away from the zone axis so that the atomic
columns appear as lines instead of points, the dynamical effects will be reduced since the variations in ϕ(r)
are smaller.
Dynamical scattering results in the presence of a kinematically extinct reflection h3 k3 l3 that is the result of
diffraction of the electron wave by two or more sets of planes. For example, in the case of double diffraction,
the wave is first diffracted by the planes (h1 k1 l1 ) and then by the planes (h2 k2 l2 ) according to the following
equations:
h3 = h1 + h2 ,
k3 = k1 + k2 ,
l3 = l 1 + l2 . (2.10)
This means that reflections that are kinematically forbidden due to the presence of screw axes or glide
planes will be present in the diffraction pattern of a crystal that scatters dynamically. However, kinematically
forbidden reflections due to unit-cell centering (Sands, 1993) do not appear in dynamical scattering (Denley
and Hart, 2002). The reflection conditions imposed by the different types of cell centering are listed in
table 2.1
Type of Condition limiting possible

centering reflections
A k + l = 2n
B h + l = 2n
C h + k = 2n
I h + k + l = 2n
F h + k, k + l, l + h = 2n
Table 2.1: Reflection conditions due to cell centering. These conditions apply to all reflections hkl.
2.4 Imaging
The purpose of HRTEM is the imaging of the electron waves. Using film, or more commonly a CCD camera,
the intensity I(r) = |ψim (r)|2 , of the waves is recorded, where ψim (r) is the electron wave reaching the
5
detector. In order to identify a nanocrystal from HRTEM images, these intensities must be related back to the
crystal structure. However, before the exit-surface waves reach the recording medium, they are focused by
the objective lens and magnified by the projection system. The effect of the projection system on the electron
wave is small compared to the effect of the objective lens. ψim (r) can therefore be taken to be the electron
wave in the image plane of the objective lens.
The effect of the objective lens is the convolution of the exit-surface wave with a spread function, t(r), of the
objective lens: ψex (r) ⊗ t(r). Using the convolution theorem we can write
ψim (r) = ψex (r) ⊗ t(r) = F −1 [Ψex (u) T (u)] , (2.11)
where Ψex (u) is the Fourier transform of ψex (r) and T (u) is called the transfer function of the microscope.
u is a two-dimensional vector in the back focal plane of the objective lens.
The transfer function of a perfectly coherent microscope can be expressed as the product of an aperture
function A(u), due to the objective aperture, and a phase factor exp{iχ(u)}, due to the defocus and aberra-
tions of the objective lens. The aperture function is a simple step function with a value of unity for u < a/2,
where a is the diameter of the objective aperture, and zero everywhere else. The phase factor will depend on
the defocus and any aberrations of the objective lens. Assuming the two-fold astigmatism has been corrected
for, the spherical aberration, Cs , will be the most significant aberration of the objective lens. If we only take
the defocus and Cs into account, then
1
χ(u) = πλ∆f u2 + πCs λ3 u4 , (2.12)
2
where ∆f is the defocus of the objective lens. Williams and Carter (1996) call χ(u) the phase-distortion
function.
Following Cowley (1988), we rewrite the spread function as the sum of a real and imaginary part: t(r) =
c(r) + is(r), where c(r) = F[A cos χ(u)] and s(r) = F[A sin χ(u)]. Using this expression we can find a
simple relationship between an image and the projected electrostatic potential in the range of validity of the
WPOA. Since ψex (r) = qe (r) = 1 − iσϕp (r), I(r) = |[1 − iσϕp (r)] ⊗ [c(r) + is(r)]|2 . Multiplying this out
and ignoring terms of [σϕp (r)]2 since we assume this product is small, we get I(r) = 1 + 2σϕp (r) ⊗ s(r).
Hence, taking the Fourier transform we get
F [I(r)] = δ(u) + 2σΦp (u) A(u) sin χ(u), (2.13)
where Φp (u) is the Fourier transform of the projected electrostatic potential. The Dirac delta function, δ ,
corresponds to the central direct beam. Such a simple linear relationship between the projected electrostatic
potential and the image is only possible when the WPOA is valid.
From equations (2.12) and (2.13) we see that the presence or absence of information in the image depends
on the complicated oscillations of sin χ(u), often called the contrast transfer function (CTF). Scherzer (1949)
showed that these oscillations can be suppressed
q out to a limit uSch by suitable adjustment of the defocus.
4
The so-called Scherzer defocus is ∆f = − 3 Cs λ. The first crossover of sin χ(u) will then occur at uSch =
− 14
1.51(Cs λ3 ) . Taking the reciprocal of this gives the Scherzer or point resolution of the microscope: ρSch =
1
0.66(Cs λ3 ) 4 . Images with spacings greater than ρSch are said to be directly interpretable.
A real microscope will not have a perfectly coherent electron source. This means that there will be a range
of values for the kinetic energy of the electrons and there will be a certain spread of angles from the source.
These imprecisions will affect the transfer function, T (u), of the microscope. There is no simple way of
expressing this effect in general. However, in the case of the WPOA these effects can be represented by
envelope damping functions that are multiplied by the transfer function. The most important of these are the
envelope functions due to chromatic aberration and the angular spread of the source.
6
The envelope functions put an absolute limit on the information obtainable from a specimen. In an field
emission gun (FEG) TEM the information-limit resolution is often much greater than the Scherzer resolution
of the microscope. This makes it important to be careful when interpreting an image from such a microscope.
It is possible to define a third type of resolution in HRTEM that is due to dynamical scattering effects. This is
called “fringe” resolution (O’Keefe, 1992). This name is derived from the fact that it is the smallest spacing
between lattice fringes visible in the image. In dynamical scattering the diffracted beams are not necessarily
much weaker than the direct beam. These diffracted beams can therefore interfere with one another creat-
ing peaks in the image intensity spectrum (i. e., Fourier transform of the image) beyond spatial frequencies
passed by the transfer function. This non-linear interference might be understood from the general equation
∗ ∗ ∗
for the image intensity spectrum, I(u) = F[ψim (r)ψim (r)] = F[ψim (r)] ⊗ F[ψim (r)] = Ψim (−u) ⊗ Ψim (u),
∗
where in this case denotes the complex conjugate and Ψim is the Fourier transform of ψim . The convolu-
tion of one diffracted beam with another diffracted beam will give an intensity spectrum peak with a spatial
frequency |u|, possibly larger than the spatial frequencies of the diffracted beams.
2.5 Lattice-Fringe Visibility
The theory of lattice-fringe visibility developed by Fraundorf et al. (2005) is potentially useful for the identifi-
cation of nanocrystals. This theory calculates the probability of seeing a set of lattice fringes for a randomly
oriented nanocrystal using the concept of lattice-fringe visibility bands. A visibility band is the solid angle
consisting of the ensemble of electron beam incident directions for which a set of parallel lattice planes is
visible (figure 2.1). Assuming a spherical crystal, this visibility band will be symmetric about a great circle.
The visibility-band half-width is given as
( " 2 #)
Γ λ Γ
αmax = arcsin d + 1− d , (2.14)
t 2d t
where t is the crystal thickness and Γ is a “visibility” factor taking into account non-ideal imaging conditions.
R π/2+αmaxR 2π
The solid angle subtended by a visibility band with half-width αmax is π/2−αmax 0
sin θ dθdφ = 4π sin αmax .
The probability of seeing a family of symmetrically equivalent planes {hkl} with spacing d is therefore
sin αmax times the multiplicity of the planes.
The solid angle, Ω , subtended by the intersection of two visibility bands with half-widths αmax and βmax
intersecting at an angle γ is approximately given by the equation
2(2αmax )(2βmax )
Ω≈ . (2.15)
sin γ
The probability, Puvw , of seeing a family of zone axes huvwi is therefore
2αmax βmax
Puvw = × (multiplicity) . (2.16)
π sin γ
7
Figure 2.1: Lattice-fringe visibility band (shaded) for a set of lattice planes parallel to the great circle shown
passing through A. The sphere represents all possible electron beam directions incident on the specimen
(converging on O). The lattice fringes are visible when the electron beam passes through the visibility band.
The visibility-band half-width, 6 AOB , is equal to αmax in (2.14). The solid angle subtended by the visibility
band is 4π sin αmax (Fraundorf et al., 2005).
8
2.6 Fourier Coefficients of the Electrostatic Potential
The atomic scattering factor, f (θ), gives the probability of scattering by a single atom at a certain angle θ. By
using Bragg’s law (2.9), we can relate this scattering angle to a set of parallel planes with normal vector g .
For the scattering of electrons by atoms, the atomic scattering factor, f e , is defined as the Fourier transform
of the electrostatic potential (Cowley, 1981):
Z
e
f (g) = ϕ(r)e2πig·r dr. (2.17)
From this one can derive the Mott-Bethe formula as given by De Graef (2003):
|e|
f e (s) = Z − f X (s) , (2.18)

16π 2 0 |s|2
where s = |g|/2, e is the elementary charge and f X is the atomic scattering factor for x-rays.
Instead of using (2.18) directly, this equation is typically parametrized with a set of Gaussians. One such
parametrization, by Doyle and Turner (1968), gives the scattering factors as
4
X 2
e
f (s) = 0.04787 801 aj e−bj s , (2.19)
j=1
where aj and bj are listed for each element in a table.

From the atomic scattering factors for single atoms, one can calculate the scattering due to a whole unit cell
assuming kinematical (i. e., single) scattering. This is called the structure factor, F (g), and is a summation
of f e (g) over all the atoms in the unit cell located at positions ri :
X X
F (g) = fie eiφi = fie e2πig·ri . (2.20)
i i
The different positions of the atoms in the unit cell give a path difference between contributions from different
scattering centers. These path differences give rise to the phase, φ, of the structure factor. It is apparent
from (2.20) that the structure factor of a centrosymmetric unit cell will be real since the contribution to the
imaginary part from an atom at r will be canceled by the contribution from the symmetrically equivalent atom
at −r :
f e e2πig·r + f e e2πig·(−r) = 2f e cos(2πg · r). (2.21)
In the weak phase-object approximation, the structure factor corresponding to a set of parallel planes (hkl),
F (g hkl ), is proportional to Φp (u) in equation (2.13), the Fourier transform of the projected electrostatic
potential, ϕp (r). This means that the structure factor amplitudes should, in theory, be obtainable from the
amplitudes of the peaks in the Fourier transform of an HRTEM image. However, the amplitudes are strongly
affected by oscillations of the transfer function and crystal tilt (Zou and Hovmöller, 2002). The phase of Φp (u)
is much more reliable though. Oscillations of the transfer function and zone axis misalignment only lead to
phase shifts in jumps of 180◦ (Zou, 1995). For small tilts, the phases are unaffected. Hence, the Fourier
coefficient phases will either equal the structure factor phases or differ by 180◦ . The phases of peaks in the
Fourier transform of HRTEM images can therefore assist in the identification of nanocrystals. The fact that
the structure factor phases are preserved in a TEM image was first noted by De Rosier and Klug (1968).
9
Chapter 3
Lattice-Fringe Fingerprinting
Lattice-fringe fingerprinting is the name given to the method of identifying nanocrystals using high-resolution
phase-contrast TEM images. There are different pieces of information that can be used in this method. These
different pieces are lattice-fringe vectors, lattice-fringe probability, in the case of studying many nanocrystals,
and phases of the Fourier coefficients of the image. The identification of an unknown nanocrystal becomes
more likely if more of the available information in the image is used.
Identifying an unknown nanocrystal using lattice-fringe fingerprinting is only possible with a database of
lattice-fringe fingerprinting information. A crystallographic database containing lattice-fringe fingerprint infor-
mation combined with search/match algorithms is therefore a work in progress in the Nanocrystallography
Group at Portland State University. A flowchart outlining the steps involved in lattice-fringe fingerprinting is
shown in figure 3.1.
3.1 Lattice-Fringe Vectors
The main component of lattice-fringe fingerprinting is using the characteristic spacing between lattice fringes
and the angles at which different sets of lattice fringes intersect. Areas showing crossed lattice fringes
are used since lattice-fringe spacings are more reliable when the nanocrystal is oriented close to a zone
axis (Malm and O’Keefe, 1997). The measurements can be made by directly inspecting the high-resolution
image, but it is much more convenient to work in reciprocal space by means of the Fourier transform.
A fast Fourier transform (FFT) is therefore computed of a region showing crossed lattice fringes after appro-
priate filters have been applied to the image (figure 3.2). Any periodicity in the image will show up as peaks
in a plot of the modulus of the Fourier transform, also called the power spectrum. Each set of lattice fringes
is transformed into two diametrically opposed peaks in the power spectrum. The radial positions of the peaks
can then be measured. The distance from each peak to the center of the Fourier space corresponds to the
inverse spacing between the lattice fringes. The angles between the different sets of lattice fringes, the in-
terfringe angle, can also be found by measuring the central angle between the peaks of the power spectrum.
Fourier coefficients on opposite sides of the center are conjugate pairs. Therefore, not all of the peaks and
angles in the power spectrum need to be measured.
The lattice-fringe spacing corresponds to the reciprocal lattice spacing, ghkl , of a set of parallel planes (hkl).
The reciprocal lattice spacing and interfringe angles can be displayed in a lattice-fringe fingerprint plot, in
which interfringe angle is plotted versus reciprocal spacing (Fraundorf et al., 2005). Intersections between
two lattice fringes of different spacing appear as two data points in the lattice-fringe fingerprint plot, whereas
intersections between two symmetrically equivalent lattice fringes give only a single data point in the plot.
The lattice-fringe fingerprint plot provides a convenient way of displaying recorded data and facilitates the
comparison between experimental data and theoretical lattice-fringe fingerprint plots calculated from lattice
parameters.
Measuring the reciprocal lattice vectors using the power spectrum is a common method in high-resolution
electron microscopy. In fact, before the widespread use of computers a diffractogram of an image was
10
Find crossed
HRTEM image
lattice-fringes
Run
Select rectangular
hanning_FFT
region
script
Select Fourier Run measure_FT

transform peaks script
Find origin and

Measure relative measure phases
abundance of zone
axes
Compare with
calculated data
Match
Figure 3.1: Lattice-fringe fingerprinting flowchart.
11
created by using a light source and the image on a transparent film as a diffraction grating on an optical
bench. Using the FFT, one can make much more precise measurements. This precision can be increased
through so-called sub-pixel interpolation.
12
004
Interfringe angle
0
22 022
°
45
0 4 0 000 0 40
0
22 02
2
00
4
(a) (b)
90
80 Intersection of
symmetrically Intersection of
Interfringe angle (degrees)
70 equivalent {022} symmetrically

planes equivalent {004}
60 planes
50
40
30 Intersection of {022}
and {004} planes
20
10
0
5.0 5.5 6.0 6.5 7.0 7.5
-1
g (nm )
(c)
Figure 3.2: (a) Simulated HRTEM image of silicon in the [100] orientation (Zuo and Mabon, 2004). (b) Fourier
transform of the HRTEM image. The contrast has been inverted for clarity. The dashed lines represent recip-
rocal lattice vectors. We see, for example, that the (022) and (004) lattice fringes intersect at an interfringe
angle of 45◦ . (c) Lattice-fringe fingerprint plot based on measurements of the Fourier transform.
13
3.2 Sub-Pixel Interpolation
Precision is an obvious concern when measuring reciprocal lattice vectors. Measuring the reciprocal lattice
vectors is equivalent to determining the peaks of the power spectrum. Sub-pixel interpolation, as applied
by de Ruijter (1994) to two-dimensional lattice-fringe images, was used to make these measurements. This
method determines a more precise position of each individual peak. It is also possible to refine the positions
of all the peaks in the power spectrum by using a least-squares method to fit the peaks to a periodic grid.
This could perhaps be used in conjunction with sub-pixel interpolation, but has not been implemented in this
thesis.
To use sub-pixel interpolation, the average intensity must first be subtracted from the image. There will usually
be artifacts caused by the edges of the Fourier transformed region because the Fourier transform assumes
the transformed region repeats indefinitely. This edge effect appears as streaking of the power spectrum
peaks. This causes the intensity of the peaks to decrease. To reduce this effect, the image selection should
be multiplied by a circular window function before Fourier transforming. The two-dimensional hanning window
h m i h n i
Wh (m, n) = 1 − cos 2π 1 − cos 2π (3.1)
M N
is suitable for this purpose. Here M and N are the total number of pixels in the m and n direction, respectively
(figure 3.3).
Sub-pixel interpolation starts with the brightest pixel of a power spectrum peak as a first-order approximation.
A more accurate position of the power spectrum peak is determined by interpolating between the nearest-
neighbor pixels under the assumption that the intensity in the image varies sinusoidally (figure 3.4). If the
position of the brightest pixel is (k, l), fractions of a pixel, k 0 and l0 , are added in each direction. Thus, the
interpolated power spectrum peak will be located at (k + k 0 , l + l0 ). k 0 and l0 are given by the expressions
(de Ruijter, 1994)
c1 |Xk+α,l | − c2 |Xkl |
k0 = α ,
c3 |Xk+α,l | + |Xkl |
c1 |Xk,l+β | − c2 |Xkl |
l0 = β , (3.2)
c3 |Xk,l+β | + |Xkl |
where Xkl is the complex Fourier coefficient of the pixel located at (k, l), and α = ±1 and β = ±1 indicated
the positions of the brightest neighbors of the brightest pixel. c1 , c2 and c3 depend on the window function
used. For the Hanning window, c1 = 2 and c2 = c3 = 1.
Sub-pixel interpolation can be used for more than just determining the position of power spectrum peaks.
Interpolated values can also be found for the amplitude and the phase of the complex Fourier coefficients.
These are given by
2|Xkl | πk 0 πl0
1 − k 02 1 − l02 , (3.3)

A =
M N sin πk 0 sin πl0
φ = arg (Xkl ) + πk 0 + πl0 , (3.4)
where arg(Xkl ) is the argument, or phase, of the complex Fourier coefficient. The terms involving π in (3.4)
are due to the position of the real-space origin in the upper left-hand corner ((0, 0) in figure 3.3) instead of
in the center (de Ruijter, 1994, p. 200). To make use of sub-pixel interpolation, Digital Micrograph scripts
were written that allow lattice-fringe spacings, angles, amplitudes and phases to be found for any number of
selected power spectrum peaks (Appendix).
Sub-pixel interpolation improves the precision of lattice-fringe measurements. The exact precision and ac-
curacy of measurements of nanocrystals have been investigated in several papers. De Ruijter et al. (1995)
14
0 m M −1
0
N −1
(a)
1.5
Wh 1
1
0.5
0
2 4 6 8 M
10
m
(b)
of an M × N pixel image. (b) Plot of the one-dimensional Hanning window

Figure 3.3: (a) Schematic
m
Wh (m) = 1 − cos 2π M .
15
7
4 10
7
3 10
7
k 2 I10
7
1 10
l
k−4 k−3 k−2
-2 k−1 0k k1 k2
2 k3 k4
4
k−0.34
(a) (b)
Figure 3.4: (a) Closeup of a Fourier transform peak (without inverted contrast). The brightest pixel is at (k, l).
(b) Plot of the intensity of the pixels along the horizontal line through (k, l) (black dots) and the interpolating
intensity curve (solid curve) using the pixel values at k and k − 1 to fit the curve to the experimental data. k 0
is found to be −0.34 using (3.2). In this case, α = −1. The same method is applied in the vertical direction
to determine l0 .
16
found for a 15x15 Å region of a reduced oxide phase a precision of 1 %–3 % for the spacing and 0.5◦ –2◦ for
the angle. They concluded that the accuracy, i. e., deviation from expected values, in the measurements for
such small crystals would depend more on thickness variations and misorientation than statistical deviations,
such as shot noise.
It is well-known that for nanocrystals the lattice parameters are dependent on the grain size. Tonejc et al.
(2002) studied anatase nanocrystals with a grain size down to about 5 nm. They reported a deviation from
the x-ray powder diffraction values of up to −1.4 % for the lattice parameter a, and up to −4.1 % for c. Lu
and Zhao (1999) summarize results on lattice distortions found in the literature for various inorganic materials
down to a grain size of 4 nm. None of the lattice parameters were distorted by more than 0.30 %. Table 3.1
shows the effect of a pessimistic distortion of −4.1 % of c in the case of rutile. Using more calculations like
the ones shown, the average angle difference was found to be 0.7◦ , with a maximum angle difference of 2.4◦ .
hkl g g† hkl g g† Angle Angle† Angle differ-

(nm−1 ) (nm−1 ) (nm−1 ) (nm−1 ) (◦ ) (◦ ) ence (◦ )
110 3.08 3.08 11̄0 3.08 3.08 90.0 90.0 0.0
110 3.08 3.08 011 4.02 4.14 67.5 68.2 0.7
101 4.02 4.14 011 4.02 4.14 45.0 43.6 1.4
101̄ 4.02 4.14 1̄01̄ 4.02 4.14 65.6 63.4 2.2
110 3.08 3.08 020 4.35 4.35 45.0 45.0 0.0
101 4.02 4.14 200 4.35 4.35 57.2 58.3 1.1
Table 3.1: The effect of lattice parameter distortions on rutile shown by comparing reciprocal lattice spacings,
g , and interplanar angles. † Values calculated using c decreased by 4.1 %.
In an HRTEM image, there may also be a foreshortening of the lattice-fringe spacings when tilting away,
perpendicular to the lattice fringes (i. e., perpendicular to the visibility band in figure 2.1 on page 8), from
the edge-on view of the lattice fringes. The spacings will be shrunk by a factor of cos α, where α is the
amount of tilt perpendicularly away from the edge-on view. The maximum foreshortening is therefore equal
to cos αmax . This projection effect depends on the lattice-plane spacing and the thickness of the crystal, but
calculations using (2.14) show that this effect will usually be less than half of one percent. For example, the
{111} spacings of magnetite (d111 = 4.80 Å) will be decreased by 0.49 %, assuming a visibility factor, Γ ,
equal to unity and a crystal thickness of 5 nm. These calculations show that lattice parameter distortions due
to nanocrystallinity will not make identification through lattice-fringe fingerprinting impossible.
3.3 Lattice-Fringe Visibility and Probability
The theory of lattice-fringe visibility, as described in section 2.5, can serve as the basis of an additional
method of identifying nanocrystals. The solid angle subtended by crossed lattice fringes, multiplied by the
multiplicity and divided by 4π , can be interpreted as the probability of seeing crossed lattice fringes in a
randomly oriented spherical nanocrystal. This probability can be calculated using (2.15). The probability
gives an idea of which zone axes are most likely to be observed.
Experimental data on the visibility of crossed lattice fringes from a collection of many nanocrystals, such
as a nanopowder, can then be compared with theoretical values. Combined with lattice-fringe vectors, this
information can be used to confirm the identification of a crystal phase. The abundance of certain crossed
17
lattice fringes obtained from a limited set of nanocrystals cannot serve as a method of determining the crystal
phase by itself, but it might serve as a check. The lattice-fringe visibility can also be included in a lattice-fringe
fingerprint plot (Fraundorf et al., 2005).
3.4 Phases of the Fourier Coefficients of Images
The fast Fourier transform is a convenient tool for extracting information from high-resolution images. All the
information contained in the image is contained in the complex Fourier coefficients of the FFT. The positions
of the peaks can be used to measure the lattice-fringe vectors, whereas the Fourier coefficient amplitudes
have been shown to be unreliable (Zou and Hovmöller, 2002). The only other piece of information is the
phase of the Fourier coefficients. The phase of a Fourier coefficient corresponding to a set of lattice fringes
determines the position of the bright lines in the image. Equivalently, the phase determines the relative
intensity of the lattice fringes at the origin of the FFT (figure 3.5). This is analogous to the oscillations of a
spring, f (t) = A cos(ωt + φ), where the phase, φ, determines the amplitude at t = 0.
origin
Figure 3.5: Simulated image showing sinusoidally varying fringes. If the upper left-hand corner is chosen as
the origin, the phase of the fringes will be 180◦ , since the brightness is at a minimum at that point.
This dependence on origin means that before phases measured from the FFT of an image can be compared
with theoretical values, the origin of the image must be determined. The origin of the crystal is chosen
to correspond to the unit cell origin given in the International Tables for X-ray Crystallography (Henry and
Lonsdale, 1952). An HRTEM image is in the WPOA a two-dimensional projection of the crystal structure,
therefore it is the origin of the projected symmetry that must be used.
In order to find the unit cell origin of a high-resolution image we adopt the method developed by Zou and
Hovmöller (2002) which is implemented in the computer program CRISP (Hovmöller, 1992). In this approach
the origin is found by minimizing the so-called phase residual, φres . The phase residuals are calculated by
using phase relations and restrictions present in each of the 17 two-dimensional space groups (table 3.2 on
page 21). Each observed phase, φobs , is compared to a phase determined from symmetry relations and
18
restrictions, φsym , using the formula
P
[w(hk)|φobs (hk) − φsym (hk)|]
hk
φres = P , (3.5)
w(hk)
hk
where w(hk) is the weighting factor given to the reflection (hk).1 In the case of a centrosymmetric space
group for example, φsym is set to either 0◦ or 180◦ . For non-centrosymmetric space groups, the phases
can take on any value (from −180◦ to 180◦ ). If there are no symmetry relations or restrictions for a given
reflection, φsym is set equal to φobs . Hence, this reflection is not used in calculating the phase residual.
The phase residual is calculated for each possible unit cell origin for each of the 17 two-dimensional space
groups since the phase relations and restrictions are different for each of these space groups, giving different
φsym . Hence, the projected symmetry is determined in addition to the unit cell origin.
After the FFT of the image is calculated using the correct two-dimensional space group origin, the sym-
metrized phases, φsym , can be compared to theoretical values. However, if the two-dimensional space group
origin is not a unique point, but for example a line, it is not useful in general to compare the symmetrized
and theoretical phases. This is the case only for the two-dimensional point groups 1 and m. The phases of
Fourier transform peaks corresponding to planes parallel to the mirror or glide line are not affected by this
limitation though.
The defocus of the objective lens is important when using the phases. A change in sign of the contrast
transfer function will result in a 180◦ phase shift. There are two general ways of dealing with this. Either
full-fledged CTF correction can be applied to the high-resolution image using software such as CRISP before
measuring the phases, or the measured phases in bands of reversed contrast are simply shifted 180◦ . The
spatial frequencies for which the contrast is reversed is in practice found by looking at the Fourier transform
of an amorphous region. The contrast reversal, that is sin χ = 0, will coincide with the middle of the dark
circular bands in the power spectrum (figure 3.6). In the case of simulations, the CTF is known and can be
used to shift the phases of the peaks in the regions of reversed contrast. When the CTF is negative, such as
in the large band at Scherzer defocus, the phases are shifted 180◦ from the theoretical phases.
Another parameter one might think would affect the phases, is crystal tilt. When a crystal zone axis is not
perfectly aligned along the incident direction of the electron beam the atomic columns appear as lines instead
of points in the image. Being off the axis will decrease the intensity of some of the diffracted beams, this
makes the amplitude of Fourier coefficients sensitive to tilt. The phases, however, are not as sensitive to tilt.
Zou (1995, pp. 50–54) show using a simple model that the phases of thin crystals are not severely affected
by crystal tilt. If the tilt of the crystal is known, it can be corrected for. The tilt can be determined from the
amplitudes of the peaks in the Fourier transform.
1 The indices hk are only used to index the two-dimensional Fourier transform and are not necessarily related to the Miller indices of
the lattice planes.
19
(a)
−1
−1
k nm  1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0
(b)
Figure 3.6: (a) Fourier transform of a TEM image of amorphous carbon film showing the dependence of the
contrast transfer function on the magnitude of u (i. e., distance from the center of the Fourier transform).
The arrows point to the first two zero crossings of the contrast transfer function. (b) Simulated graph of a
contrast transfer function at Scherzer defocus. The black areas correspond to a positive contrast transfer
function where the structure factor phases are not shifted. The graph was created using the Contrast Transfer
Function Explorer by Sidorov (2002)
20
Phases
No. Space Point Origin Phase relations 0◦ or
group group 180◦
1 p1 1 on 1 - -
2 p2 2 at 2 - All
3 pm on m φ(hk) = φ(h̄k) (h0)

4 pg m on g φ(hk) = φ(h̄k) + k · 180◦ (h0)
5 cm on m φ(hk) = φ(h̄k) (h0)
6 pmm at 2mm φ(hk) = φ(h̄k) All
7 pmg at 2 φ(hk) = φ(h̄k) + k · 180◦ All

2mm
8 pgg at 2 φ(hk) = φ(h̄k) + (h + k) · 180◦ All
9 cmm at 2mm φ(hk) = φ(h̄k) All
10 p4 4 at 4 φ(hk) = φ(k̄h) All
11 p4m at 4mm φ(hk) = φ(k̄h) = φ(h̄k) All
4mm φ(hk) = φ(k̄h) =

12 p4g at 4 All
φ(h̄k) + k · 180◦
φ(hk) = φ(k, h̄ + k̄) =
13 p3 3 at 3 -
φ(h̄ + k̄, h)
(hh)
φ(hk) = φ(k, h̄ + k̄) =
14 p3m1 at 3m1 φ(h̄ + k̄, h) = φ(k̄ h̄) (h2h̄)
(2k̄k)
3m
(hh̄)
φ(hk) = φ(k, h̄ + k̄) =
15 p31m at 31m φ(h̄ + k̄, h) = φ(kh) (h2h)
(2kk)
φ(hk) = φ(k, h̄ + k̄) =
16 p6 6 at 6 All
φ(h̄ + k̄, h)
φ(hk) = φ(k, h̄ + k̄) =
17 p6m 6mm at 6mm All
φ(h̄ + k̄, h) = φ(kh)
Table 3.2: Phase relations of the 17 two-dimensional space groups. After Zou (1995).
21
3.5 Database Support
A crucial component of the method of lattice-fringe fingerprinting is comparing experimental data with ac-
cepted values in order to identify the unknown structure. This requires a searchable database of known
crystal structures. The database must contain the type of information used in lattice-fringe fingerprinting
explicitly, or make it possible for such data to be derived.
The Crystallographic Information File (CIF) format (Hall et al., 1991) of the International Union of Crystallog-
raphy provides a convenient way for electronic storage and interchange of crystal structure information. Data
on any crystal can be stored as a CIF. The format allows for basic definitions such as chemical composition,
space group, equivalent positions and atomic positions. More advanced information can also be stored.
The CIF format is used in the Crystallography Open Database (http://www.crystallography.net/). The
format is also used in the Nano-Crystallography Database (NCD) being developed at Portland State Univer-
sity, where lattice-fringe fingerprint plots can be generated for an arbitrary resolution using the information
contained in the CIFs.
3.6 Search/Match Procedure
The goal of lattice-fringe fingerprinting is to identify an unknown nanocrystal by comparing experimental data
with the corresponding theoretical values for a set of candidate structures. There is therefore a need for
search/match algorithms. This thesis does not attempt to provide a way to meet this need. However, a
simple search algorithm based on pseudo-code given in De Graef (2003, p. 522) was implemented in order
to compare lattice-fringe vector data.
The simple program, working one zone axis at a time, first finds the calculated lattice vector that best fits
each experimental lattice vector. The best fit for a certain experimental lattice vector is the calculated lattice
vector that gives the lowest difference parameter, ∆, where
v
u 2
uX 2 2
∆=t (g i,exp − gi,cal ) + ((γexp − γcal ) wγ ) . (3.6)
i
The angle is given a weight, wγ , of 0.1 to take into account the difference in magnitude when lengths are
measured in nanometers and angles in degrees.
Once the best match for each experimental lattice vector has been found, the total difference parameter,
∆tot , for the zone axis is calculated by simply summing the individual difference parameters together. This
procedure is applied to all the different zone axis. The program then selects the zone axis with the lowest
∆tot as the correct match. By expanding the search to zone axes of different crystal structures, this method
can be used to find the best match between measurements from the FFT of an image and one of many
known crystal structures in a database. This algorithm was used to find the best match of measured values
to calculated values of magnetite and maghemite. Structure factor phase information can be included in this
search by including an extra term in the radicand in (3.6).
This algorithm works for a small database containing a limited number of crystal structures. For a database
of a reasonable size however, this method is too inefficient. It might be easier to perform a coarse search
first using for example only the largest lattice vectors and angles in order to reduce the search space. More
parameters can then be added to the search successively until the actual crystal structure is determined.
22
Chapter 4
Application of Lattice-Fringe Fingerprinting
To determine the possibilities and limitations of lattice-fringe fingerprinting, the method was applied to HRTEM
images of three different materials: titania, iron oxide and gallium nitride.
4.1 Computer Implementation
Lattice-fringe fingerprinting HRTEM images was made easier by using Digital Micrograph scripts. Digital
Micrograph is a proprietary computer program that is commonly used by electron microscopists for, among
other things, analyzing TEM images. Three scripts were created (Appendix). One script calculates the
Fourier transform of a selection after subtracting the average and multiplying by a Hanning window. The
selection must be rectangular and the number of pixels along each side must be a power of two. The result
of the Fourier transform is displayed in an image of the logarithm of the modulus of the Fourier coefficients,
but the complex numbers are available and used for all further calculations.
A second script finds the peak of the intensity spectrum inside each of several user-made selections using
sub-pixel interpolation and measures the lattice-fringe spacings and angles. The lengths are measured
in pixels and then divided by the dimensions of the Fourier transform in order to get a spatial frequency
independent of the image size. The reciprocal of this spatial frequency will be proportional to the direct space
lattice-fringe spacing. This length can then be multiplied by a scale factor, dependent on the magnification,
to obtain the actual length.
A third script gives the spacing, the amplitude and the phase of each of the intensity spectrum peaks. The
amplitude and phase is calculated from the Fourier coefficients using (3.3) and (3.4). The origin of the Fourier
transform in Digital Micrograph is always the upper left-hand corner of the selection.
4.2 Titania
The first set of images that was analyzed was eight images of titanium dioxide, or titania, nanocrystals. These
images were taken by Modesto Godinez at Portland State University.1 Titania crystallizes into three different
structures, anatase (I41 /amd, no. 141), brookite (P bca, no. 61) and rutile (P 42 /mnm, no. 136), where the
numbers refer to the numbers assigned in the International Tables. Anatase and rutile are tetragonal whereas
brookite is orthorhombic. Theoretical lattice-fringe fingerprint plots of these three crystal structures are shown
in figures 4.1–4.3.
To lattice-fringe fingerprint titania from the TEM images, areas with crossed lattice fringes were first located.
The appropriate scripts were then applied to measure the lattice-fringe spacing and angles. Six different
regions showing crossed lattice fringes were found in three different images. A part of one image and the
corresponding Fourier transform are shown in figure 4.4.
1 The images were taken by Godinez under the supervision of Chunfei Li and Bjoern Seipel.
23
The magnification of the images was not known in advance. This meant that only the angles and the ratios of
the lattice-fringe spacings could be used in determining the structure and not the actual spacings. Comparing
the measurements from the three largest lattice-fringe spacings with calculated data for anatase, brookite and
rutile, we find two possible candidates for the structure: brookite in the [011] orientation and rutile in the [111]
orientation. However, for brookite one would expect to see many more reflections due to a larger unit cell,
as is indicated by the lattice-fringe fingerprint plot in figure 4.2. This means that the nanocrystal probably is
rutile. With this information the image magnification could be determined and the Fourier transform indexed
(figure 4.5).
None of the other nanocrystals showed the (21̄1̄) reflection. Using only the (11̄0), (101̄) and (011̄) reflections,
the experimental data gives three clusters of data points in the lattice-fringe fingerprint plot (figure 4.6). These
data correspond fairly well to the expected results from rutile oriented close to the [111] direction, as shown in
the plot in figure 4.3. Assuming each of the three clusters correspond to three theoretical values, the average
and standard deviation can be calculated (figure 4.7). The large spread of the experimental data might be
due to the small size of the nanocrystals.
90
80
〈111 〉 〈100 〉
〈131 〉 〈131 〉
70 〈100 〉 〈100 〉
60
〈 331〉
50
〈100 〉
40
30
〈100 〉 〈100 〉
20
2.8 3.0 3.2 3.4 3.6 3.8 4.0 4.2
-1
g (nm )
Figure 4.1: Theoretical lattice-fringe fingerprint plot of anatase, assuming kinematic scattering and 0.24 nm
microscope resolution. The zone axis corresponding to each data point is indicated.
24
〈 001〉 〈 001〉 〈100 〉
90 〈 010〉 〈120 〉 〈 012〉
〈100 〉 〈 010〉 〈 201〉
〈 012〉 〈110 〉 〈 201〉 〈120 〉
〈123 〉
〈124 〉 〈123 〉 〈124 〉
80 〈 001〉 〈101 〉〈 231〉 〈 231〉 〈 324〉
〈 241〉 〈 011〉 〈 241〉
〈 010〉 〈 312〉 〈 312〉
〈 010〉

〈 213〉 〈 213〉
70 〈 011〉 〈120 〉
〈 011〉 〈 251〉 〈 251〉
〈102 〉 〈 412〉 〈 412〉
〈 011〉 〈 011〉 〈100 〉 〈100 〉
60 〈102 〉 〈102 〉
〈 231〉 〈 231〉 〈100 〉
〈124 〉 〈120 〉 〈120 〉
〈124 〉
〈 011〉 〈 001〉 〈101 〉 〈 011〉 〈101 〉
50 〈121 〉〈110 〉 〈 001〉 〈110 〉
〈121 〉 〈 231〉 〈 231〉
〈 011〉
〈 211〉 〈124 〉 〈 211〉 〈124 〉
40 〈 001〉 〈 001〉
〈120 〉 〈120 〉
30 〈 010〉 〈112 〉
〈112 〉 〈100 〉 〈100 〉
20
〈 011〉 〈 011〉
〈 010〉 〈 010〉
10
2.0 2.5 3.0 3.5 4.0 4.5
-1
g (nm )
Figure 4.2: Theoretical lattice-fringe fingerprint plot of brookite, assuming kinematic scattering and 0.24 nm
microscope resolution. The zone axis, or in some cases the zone axes, corresponding to each data point is
indicated.
90 〈 001〉
80
70
〈111 〉 〈111 〉
〈100 〉
60
50
〈111 〉
40
3.0 3.2 3.4 3.6 3.8 4.0
-1
g (nm )
Figure 4.3: Theoretical lattice-fringe fingerprint plot of rutile, assuming kinematic scattering and 0.24 nm
microscope resolution. The zone axis corresponding to each data point is indicated.
25
32.5
30.2
24.2
4.6
(a) (b)
Figure 4.4: (a) HRTEM image of a titania nanocrystal. The white square surrounds the Fourier transformed
region. (b) The Fourier transform of the area inside the white square. A black circle marks the position of the
weakest visible reflection. The amplitude of the Fourier transform peaks, calculated using (3.3), is indicated
next to the dark spots. The amplitudes of diametrically opposed points are identical, according to Friedel’s
law and the symmetry of the two-dimensional Fourier transform.
10 1 2
11
0 1 1
1
10
000
Figure 4.5: Indexed Fourier transform of the region in figure 4.4 assuming [111] rutile.
26
70
65

60
55
50
45
40
2.8 3.0 3.2 3.4 3.6 3.8 4.0 4.2 4.4
-1
g (nm )
Figure 4.6: Lattice-fringe fingerprint plot from titania images.
70
65
60
55
50
45
40
2.8 3.0 3.2 3.4 3.6 3.8 4.0 4.2 4.4
-1
g (nm )
Figure 4.7: Averaged lattice-fringe fingerprint plot from titania images. The error bars correspond to one
standard deviation in each direction.
27
4.3 Iron Oxide
Iron oxide exists in different crystal structures. Two of these are magnetite and maghemite. Magnetite,
Fe3 O4 , is face-centered cubic with space group F d3̄m (no. 227). Maghemite, γ -Fe2 O3 , is primitive cubic
with space group P 41 32 (no. 213). These crystal structures have very similar lattice constants with a =
8.32 Å (Bragg, 1915) and a = 8.33 Å (Pecharromán et al., 1995), for magnetite and maghemite respectively.
The only difference between the two crystal structures is a larger number of cation vacancies in maghemite.
The iron oxide nanocrystals are known to exist in solid solution between magnetite and maghemite (Lovely
et al., 2006). The objective of lattice-fringe fingerprinting was in this case to see whether it would be possible
to distinguish between these two crystal phases.
The first set of images were taken by Eric Mandell at the University of Missouri-St. Louis using a Philips EM
430ST with a point resolution of 0.19 nm. This means that spatial frequencies out to 5.26 nm−1 are directly
interpretable. Kinematic lattice-fringe fingerprint plots of magnetite and maghemite are shown in figures 4.8
and 4.9. These plots are quite a bit more complex than the plots of rutile. In these plots, some lattice planes
intersect multiple other lattice planes at the same angle. For example, the (022) planes intersect both (111̄)
and (311̄) at 90◦ , in the [2̄11̄] and [2̄33̄] zone axis, respectively. Also, many of the data points are very
close together. This makes it virtually impossible to identify these nanocrystals only by inspecting these
lattice-fringe fingerprint plots.
The lattice-fringe fingerprint plots become less crowded, however, if we consider a single zone axis at a
time. That is, instead of trying to identify the crystal structure using all possible lattice plane intersections, we
identify the crystal structure and the zone axis. Identifying the crystal structure from HRTEM images is then
similar to indexing an electron diffraction pattern. Each nanocrystal must be identified separately since the
nanocrystals might be oriented differently. First we consider four nanocrystals imaged with the Philips EM
430ST.
The nanocrystal shown in figure 4.10 appeared in five images acquired with slightly different goniometer
settings. The lattice-fringe fingerprint plot that was obtained from Fourier transforms like the one in figure 4.10
is shown in figure 4.11. It is not evident from comparing this plot with figures 4.8 and 4.9 what the zone axis
orientation is. However, if we consider only the h211i directions, as in figure 4.12, the plots look very similar.
We then conclude that this nanocrystal consists mostly of magnetite oriented close to a h211i zone axis. We
can then index the Fourier transform of the image of the nanocrystal as shown in figure 4.13. For maghemite
in the h211i orientation, we would also expect to see the {110}, {210} and {321} planes. These reflections
are kinematically and dynamically forbidden in magnetite due to F -centering.2
Several other nanocrystals showing crossed lattice fringes were identified in a similar fashion. However, to
make the process less tedious the search/match procedure outlined in section 3.6 was implemented. All the
possible lattice-plane intersections were stored together with the zone axis in a data file, one for magnetite
and another for maghemite. The experimental lattice-fringe vector measurements were stored in a different
data file. A simple program which calculates the difference parameter in equation 3.6 for a measured lattice-
fringe vector and the theoretical calculations was then used. The zone axes with the lowest total difference
parameters were then studied more closely to determine the most likely match.
This program was used in finding the best match for the nanocrystal pictured in figure 4.14. As it turns
out, this nanocrystal is also oriented close to the h211i direction, as shown in the Fourier transform. What
is interesting to note in this case though, is the faint presence of the (1̄20) reflection. As mentioned, this
reflection should not be seen in magnetite, but is expected in maghemite. The (011̄) reflection is not seen,
but the (1̄20) reflection suggests the presence of maghemite in this nanocrystal.
2 Reflections that are forbidden due to centering might be present nonetheless due to atomic ordering. Such effects are not considered
any further in this thesis.
28
A third nanocrystal is shown in figure 4.15. The corresponding Fourier transform shows three {022} planes
intersecting at angles of 59.6◦ and 63.1◦ . The closest match is the intersection of three {022} planes at 60◦
in the h111i zone axis.
A fourth nanocrystal is shown in figures 4.16. The lattice-fringe fingerprint plot is shown in figure 4.17. Using
the computer program, the best match was found to be maghemite in a h332i orientation. This even though
two expected reflections are missing in the Fourier transform, as shown in figure 4.18. The (203̄) and (1̄10)
reflections are not expected in magnetite, again due to F -centering. The absence of (3̄30) might be due to a
damping of the transfer function in this region. The 023̄ reflection is also absent.
{111}
{133}
{022}
{113}
{222}
{004}
90
80
70
60
50
40
30
20
10
2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5
-1
g (nm )
Figure 4.8: Theoretical lattice-fringe fingerprint plot of magnetite, F d3̄m, assuming kinematic scattering and
0.19 nm microscope resolution. The plane family is indicated above the plot.
29
{033} {114}
{112}
{113}
{222}
{004}
{011}
{111}
{012}
{022}
{013}
{023}
{123}
{133}
90
80
70
60
50
40
30
20
10
0
1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5
-1
g (nm )
Figure 4.9: Theoretical lattice-fringe fingerprint plot of maghemite, P 41 32, assuming kinematic scattering and
0.19 nm microscope resolution. The plane family is indicated above the plot.
30
(a)
(b)
Figure 4.10: (a) HRTEM image of iron oxide nanocrystal. (b) Fourier transform of the nanocrystal.
31
90
80

70
60
50
40
30
2.0 2.5 3.0 3.5 4.0 4.5

-1
g (nm )
Figure 4.11: Lattice-fringe fingerprint plot from iron oxide nanocrystal.
90
80
70
60
50
40
30
2.0 2.5 3.0 3.5 4.0 4.5

-1
g (nm )
Figure 4.12: Lattice-fringe fingerprint plot of magnetite in the h211i direction.
32
2 0 4

113
0
22
3 33
1,691 2 2 2
386

111
000
1,062 2 4 0
380
39 
13 
1
808
313
36
Figure 4.13: Indexed Fourier transform of an image of a magnetite nanocrystal assuming it is oriented close
to the [211] direction. The amplitude and index is given for each Friedel pair.
33
(a)
2 2 2
2 4 0
489 
111
1 2 0 1 3 1
1,499
000 02
2
586 77
1,404 11 3
50
(b)
Figure 4.14: (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image
assuming the nanocrystal is oriented close to the [211] direction.
34
0 2 2
2 0 2
531
000
2
20
2,262
1,022
(a) (b)
assuming the nanocrystal is oriented close to the [111] direction.
35
(a)
(b)
Figure 4.16: (a) HRTEM image of iron oxide nanocrystal. (b) The Fourier transform of the image.
36
90
80

70
60
50
40
30
20
10
1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5
-1
g (nm )
Figure 4.17: Lattice-fringe fingerprint plot from the iron oxide nanocrystal in figure 4.16.

3 30 
13 
3
2 20 02
3
55 
11 0
11
3
59 000 20 
3
957 3
13
435
140
17
Figure 4.18: Indexed Fourier transform of the nanocrystal in figure 4.16, assuming [332] orientation. The
arrows point to where there are absent reflections.
37
We consider next images taken on a Philips CM20 at Technische Universität Chemnitz, with a theoretical
point resolution of 0.24 nm. The HREM AutoTune software by Gatan was used in order to minimize astig-
matism and coma. The specimen was not tilted in order to orient the nanocrystals. Instead, nanocrystals
that were showing crossed lattice fringes were imaged. The images are therefore more typical, than ideal,
HRTEM images.
The best match for the nanocrystal in figure 4.19 is magnetite in a h110i orientation. Those reflections that
correspond to {022}, {222} and {133} planes are missing, but that is because there is no information in that
region of reciprocal space. This might be due to specimen drift since the astigmatism has been corrected for.
For maghemite we would expect to see the (1̄10) reflection for example, which is not present.
The nanocrystal in figure 4.20 could be maghemite in a h211i orientation. The presence of a (011̄) reflection
suggests this. The same goes for the (102̄) reflection, barely seen in the Fourier transform.
The nanocrystal in figure 4.21 is also oriented close to the h211i zone axis. However, in this case all the visible
reflections that are expected in magnetite are present in this orientation. There is therefore no evidence of
maghemite in this nanocrystal.
The nanocrystal in figure 4.22 is probably maghemite in a h211i orientation by the same reasoning as above.
In this case the (011̄) and (1̄20) reflections are fairly strong.
The nanocrystal in figure 4.23 could also be maghemite close to h211i since the 011̄ reflection is visible.
Figure 4.24 is a nanocrystal oriented close to the h110i zone axis. The absence of the (1̄10) reflection
suggests that the structure of this nanocrystal is close to that of magnetite. All the expected reflections are
seen except for the {133} which is probably beyond the resolution of this image.
The nanocrystal in figure 4.25 is another nanocrystal in a h211i orientation. Again, the presence of (011̄) and
(1̄20) suggest the presence of maghemite.
Finally, the nanocrystal in figure 4.26 was found to be oriented close to a h310i zone axis. The (004) reflection
is not visible. Instead, there is a (002) reflection. This reflection should be absent in the kinematic limit, which
suggests that there is dynamical scattering in this case.
38
(a)
004
002
9.1 1 11
3.2 1 1 1
000
13.0 1 1 3
14.3
3.1
(b)
Figure 4.19: (a) HRTEM image of iron oxide nanocrystal. (b) The Fourier transform of the image assuming
[110] orientation.
39
(a)
1 11 1 3 1
02
2
0 1 1
3.9 3.6 000
1.7 23.6
(b)
assuming [211] orientation.
40
(a)
0
22 1 1 3
8.4
5.7 1 11
000
1 3 1
3.4 12.0
(b)
41
(a)
2 2 2
0.4 0.3 
1 11 1 3 1

1 20
0.8 1.5 022

000 0 1 1
3.2 1.4 11 3
10 
2
1.5 4.3 30.4 2 0 4
7.6 2 1 3
(b)
42
(a)

113
1 1 1
4.9
000
8.5 02
2
6.4
(b)
43
(a)
004
1 1 3
002 2 2 2
17.1
1 11
3.5 2 20
22.7
000 1 1 1
28.1 2 2 2
28.1
22.7 1 1 3
5.8
17.7
7.9
(b)
44
(a)

3 33
2 2 2
1 1 1 
1 20 1 3 1
000 0 1 1 0 2 2
2.3 12.7
5.0 9.1 48.8
4.8
3.6
(b)
45
(a)
1 3 3
1 3 1
1
31
9.3
000
7.8 002
1.7
2.2
(b)
46
4.4 Fourier Coefficient Phases
4.4.1 Gallium Nitride
HRTEM computer simulations were used to further study using Fourier coefficient phases in characteriz-
ing nanocrystals. The WebEMAPS program developed by Zuo and Mabon (2004) was utilized to simulate
HRTEM images of gallium nitride. The WebEMAPS program uses Bloch waves, and hence takes into ac-
count dynamical scattering. Microscope parameters such as spherical and chromatic aberration, energy
spread and defocus can be input into the program, in addition to specimen tilt and thickness.
Gallium nitride, Ga3+ N3− , has a wurtzite crystal structure (space group P 63 mc, no. 186). In this study, GaN
in the [010] orientation was used. As described in section 3.4, to use the phases we must also find the correct
symmetry. The projected symmetry of all three-dimensional point groups can be found from the International
Tables (table 3.7.1, Point-group projection symmetry). In a hexagonal crystal system, the [010] direction
is perpendicular to the (1̄21̄0) plane. From the International Tables we then find that a projection onto the
(1̄21̄0) plane will have m point-group symmetry. This leaves three possible two-dimensional space groups:
pm, pg and cm. The screw axis in the crystal structure will result in a glide line. Hence, the two-dimensional
space group will be pg , with the origin on the glide line. The symmetry elements in this two-dimensional
space group are illustrated in figure 4.27.
Figure 4.27: Symmetry elements of the pg two-dimensional space group. The dashed lines represent glide
lines.
Lattice planes that are parallel to the glide line will have real structure factors, so the phases will be either 0◦
or 180◦ . There is no other restriction on the phases. However, there will be phase relations due to the glide
line: φ(hk) = φ(h̄k) + k · 180◦ , where the glide line is in the k -direction and φ(hk) means the phase of the
(hk) reflection. So for example, if φ(11) = 25◦ , then φ(1̄1) = −155◦ .
To study the simulated images one can make use of the program CRISP, but Digital Micrograph was also
used in order to study the method in more detail. In order to get theoretical values for the structure factor
phases, the structure factors were calculated using the values from Doyle and Turner (1968) as described
in section 2.5. The aj and bj coefficients were first converted into the correct units. It was then possible to
compare the calculated structure factor phases with the phases measured in the simulated images of GaN.
The structure factor phases were calculated in Microsoft Excel, although the complex addition was done in
Mathematica.
A simulated HRTEM image of gallium nitride with 5 nm thickness is shown in figure 4.28. The screw axis,
parallel to the c-axis, causes the (001) and (003) reflection to be absent in the Fourier transform. Since the
47
projected symmetry was known, only the unit cell origin had to be determined. This was done by manually
shifting the Fourier transform pixel by pixel and checking the phase restrictions and relations at each position.
The calculated structure factor phases, together with the measured Fourier coefficient phases with the Fourier
transform origin on the glide line, are listed in table 4.1. We see that there is no correlation between the
theoretical and measured phases or between different thicknesses, except for the (100) and (200) reflections
since these are restricted to 0◦ or 180◦ . However, the measured phases follow closely the phase relations,
obeying φ(h0l) = φ(h̄0l) + l · 180◦ (using Miller indices). For example, φ(202̄) ≈ φ(2̄02̄) and φ(201̄) ≈
φ(2̄01̄)+180◦ . In this case, since the origin is anywhere on the glide line, one could not expect the theoretical
and measured values to be the same, except for the case of reflections due to lattice planes parallel to the
glide line. As the origin of the Fourier transform is shifted along the glide line, all the phases change except
for these reflections. This means that when the projected symmetry is that of the two-dimensional point group
m, only a few measured phases can be compared directly to the theoretical phases.
48
(a)
0 0 4

10 
3 10 
3
2 0 2 1 0 2 0 0 2 10 2 20 2
2 0 1 1 0 1 10 1 20 1
4,162 5,709 000 10 0 20 0
3,338 7,970 7,959 3,336
1,979 3,334 9,511 3,332 1,978
6,183 6,171
547
(b)
Figure 4.28: (a) Simulated image of GaN, 5 nm thickness oriented along [010]. Electron potential: 200 kV,
x-axis: [100], defocus: −67 nm, energy spread: 1.0 eV, spherical aberration: 1.2 mm, chromatic aberration:
1.2 mm, output limit: 4.5 nm−1 . (b) The indexed Fourier transform of the image. The amplitudes are shown
for the reflections in the bottom half.
49
hkl Calculated Phase Differ- Phase Differ-
phase t = 5 nm ence t = 10 nm ence
100 180◦ −179.1◦ - 179.4◦ -
200 180◦ 179.1◦ - −179.4◦ -
101̄ −68.4◦ −124.5◦ −35.3◦

◦
180.4 180.7◦
1̄01̄ 111.6◦ 55.9◦ 145.4◦
201̄ 109.5◦ 78.6◦ −137.1◦

◦
179.9 180.4◦
2̄01̄ −70.5◦ −101.3◦ 43.3◦
002̄ −21.7◦ 164.0◦ - −170.6◦ -
102̄ 158.3◦ −76.6◦ 8.0◦

◦
0.5 1.1◦
1̄02̄ 158.3◦ −77.1◦ 6.9◦
202̄ 160.4◦ 150.0◦ −155.4◦

◦
0.6 0.3◦
2̄02̄ 160.4◦ 149.4◦ −155.7◦
103̄ −77.4◦ 4.9◦ −108.8◦

◦
180.1 180.2◦
1̄03̄ 102.6◦ −175.2◦ 71.4◦
004̄ −1.7◦ −172.7◦ - −7.6◦ -
Table 4.1: Calculated structure factor phases and measured Fourier coefficient phases (from two images of
crystals with different thicknesses, t) for the reflections present in gallium nitride in the [010] orientation. The
difference columns show the phase difference between reflections that have a phase relation. The phase
differences are close to the theoretical value of l · 180◦ . Note also that the phases for the (100) and (200)
reflections are close to the calculated value.
50
4.4.2 Titania
The titania nanocrystal shown in figure 4.4 on page 26 could also be used to study the phases. Since rutile
is centrosymmetric, all the phases must be 0◦ or 180◦ . The [111] direction is perpendicular to the plane
(hhl), where l/h = c2 /a2 . The International Tables give the two-dimensional point group of the projected
symmetry as 2mm. From looking at a model of the structure in the [111] direction, it is clear that there are
two perpendicular mirror planes in the projection. The two-dimensional space group is therefore pmm. This
gives the phase relation of φ(hk) = φ(h̄k). Calculations show that reflections due to the {110} and {011}
lattice planes will have a phase of 0◦ . In the case of contrast reversal in the image, the phase of the Fourier
coefficients of the image should be 180◦ .
To find the correct origin, the origin of the image selection was shifted pixel by pixel. Using the origin with
the lowest phase residual, the phases of the Fourier coefficients were −9◦ , −22◦ , and −16◦ for the three
reflections, as shown in figure 4.29. The deviation from the theoretical value might be due to the low resolution
of the image. The separation between two bright dots in the HRTEM image (figure 4.30) is about seven pixels.
This means that shifting the origin by one pixel can change the phases by roughly 360◦ /7 ≈ 51◦ . It might be
possible to use sub-pixel interpolation to get more accurate phase measurements. The fact that the phases
are not shifted by 180◦ with respect to the calculated values imply that the contrast transfer function is positive
in the corresponding region of reciprocal space, making the atoms appear white.
10 1 °
=−22
0 1 1
=−16
° 1
10 °
=−9
29.9 28.6
18.5
Figure 4.29: Fourier transform with measured Fourier coefficient phases and amplitudes.
51
Figure 4.30: HRTEM image of a titania crystal. The white square surrounds the Fourier transformed region.
The real-space origin is in the upper left-hand corner of the white square.
52
Chapter 5
Discussion
The results show that it is possible to identify the crystal structure of a nanocrystal using lattice-fringe finger-
printing. With the support of a comprehensive database and search/match procedures, this method can also
be made as automatic as any other microscopic analysis method.
The nanocrystals that were known to be titania were determined to have the rutile crystal structure. The
crossed lattice fringes that were visible could only be explained with the crystal structure of rutile. Nanocrys-
tals that did not show crossed lattice fringes could, of course, have had a different structure.
The results for the iron oxide nanocrystals suggest that some of the nanocrystals had a structure closer to
that of magnetite, and others had a structure closer to that of maghemite. This corresponds with the two
crystal structures coexisting in a solid solution. The nanocrystals might have been too thick to draw any
conclusions from the phases. Under kinematical conditions it should be possible to distinguish between the
two crystal structures also using phases of the Fourier coefficients because of the difference in symmetry.
Seven out of the 12 nanocrystals studied were oriented along h211i.
The analysis of the simulated images of gallium nitride demonstrate how the phases of the Fourier coefficients
of HRTEM images can be used to identify a nanocrystal. When the projection of the symmetry element
defining the unit cell origin is a point, the exact crystal origin of an imaged nanocrystal can be determined
and the measured and calculated phases can be compared directly. This is sometimes not the case, such
as with gallium nitride in any other than the [001] orientation, which is parallel to the hexad screw axis. When
the phases can not be directly compared to calculated phases the symmetry can still be used, in the form of
phase restrictions and phase relations. In either case, the symmetry of the crystal structure must be present
in the image.
The increase in microscope point resolution through abberation-corrected lenses will make lattice-fringe fin-
gerprinting more viable. First, more lattice fringes will be visible, making more information available. This
also makes it more likely for a randomly oriented nanocrystal to have visible lattice fringes. Secondly, by
resolving more lattice fringes, more information on the symmetry of the nanocrystal will be present in the
image.
5.1 Limitations
Since lattice fringes depend on the structure of the nanocrystal, lattice-fringe fingerprinting cannot easily
distinguish between materials of very similar structure. This goes for homologous structures such as gallium
nitride and zinc oxide. These two compounds crystallize in the wurtzite structure. To distinguish between
such structures one might use X-ray fluorescence, in which the chemical composition of the material can be
determined without the need of a focused beam.
Another factor that affects the applicability of lattice-fringe fingerprinting is the difficulty of obtaining good
HRTEM images. Aligning the microscope is very important for high-resolution imaging, and this requires
some time and experience. However, the alignment and the general operation of TEMs have become simpler
over the years with for example auto-alignment software.
53
The Fourier coefficient phases are resistant to small tilts and simply shifted 180◦ by contrast transfer oscilla-
tions. However, the phases are not usable when dynamical scattering is dominant. When the electron waves
are diffracted more than once the path length changes and the path differences, and hence phases, are no
longer reliable.
One caveat when working with nanocrystals is that these crystals often have lattice parameters that are dif-
ferent from that of the bulk crystal. The effect on the lattice spacings and angles when the lattice parameters
are perturbed was shown above. When the structure of the nanocrystal varies dramatically from the crystal in
its bulk form this structure should be included in a database, with a note on the size range of the nanocrystal.
54
Chapter 6
Conclusion
Lattice-fringe fingerprinting is a novel method of identifying nanocrystals using HRTEM images. In its most
basic form, the reciprocal lattice vectors and the interfringe angles are used to fingerprint the crystal structure.
For nanocrystals that are sufficiently thin it is also possible to use the phases of the Fourier coefficients of the
projected electrostatic potential. For an abundance of nanocrystals, such as in a nanopowder, the probability
of seeing certain zone axes can be taken into account as well.
Lattice-fringe fingerprinting was applied to three different crystal systems: titania, iron oxide and simulated
images of gallium nitride. The titania nanocrystals that showed crossed lattice fringes were found to be rutile
in the [111] orientation. For iron oxide, the zone axis was determined for each of the nanocrystals showing
crossed lattice fringes. The majority of nanocrystals showing crossed lattice fringes were oriented close to
the h211i direction. The simulated images of gallium nitride demonstrated the possibility of using the phases
of the Fourier coefficients in identifying the crystal structure. These phases can often not be compared
directly with calculated structure factor phases, but instead the phase restrictions and phase relations due to
the projected symmetry can be used as another component of the lattice-fringe fingerprint.
55
References
W. H. Bragg. The structure of magnetite and the spinels. Nature, 95:561, 1915.
J. M. Cowley. Diffraction physics. North-Holland, 2nd edition, 1981.
J. M. Cowley. High-resolution transmission electron microscopy and associated techniques, chapter 2, pages
38–57. Oxford University Press, 1988.
M. De Graef. Introduction to conventional transmission electron microscopy. Cambridge University Press,

2003.
D. J. De Rosier and A. Klug. Reconstruction of three dimensional structures from electron micrographs.
Nature, 217:130–134, 1968.
W. J. de Ruijter. Measurement of lattice-fringe vectors from digital HREM images: theory and simulations.
Journal of Computer-Assisted Microscopy, 6(4):195–212, 1994.
W. J. de Ruijter, R. Sharma, M. R. McCartney, and D. J. Smith. Measurement of lattice-fringe vectors from

digital HREM images: experimental precision. Ultramicroscopy, 57:409–422, 1995.
D. R. Denley and H. V. Hart. RINGS: a new search/match database for identification by polycrystalline
electron diffraction. Journal of Applied Crystallography, 35:546–551, 2002.
P. A. Doyle and P. S. Turner. Relativistic Hartree-Fock x-ray and electron scattering factors. Acta Crystallo-
graphica, A24:390–397, 1968.
P. Fraundorf, W. Qin, P. Moeck, and E. Mandell. Making sense of nanocrystal lattice fringes. Journal of
Applied Physics, 98:114308, 2005.
S. R. Hall, F. H. Allen, and I. D. Brown. The Crystallographic Information File (CIF): a new standard archive
file for crystallography. Acta Crystallographica, A47:655–685, 1991.
H. V. Hart. ZONES: a search/match database for single-crystal electron diffraction. Journal of Applied
Crystallography, 35:552–555, 2002.
N. F. M. Henry and K. Lonsdale, editors. International tables for x-ray crystallography, volume 1. The Kynoch
Press, Birmingham, England, 1952.
S. Hovmöller. CRISP: crystallographic image processing on a personal computer. Ultramicroscopy, 41:

121–135, 1992.
F. H. Li and D. Tang. Pseudo-weak-phase-object approximation in high-resolution electron microscopy I.

Theory. Acta Crystallographica, A41:376–382, 1985.
J. A. López Pérez, M. A. López Quintela, J. Mira, J. Rivas, and S. W. Charles. Advances in the preparation
of magnetic nanoparticles by the microemulsion method. Journal of Physical Chemistry B, 101(41):8045–
8047, 1997.
56
G. R. Lovely, A. P. Brown, R. Brydson, A. I. Kirkland, R. R. Meyer, L. Chang, D. A. Jefferson, M. Falke, and
A. Bleloch. Observation of octahedral cation coordination on the {111} surfaces of iron oxide nanoparti-
cles. Applied Physics Letters, 88:093124, 2006.
K. Lu and Y. H. Zhao. Experimental evidences of lattice distortion in nanocrystalline materials. Nanostruc-

tured Materials, 12:559–562, 1999.
J.-O. Malm and M. A. O’Keefe. Deceptive “lattice spacings” in high-resolution micrographs of metal nanopar-
ticles. Ultramicroscopy, 68:13–23, 1997.
M. A. O’Keefe. “Resolution” in high-resolution electron microscopy. Ultramicroscopy, 47:282–297, 1992.
C. Pecharromán, T. Gonzáles-Carreño, and J. E. Iglesias. The infrared dielectric properties of maghemite,

γ -Fe2 O3 , from reflectance measurement on pressed powders. Physics and Chemistry of Minerals, 22(1):
21–29, 1995.
C. Saltiel and H. Giesche. Needs and opportunities for nanoparticle characterization. Journal of Nanoparticle
Research, 2(3):325–326, 2000.
D. E. Sands. Introduction to crystallography. Dover Publications, 1993.
O. Scherzer. The theoretical resolution limit of the electron microscope. Journal of Applied Physics, 20:
20–29, 1949.
M. V. Sidorov. Contrast transfer function explorer [computer software], 2002. URL http://clik.to/
ctfexplorer.
A. M. Tonejc, I. Djerdj, and A. Tonejc. An analysis of evolution of grain size-lattice parameters dependence
in nanocrystalline TiO2 anatase. Materials Science and Engineering C, 19:85–89, 2002.
D. B. Williams and C. B. Carter. Transmission electron microscopy. Plenum Press, 1996.
X. Zou. Electron crystallography of inorganic structures—theory and practice. PhD thesis, Stockholm Uni-
versity, 1995.
X. Zou and S. Hovmöller. Industrial applications of electron microscopy, chapter 22, pages 583–614. Marcel
Dekker, 2002.
J. M. Zuo and J. C. Mabon. Web-based electron microscopy application software: Web-EMAPS. Microscopy
and Microanalysis, 10(Suppl 2):1000–1001, 2004. URL http://emaps.mrl.uiuc.edu/.
57
Appendix
Scripts
A.1 hanning_FFT.s
The following script subtracts the average from the image, applies a Hanning window and then computes the
fast Fourier transform. The ‘\’ symbol means that the line continues on the following line.
/*******************************************************
Digital Micrograph script 'hanning_FFT.s' */
number size, sizeX, sizeY, top, left, bottom, right, ii, posX, posY
number zoom, test
image front, hannX, hannY, hann, avg, hannout
compleximage fft
front := GetFrontImage();
GetSize(front, sizeX, sizeY);
GetSelection(front, top, left, bottom, right);
GetWindowPosition(front, posX, posY);
zoom = GetZoom(front);
// Test if image/selection has dimensions of the power of two.

test = bottom - top;
while( test / 2 >= 1 )
test = test/2;
if( test != 1 )
Throw( "Only for images (selections) of the power of two!" );
test = right - left;
while( test / 2 >= 1 )
test = test/2;
if( test != 1 )
Throw( "Only for images (selections) of the power of two!" );
// Create Hanning window.

ii = 1;
hannX := CreateFloatImage("", (right-left), (bottom-top));
hannX = 0;
hannX[0, 0, 1, (right-left)] = \
1 - cos( 2 * Pi() * icol / (right-left));
while( ii < (bottom-top) )
{
hannX[ii, 0, 2*ii, (right-left)] = \
hannX[0, 0, ii, (right-left)];
58
ii = ii * 2;
}
ii = 1;
hannY := CreateFloatImage("", (right-left), (bottom-top));
hannY = 0;
hannY[0, 0, (bottom-top), 1] = \
1 - cos( 2 * Pi() * irow / (bottom-top));
while( ii < (right-left) )
{
hannY[0, ii, (bottom-top), 2*ii] = \
hannY[0, 0, (bottom-top), ii];
ii = ii * 2;
}
hann = hannX * hannY;
// Subtract average from image.

avg = front - Average(front);
// Multiply with Hanning window.

hannout = avg[top, left, bottom, right] * hann;
// Do fast Fourier transform and display image.

fft = RealFFT(hannout);
SetName(fft, GetName(front) + "H");
DisplayAt(fft, posX + 14, posY + 21);
A.2 measure_FT.s
The next script finds the position of selected Fourier transform peaks using sub-pixel interpolation and calcu-
lates reciprocal spacing in units of pixel−1 and angles between the reciprocal space vectors in degrees.
/*******************************************************
Digital Micrograph script 'measure_FT.s'
Get image and selections and make sure they are okay. */
ComplexImage img := GetFrontImage()

Number xsize, ysize
GetSize(img, xsize, ysize)
// Find the central bright spot, assuming it is in the middle.

Number centerx = xsize / 2
Number centery = ysize / 2
ImageDisplay imgdisp = img.ImageGetImageDisplay(0)
Number roinumber = imgdisp.ImageDisplayCountROis()

if(roinumber < 2)
59
{
OkDialog("This script requires at least two \
rectangular selections.")
Exit(0)
}
Number i
ROI iroi
for(i = 0; i < roinumber; i++) {
iroi = ImageDisplayGetROI(imgdisp, i)
if(!ROIIsRectangle(iroi))
{
OkDialog("Only rectangular selections can \
be used with this script.")
Exit(0)
}
}
/*******************************************************
Find the interpolated brightest spot in each selection
and save thecoordinates as a number note. */
Number top, left, bottom, right

Number x, y, maxx, maxy, pixelintensity, maxintensity
Number alpha, beta, xx, xa, xb
Number kprime, lprime, spotx, spoty
ROIGetRectangle(iroi, top, left, bottom, right)
maxintensity = 0
for(y = top; y < bottom; y++) {
for(x = left; x < right; x++) {
pixelintensity = Abs(GetPixel(img,x,y))
if(pixelintensity > maxintensity) {
maxintensity = pixelintensity
maxx = x
maxy = y
}
}
}
// Find brightest neighboring pixel horizontally.

if(Abs(GetPixel(img,maxx+1,maxy)) > \
Abs(GetPixel(img,maxx-1,maxy)))
alpha = 1
else
alpha = -1
// Find brightest neighboring pixel vertically.

if(Abs(GetPixel(img,maxx,maxy+1)) > \
Abs(GetPixel(img,maxx,maxy-1)))
beta = 1
60
else
beta = -1
// Absolute value of brightest pixel.

xx = maxintensity
// Absolute value of brightest neighbor horizontally
// and vertically.
xa = Abs(GetPixel(img,maxx+alpha,maxy))
xb = Abs(GetPixel(img,maxx,maxy+beta))
// Calculate sub-pixel interpolation distance.

kprime = alpha * (2*xa - xx) / (xa + xx)
lprime = beta * (2* xb - xx) / (xb + xx)
spotx = maxx + kprime

spoty = maxy + lprime
// Save the coordinates as number notes.

SetNumberNote(img, "Spotx"+i,spotx)
SetNumberNote(img, "Spoty"+i,spoty)
}
/*******************************************************
Calculate the lengths of the reciprocal lattice vectors
and the angles between them. */
// Open result window and write header.

DocumentWindow reswin = GetResultsWindow(1)
Result("Angle"+"\t"+"Length"+"\t\t"+"Length"+"\n")
Number j, spotx1, spoty1, length1, spotx2, spoty2

Number length2, length3, theta, angle
// Loop for the first leg of the angle.

for(i = 0; i < roinumber-1; i++) {
// Retrieves the coordinates from the number notes.

GetNumberNote(img, "Spotx"+i, spotx1)
GetNumberNote(img, "Spoty"+i, spoty1)
length1 = sqrt( ( (spotx1 - centerx)/xsize )**2 + \
( (spoty1 - centery)/ysize )**2 )
// Loop for the "second leg".

for(j = i+1; j < roinumber; j++) {
GetNumberNote(img, "Spotx"+j, spotx2)
GetNumberNote(img, "Spoty"+j, spoty2)
// Side opposite angle of interest.

length3 = sqrt( ( (spotx2 - spotx1)/xsize )**2 + \
( (spoty2 - spoty1)/ysize )**2)
61
// Find cos(angle) by cosine rule.
theta = (length1**2 + length2**2 - length3**2) / \
(2 * length1 * length2)
// Find angle and convert to degrees.

angle = ACos(theta) * (180/Pi())
if(angle <= 90 && angle > 0.5) {
// Put tab-delimited values in results window.
Result(angle+"\t"+length1+"\t"+length2+"\n")
}
}
}
A.3 amplitude.s
This script is similar to the previous script, but instead of giving the angles it returns the reciprocal spacing,
the amplitude, and the phase of the Fourier coefficients using 3.3.
/*******************************************************
Digital Micrograph script 'amplitude.s'
Get image and selections and make sure they are okay. */
ComplexImage img := GetFrontImage()

Number xsize, ysize
GetSize(img, xsize, ysize)
// Find the central bright spot, assuming it is in the middle.

Number centerx = xsize / 2
Number centery = ysize / 2
ImageDisplay imgdisp = img.ImageGetImageDisplay(0)
Number roinumber = imgdisp.ImageDisplayCountROis()

if(roinumber < 1)
{
OkDialog("This script requires at least one \
rectangular selection.")
Exit(0)
}
Number i
ROI iroi
if(!ROIIsRectangle(iroi))
{
OkDialog("Only rectangular selections can \
62
be used with this script.")
Exit(0)
}
}
/*******************************************************
Find the interpolated brightest spot in each selection
and save the coordinates as a number note. */
Number top, left, bottom, right

Number x, y, maxx, maxy, pixelintensity, maxintensity
Number alpha, beta, xx, xa, xb
Number kprime, lprime, spotx, spoty, amplitude, phase
ComplexNumber xxc
ROIGetRectangle(iroi, top, left, bottom, right)
maxintensity = 0
for(y = top; y < bottom; y++) {
for(x = left; x < right; x++) {
pixelintensity = Abs(GetPixel(img,x,y))
if(pixelintensity > maxintensity) {
maxintensity = pixelintensity
maxx = x
maxy = y
}
}
}
//Find brightest neighboring pixel horizontally.
if(Abs(GetPixel(img,maxx+1,maxy)) > \
Abs(GetPixel(img,maxx-1,maxy)))
alpha = 1
else
alpha = -1
//Find brightest neighboring pixel vertically.

if(Abs(GetPixel(img,maxx,maxy+1)) > \
Abs(GetPixel(img,maxx,maxy-1)))
beta = 1
else
beta = -1
//Complex value of the brightest pixel.

xxc = GetPixel(img,maxx,maxy)
//Absolute value of brightest pixel.
xx = Abs(xxc)
//Absolute value of brightest neighbor horizontally
// and vertically.
xa = Abs(GetPixel(img,maxx+alpha,maxy))
xb = Abs(GetPixel(img,maxx,maxy+beta))
//Calculate sub-pixel interpolation distance.
63
kprime = alpha * (2*xa - xx) / (xa + xx)
lprime = beta * (2* xb - xx) / (xb + xx)
spotx = maxx + kprime

spoty = maxy + lprime
amplitude = (2*xx/(xsize * ysize))* \

((Pi()*kprime)/(Sin(Pi()*kprime)))* \
((Pi()*lprime)/(Sin(Pi()*lprime)))* \
(1-kprime**2)*(1-lprime**2)
phase = ( Phase(xxc) + kprime*Pi() + lprime*Pi() )* \
(180/Pi())
//Save the coordinates as number notes.

SetNumberNote(img, "Spotx"+i,spotx)
SetNumberNote(img, "Spoty"+i,spoty)
SetNumberNote(img, "Amplitude"+i, amplitude)
SetNumberNote(img, "Phase"+i, phase)
SetNumberNote(img, "kprime"+i, kprime)
SetNumberNote(img, "lprime"+i, lprime)
/*******************************************************
Calculate the lengths of the reciprocal lattice vectors
and the angles between them. */
//Open result window and write header.

DocumentWindow reswin = GetResultsWindow(1)
Result("Length\t\tAmplitude\tPhase\tk'\t\t\tl'\n")
Number spotx1, spoty1, length1

Number amplitude1, phase1, kprime1, lprime1
//Retrieve the coordinates from the number notes.

GetNumberNote(img, "Spotx"+i, spotx1)
GetNumberNote(img, "Spoty"+i, spoty1)
GetNumberNote(img, "Amplitude"+i, amplitude1)
GetNumberNote(img, "Phase"+i, phase1)
GetNumberNote(img, "kprime"+i, kprime1)
GetNumberNote(img, "lprime"+i, lprime1)

//Put tab-delimited values in results window.

Result(length1+"\t"+amplitude1+"\t"+phase1+"\t"+ \
kprime1+"\t"+lprime1+"\n")
}
64

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Lattice-Fringe Fingerprinting Bjorge PDF

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Volume 1, Issue 1, 2007

Lattice-Fringe Fingerprinting: Structural Identification of Nanocrystals

A thesis submitted in partial fulfillment of the

Portland State University

List of Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii

1.1 Overview of the Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Chapter 2 High-Resolution Transmission Electron Microscopy . . . . . . . . . . . . . . . . . . . 3

2.1 The Fourier Transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Chapter 3 Lattice-Fringe Fingerprinting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

3.1 Lattice-Fringe Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Chapter 4 Application of Lattice-Fringe Fingerprinting . . . . . . . . . . . . . . . . . . . . . . . . 23

4.1 Computer Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

2.1 Reflection conditions due to cell centering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

3.1 The effect of lattice parameter distortions on rutile . . . . . . . . . . . . . . . . . . . . . . . . . . 17

3.2 Phase relations of the 17 two-dimensional space groups . . . . . . . . . . . . . . . . . . . . . . . 21

2.1 Lattice-fringe visibility band . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

3.1 Lattice-fringe fingerprinting flowchart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

3.5 Simulated image showing sinusoidally varying fringes . . . . . . . . . . . . . . . . . . . . . . . . 18

4.1 Theoretical lattice-fringe fingerprint plot of anatase . . . . . . . . . . . . . . . . . . . . . . . . . . 24

4.2 Theoretical lattice-fringe fingerprint plot of brookite . . . . . . . . . . . . . . . . . . . . . . . . . . 25

4.3 Theoretical lattice-fringe fingerprint plot of rutile . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

4.6 Lattice-fringe fingerprint plot from titania images . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

4.7 Averaged lattice-fringe fingerprint plot from titania images . . . . . . . . . . . . . . . . . . . . . . 27

4.8 Theoretical lattice-fringe fingerprint plot of magnetite . . . . . . . . . . . . . . . . . . . . . . . . . 29

4.9 Theoretical lattice-fringe fingerprint plot of maghemite . . . . . . . . . . . . . . . . . . . . . . . . 30

4.11 Lattice-fringe fingerprint plot from iron oxide nanocrystal . . . . . . . . . . . . . . . . . . . . . . . 32

4.12 Lattice-fringe fingerprint plot of magnetite in the h211i direction . . . . . . . . . . . . . . . . . . . 32

4.13 Indexed Fourier transform of an image of a magnetite nanocrystal . . . . . . . . . . . . . . . . . 33

4.17 Lattice-fringe fingerprint plot from iron oxide nanocrystal . . . . . . . . . . . . . . . . . . . . . . . 37

4.18 Indexed Fourier transform of the nanocrystal in figure 4.16 . . . . . . . . . . . . . . . . . . . . . . 37

4.27 Symmetry elements of the pg two-dimensional space group . . . . . . . . . . . . . . . . . . . . . 47

4.29 Fourier transform with measured phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

4.30 HRTEM image of a titania nanocrystal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

a Diameter of the objective aperture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

aj Parameter for the fit of f e (s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

A(u) Aperture function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

bj Parameter for the fit of f e (s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Cs Spherical aberration of the objective lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

dhkl Lattice-plane spacing of the (hkl) planes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

f (θ) Atomic scattering factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

f e (s) Atomic scattering factor for electrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

fX Atomic scattering factor for x-rays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

F (g) Structure factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

F −1 Inverse Fourier transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

g Three-dimensional position vector in reciprocal space . . . . . . . . . . . . . . . . . . . . . . . . 3

g hkl Reciprocal-space vector for the planes with indices hkl . . . . . . . . . . . . . . . . . . . . . . . 5

hkl Miller indices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

m Relativistic electron mass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Puvw Probability of seeing a family of zone axes huvwi . . . . . . . . . . . . . . . . . . . . . . . . . . 7

qe (r) Specimen transmission function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

r Three-dimensional position vector in direct space . . . . . . . . . . . . . . . . . . . . . . . . . . 3

t(r) Spread function of the objective lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

T (u) Microscope transfer function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

u Two-dimensional vector in the back focal plane of the objective lens . . . . . . . . . . . . . . . . 6

Xkl Complex Fourier coefficient of the pixel at (k, l) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

αmax Visibility band half-width . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

χ(u) Phase-distortion function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

δ Dirac delta function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

∆tot Total difference parameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

∆f Objective lens defocus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

φobs Observed phase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

φres Phase residual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18