Indian Institute of Science Education and Research

Kolkata
Integrated Dual BS MS Dissertation
Quantitative Mueller matrix polarimetry
with diverse applications
Author:
Harsh Purwar
Email: harsh@iiserkol.ac.in
Supervisor:
Dr. Nirmalya Ghosh
Email: nghosh@iiserkol.ac.in
Department of Physical Sciences,
IISER-Kolkata, Mohanpur Campus, Nadia 741 252, India
2011 2012
Certicate
This is to certify that the thesis entitled Quantitative Mueller matrix polarimetry with
diverse applications being submitted to the Indian Institute of Science Education and Research
(IISER) Kolkata in partial fulllment of the requirements for the award of the Integrated
BS MS degree, embodies the research work done by Harsh Purwar under my supervision at
IISER Kolkata. The work presented here is original and has not been submitted so far, in
part or full, for any degree or diploma of any other university/institute.
Place:
Date:
Dr. Nirmalya Ghosh
Assistant Professor
Department of Physical Sciences
Indian Institute of Science Education and Research, Kolkata
ii
Acknowledgement
It is a pleasure to thank the many people who made this thesis possible.
Foremost, I would like to express my sincere gratitude to my supervisor Dr. Nirmalya Ghosh
for his continuous support, motivation, inspiration, enthusiasm and immense knowledge. His
guidance helped me at all times, during research and also while writing this thesis. I could not
have imagined having a better supervisor and mentor for my Masters study.
Besides my advisor, I would like to thank the rest of my thesis committee: Dr. Ayan Banerjee,
Dr. Bhavtosh Bansal and Dr. Ritesh K. Singh for their encouragement, insightful comments
and for asking good questions.
I also thank Dr. Uday Kumar for important discussions on various new ideas related to the
applications of the developed strategies. I would also like to thank the Department of Chemical
Sciences at IISER-Kolkata for letting me work in their labs even at odd hours.
I thank my fellow labmates in Optics and Photonics/Biophotonics Laboratory: Jalpa Soni,
Sayantan Ghosh, Satish Kumar, Harshit Lakhotia, Shubham Chandel, Nandan K. Das and
Subhasri Chatterjee for the stimulating discussions, for the sleepless nights we were working
together before deadlines, and for all the fun we have had in the last twelve months. Also I
thank my friends and family members for motivating, encouraging, inspiring and supporting
me throughout.
Place: IISER-Kolkata, Mohanpur Campus
Date: May 7th 2012
Harsh Purwar
Department of Physical Sciences,
Indian Institute of Science Education and Research, Kolkata
iii
List of Publications
Included in thesis
Jan. 2012 Development and Eigenvalue calibration of an automated
spectral Mueller matrix system for biomedical polarimetry
Harsh Purwar, Jalpa Soni, Harshit Lakhotia, Shubham Chandel, Chitram
Banerjee, Nirmalya Ghosh Proc. of SPIE, Vol. 8230 No. 823019
(doi:10.1117/12.906668). Full length manuscript is under preparation.
Dec. 2011 Quantitative polarimetry of plasmon resonant spheroidal metal
nanoparticles: A Mueller matrix decomposition study Jalpa Soni,
Harsh Purwar, Nirmalya Ghosh Optics Communications, Vol. 285 Issue
6, pp. 15991607 (doi:10.1016/j.optcom.2011.11.066).
Nov. 2011 Enhanced polarization anisotropy of metal nano-particles and
their spectral characteristics in the surface plasmon resonance
band Jalpa Soni, Harsh Purwar, Nirmalya Ghosh appeared in paper ver-
sion of Proc. of SPIE, Vol. 8096 No. 809624.
Other related pulications
May 2012 A comparative study of dierential matrix and polar decom-
position formalisms for polarimetric characterization of complex
turbid media Satish Kumar, Harsh Purwar, Razvigor Ossikovski, I Alex
Vitkin and Nirmalya Ghosh communicated to Optics Communications.
Sep. 2011 Diering self-similarity in light scattering spectra: A poten-
tial tool for pre-cancer detection Sayantan Ghosh, Jalpa Soni,
Harsh Purwar, Jaidip Jagtap, Asima Pradhan, Nirmalya Ghosh, Pras-
anta K. Panigrahi Optics Express, Vol. 19 No. 20, pp. 1970816
(doi:10.1364/OE.19.019717). Selected for further impact by Virtual Jour-
nal for Biomedical Optics, Vol. 6 Issue 10, Nov. 2011.
iv
Preface
The work embodied in this thesis has been carried out in the Department of Physical Sci-
ences, Indian Institute of Science Education and Research (IISER) Kolkata during the period
August 2011 to April 2012. The thesis is divided into following chapters.
Chapter 1: Introduction gives a brief overview of various aspects of Mueller matrix (MM)
polarimetry and its applications. It also discusses about its applicability in the eld of biomed-
ical optics.
Chapter 2: Basics of Polarimetry discusses about the Stokes-Mueller formalism and de-
nes the basic polarization parameters. Two of the commonly used Mueller matrix measurement
techniques are also discussed very briey highlighting their major advantages and drawbacks.
Chapter 3: Our MM Measurement Strategy describes in detail about the proposed spec-
tral Mueller matrix measurement strategy and its advantages over other common approaches.
It also lays emphasis on the physical realizability of the measured Mueller matrices and how
can it be achieved through optimization of the varying parameters.
Chapter 4: Calibration and Decomposition discusses two mathematical techniques in
some detail namely, Eigenvalue calibration and Polar decomposition which form the backbone
of the proposed measurement strategy.
Chapter 5: Results and Discussion shows some of the important calibration results, mea-
sured Mueller matrices and spectral behaviour of the decomposition derived polarization pa-
rameters for some common optical elements.
Chapter 6: Applications towards Tissue Characterization: This spectral MM mea-
surement system was initially used for tissue characterization (to distinguish between normal
and cancerous tissues). Brief introduction, experimental setup and preliminary results are pre-
sented in this chapter.
Chapter 7: Applications towards Nano-plasmonics: One of the major applications of
this work is in the eld of nano-plasmonics and is discussed in this chapter. The Polar decom-
posed Mueller matrices obtained using T-matrix for spheroidal metal (silver) nanoparticles and
similar dielectric particles are investigated and some of the interesting results are shown.
Chapter 8: Conclusions and Future Directions concludes this work by describing a few
innovative ideas which may be carried out in near future.
Bibliography contains references which have been cited in the above chapters.
Appendix A: Eigenvalue Calibration - Matlab Script shows an implementation of the
Eigenvalue calibration method in Matlab.
Appendix B: Polar Decomposition - Matlab Script shows an implementation of the
Polar decomposition algorithm in Matlab.
Appendix C: Labview Automation Code shows front panel and block diagram for the
VI designed to automate the whole experimental setup.
v
Contents
Certicate ii
Acknowledgement iii
List of Publications iv
Preface v
List of Figures vii
1 Introduction 10
1.1 Review of related literature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.2 Objective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2 Basics of Polarimetry 13
2.1 Stokes-Mueller Formalism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2 Commonly used measurement approaches . . . . . . . . . . . . . . . . . . . . . . 14
2.2.1 Modulation based approaches . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.2.2 Direct measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3 Our MM Measurement Strategy 17
3.1 Dual rotating retarder approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.1.1 Polarization State Generator (PSG) . . . . . . . . . . . . . . . . . . . . . 17
3.1.2 Polarization State Analyzer (PSA) . . . . . . . . . . . . . . . . . . . . . . 18
3.2 Optimization of Generator and Aanalyzer . . . . . . . . . . . . . . . . . . . . . . 19
3.3 Experimental Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
3.4 Advantages of this strategy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
4 Calibration and Decomposition 22
4.1 Eigenvalue Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
4.1.1 Mathematical Formulation . . . . . . . . . . . . . . . . . . . . . . . . . . 22
4.1.2 Limitations and Advantages . . . . . . . . . . . . . . . . . . . . . . . . . . 24
4.2 Polar Decomposition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
4.2.1 Mathematical Formulation . . . . . . . . . . . . . . . . . . . . . . . . . . 25
5 Results and Discussion 27
5.1 Calibration Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
5.2 Polar Decomposition Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
6 Applications towards Tissue Characterization 33
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
6.2 Experimental Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
6.3 Preliminary Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
vi
7 Applications towards Nanoplasmonics 37
7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
7.2 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
7.3 Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
8 Conclusions and Future directions 46
8.1 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
8.2 Future Directions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Bibliography 49
A Eigenvalue Calibration - MATLAB Script 54
B Polar Decomposition - MATLAB Script 59
C Labview Automation Code 62
vii
List of Figures
3.1 Poincare sphere showing Stokes vectors constituting PSG (red) and PSA (blue)
matrices assuming the ideal nature of both of them. x, y and z axis are the three
elements S
1
, S
2
and S
3
of the Stokes vector respectively as dened in section 2.1. 20
3.2 Schematic of the experimental setup for elastic scattering based Mueller matrix
measurements. Key: L
1
: Lens, A: Aperture, P
1
: Fixed linear polarizers with
polarization axis oriented at any arbitrary angle (calling this polarization state as
H), Q
1
& Q
2
: Rotatable quarter waveplates (orientation angles are with respect
to P
1
), S: Sample with unknown Mueller matrix, P
2
: Fixed linear polarizer
(acting as analyzer), polarization axis crossed with polarizer P
1
. . . . . . . . . . . 20
5.1 Variation of individual elements of Polarization State Generator Matrix (W) as
a function of wavelength (). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
5.2 Variation of individual elements of Polarization State Analyzer Matrix (A) as a
function of wavelength (). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
5.3 Condition number for polarization state generator matrix (W) and polarization
state analyzer matrix (A) calculated for the spectral region ( = 500 700 nm). 28
5.4 An estimate of the error in determination of the PSG and PSA matrices for the
same spectral region. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
5.5 Variation of the individual elements of Mueller matrix for blank (no sample) over
the spectral region ( = 500 700 nm). Ideally Mueller matrix for blank should
be identity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
5.6 Null (zero) elements of the Mueller matrix for a quarter waveplate, fast axis
oriented at an angle of 23

for the spectral range = 500 700 nm. Clearly the

elemental error in the measure Mueller matrices is of the order of 0.01. . . . . . . 30
5.7 Polar decomposition derived polarization parameters namely depolarization (),
diattenuation (d) and retardance (R) for blank Mueller matrix over the spectral
region ( = 500 700 nm). Expected values of all three parameters for blank
was zero. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
5.8 Polar decomposition derived diattenuation (d) for a wide-band Glan-Thompson
linear polarizer with polarization axis oriented at an angle of 28

over the spectral

region ( = 500 700 nm). Expected value of diattenuation (d) was one. . . . . 31
5.9 Polar decomposition derived linear retardance () for a 632.8 nm quarter wave-
plate with fast-axis oriented at an angle of 23

over the spectral region ( =

500 700 nm). Expected value of linear retardance was /2 or 1.57 radians at
= 632.8 nm. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
6.1 Schematic of the experimental setup for in-elastic (uorescence) scattering with
simultaneous imaging and spectroscopic Mueller matrix measurements. Key:
L: Lens, A: Aperture, BS: Beam splitter, NDF: Neutral density lter, GT:
Wide-band Glan Thompson linear polarizer, QWP: Quarter waveplate, MO:
Mounting optics, F: Filter, LCV F: Liquid crystal variable lter. . . . . . . . . . 34
viii
6.2 First element of uorescence Mueller matrix M
11
(un-normalized) for human
cervical cancer tissue biopsy slide (thickness few m) over the spectral region
( = 450 800 nm). A bandpass lter (450 900 nm) was used to cut o the
incident wavelength 405 nm used of exciting the tissue sample. The uorescence
emission peaks of Collagen and NADH are indicated. . . . . . . . . . . . . . . . . 35
6.3 Individual elements of uorescence Mueller matrix for human cervical cancer
tissue biopsy slide (thickness few m) over the spectral region ( = 475 800
nm). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
6.4 Polar decomposition derived diattenuation (d) for human cervical cancer tissue
biopsy slide (thickness few m) over the spectral region ( = 450800 nm) for
two dierent grades (stages) of cancer determined from histo-pathology report of
the sample. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
7.1 The variation of the decomposition-derived net depolarization coecient () as a
function wavelength ( = 325525 nm) for randomly oriented silver nanoparticles
with radius r = 20 nm. The results are shown for varying aspect ratios of the
oblate spheroids ( = 1 2) and the scattering angle was chosen to be = 45

. . 42
7.2 The T-matrix computed scattering eciency (Q
sca
) as a function of wavelength
for the spheroidal silver nanoparticles of varying aspect ratios ( = 1.25 2.0)
and having a xed radius of 20 nm. . . . . . . . . . . . . . . . . . . . . . . . . . . 43
7.3 The spectral variation of the decomposition-derived linear retardance () for
preferentially oriented (see text for details on orientation) spheroidal silver nanopar-
ticles with radius r = 20 nm and varying aspect ratio = 1.02.0. The scattering
angle was = 45

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
7.4 The scattering angle () dependence of the decomposition-derived value of linear
retardance for preferentially oriented spheroidal silver nanoparticle with r = 20
nm and = 1.5. The results are shown for three dierent wavelengths: 365
nm, 440 nm (corresponding to the peaks of the transverse and the longitudinal
plasmon resonances respectively) and 400 nm (corresponding to the peak of ()
and ()). The corresponding variation of the similar dielectric particle is shown
by solid circle in the gure ( = 400 nm). . . . . . . . . . . . . . . . . . . . . . . 45
C.1 Front Panel of the automation VI. . . . . . . . . . . . . . . . . . . . . . . . . . . 62
C.2 Block Diagram of the automation VI. . . . . . . . . . . . . . . . . . . . . . . . . 63
ix
Chapter 1
Introduction
Development of optical techniques for biomedical diagnosis is an area of considerable current
research interest [1, 2]. Optical methods can facilitate non-invasive and quantitative diagnosis
[3]. For optical diagnosis, one mostly uses the light scattered from the tissue. Most of the
light scattered from tissue is scattered elastically i.e. without any change in frequency. The
elastically scattered light from tissue bears useful information on underlying morphological and
physiological state of tissue. The scattered light also has a very weak component which is
scattered in-elastically i.e. with a change in frequency via processes like uorescence, Raman
scattering etc. The in-elastically scattered light is characteristic of the chemical composition of
the tissue and thus is linked with bio-chemical properties of the tissue. Therefore by careful
analysis of elastically and in-elastically scattered light one can diagnose disease. Motivated by
this fact, various optical techniques based on scattered light (elastically or in-elastically) from
tissue are being actively perused for their diagnostic potential [2, 4, 5, 6].
With altered physiological state, the concentration, size, shape and refractive index of the
dierent extra cellular or intra-cellular organelles of tissue show prominent changes. These al-
terations have characteristic and varied impact on the measured elastic scattering signal from
tissue. The parameters of elastically scattered light that can be used to quantify these mor-
phological features in tissue are the wavelength dependence of scattered light intensity (or the
wavelength variation of the scattering coecient), the angular variation of scattering or the
polarization properties of scattered light. While considerable work has been carried out on the
use of the rst two approaches [2], there appear a few reports only on the use of polarimetric
light scattering for tissue diagnosis [7, 8]. Measurement of the polarization properties of scat-
tered light from tissue might provide additional diagnostic information on tissue as compared
to unpolarized measurements. For example, since the rate of depolarization of incident linearly
and circularly polarized light depends on the morphological parameters like the density, size
(and its distribution), shape and refractive index of scatterers present in the medium [9], this
information may be used for quantitative tissue diagnosis. In addition to isotropic depolariza-
tion property, many constituents of tissue also show intrinsic polarization properties such as
retardance (linear retardance arising due to a dierence in phase between two orthogonal linear
polarization, and circular retardance arising due to a dierence in phase between right and left
circularly polarized light) and dichroism or diattenuation (linear diattenuation arising due to the
dierential attenuation of two orthogonal linear polarization, and circular diattenuation arising
due to the dierential attenuation of right and left circularly polarized light). For example, col-
lagen is an important structural protein in the human body that has intrinsic linear retardance
property. The structural aggregates of collagen (micro-brils, brils and bers that causes the
retardance property of collagen) play an important role in maintaining the mechanical property
of tissue and the orientation and arrangement of collagen is closely related to the structural
and functional properties of tissues and organs. In various kinds of tissue abnormalities such
as, erythema, psoriasis, actinic keratosis, neurobroma and the numerous types of carcinomas
10
(like basal cell, squamous cell, melanomas etc.), the structural and functional properties of col-
lagen aggregates show distinct changes. Such changes are expected to lead to variation in their
retardance property. Measurement and quantication of linear retardance of collagen in tissue
may thus provide a useful tool for diagnosis of various kinds of tissue abnormalities. Glucose is
another important tissue constituent that possesses intrinsic circular retardance property due
to its asymmetric chiral structure. Its presence in tissue leads to rotation of the plane of linearly
polarized light about the axis of propagation (known as optical rotation). Measurement of cir-
cular retardance or optical rotation of scattered light from tissue might facilitate non-invasive
monitoring of glucose level in human tissue. Thus it appears that measurement of the dierent
polarization properties (depolarization, retardance and diattenuation) of elastically scattered
light from tissue might come out to be useful for various diagnostics applications. Mueller
matrix measurement technique is an experimental approach that can facilitate simultaneous
quantication of all these polarization parameters of a medium. We therefore propose to carry
out detailed studies on measurement of Mueller matrix of elastically scattered light from various
biological samples (including tissue samples) to explore possibility of quantitative biomedical
diagnosis using the polarization properties of scattered light. In contrast to elastic scattering
measurements, uorescence spectroscopy probes biochemical changes that take place with the
onset and progression of disease. Fluorescence spectroscopy has particularly been investigated
for diagnosis of cancer. The parameters of autouorescence (uorescence from endogenous tis-
sue uorophores) that can be used for diagnosis include dierences in the static spectra, decay
kinetics or polarization properties of uorescence. While considerable work has been carried out
on the rst two aspects [3, 10, 11], there appear only a few reports on exploiting the polariza-
tion properties of uorescence from tissue for cancer diagnosis. Limited literature available on
this aspect has demonstrated that polarized uorescence measurements have several important
advantages over unpolarized uorescence measurements for tissue diagnosis [7, 8]. As compared
to the two orthogonal polarization state measurements used in the previous polarimetric studies
[8, 12], measurements of Mueller matrix of uorescence emitted from tissue would allow one
to obtain a more complete information on polarization properties of uorescence. This there-
fore might turn out to be an ecient approach to fully exploit the advantages of polarized
uorescence measurements and design the optimal polarization scheme for quantitative tissue
diagnosis. Motivated by the promise of this approach, we also plan to investigate this aspect in
details.
1.1 Review of related literature
As noted earlier, while the inelastically scattered light (uorescence and Raman) bears useful
biochemical information on tissue, the elastically scattered light also contains useful information
on underlying morphological and physiological state of tissue. Elastic light scattering measure-
ments thus provides a tool to assess tissue morphometry by recovering typical scatterers sizes
and their refractive indices. Attempts have therefore been made by several researchers to use
elastic scattering measurements for quantitative tissue diagnosis [2, 6]. The general strategy
followed in most of these studies to quantify the morphological parameters (concentration,
size, shape and refractive index of cellular, sub-cellular or extra cellular organelles) has been
to analyze the wavelength dependence of elastic scattering signal [2] or the angular variation
of scattering [2]. Calculations based on Mie theory of light scattering have widely been used
for this purpose [13, 14]. Most of these studies have been performed using unpolarized elas-
tic scattering measurements and there appear a few reports only on the use of polarized elastic
scattering measurements for biomedical diagnosis [4]. Limited literature available on this aspect
has revealed that measurement of polarization properties of scattered light like depolarization,
retardance and diattenuation can also facilitate quantication of useful physiological and mor-
phological parameters of tissue thus, providing a useful tool for diagnosis of various kinds of
11
tissue abnormalities. Since Mueller matrix contains detailed information about all the polar-
ization properties of the medium in its dierent elements, this can be used to quantify these
parameters very eciently. This would however, require suitable theoretical approaches (math-
ematical models) to extract the dierent polarization parameters from the measured Mueller
matrix and to interpret and analyze these parameters in terms of the physiological and morpho-
logical features of tissue. This aspect has not been investigated in sucient details and there
appear only a few reports on this aspect [4, 15]. It has recently shown that the ambiguity of the
change in the orientation angle of the polarization vector due to scattering arises due to the com-
bined eect of linear diattenuation and linear retardance of light scattered at large angles and
can be decoupled from the pure optical rotation (arising due the presence of chiral molecules)
component using polar decomposition of Mueller matrix [16]. For this purpose, the method
developed earlier [15] for polar decomposition of Mueller matrix was extended to incorporate
optical rotation in the medium. The results of these preliminary studies were encouraging and
demonstrated that polar decomposition of Mueller matrix can facilitate accurate quantication
of optical rotation introduced by the presence of chiral molecules in a turbid medium, like for
example glucose in human tissue. Apart from its use in glucose sensing in tissue, the developed
polar decomposition of Mueller matrix based approach might nd wide range of applications in
quantitative biomedical diagnosis. We thus plan to investigate this aspect in more details.
1.2 Objective
The main objective of the proposed work is to develop techniques to measure the various polar-
ization properties of elastically and in-elastically (uorescence) scattered light from biological
samples, to develop methodologies to interpret and analyze the measured polarization prop-
erties in terms of the underlying morphological, biochemical features of the sample and to
use this information for quantitative biomedical diagnosis. Since, Mueller matrix provides a
complete description of the polarization characteristics of the medium, focus is on the measure-
ment of Mueller matrix and quantication of the dierent polarization parameters of scattered
light (elastically and in-elastically (uorescence) both) from the measured Mueller matrix for
biological samples.
12
Chapter 2
Basics of Polarimetry
Polarimeters are optical instruments used for determining the polarization properties of light
beams and samples [17]. Polarimetry, the science of measuring polarization, is most simply char-
acterized as radiometry with polarization elements. Typical applications of polarimeters include
the following: remote sensing of the earth and astronomical bodies, calibration of polarization
elements, measuring the thickness and refractive indices of thin lms (ellipsometry), spectro-
scopic studies of materials, and alignment of polarization-critical optical systems [17, 18, 19, 20].
2.1 Stokes-Mueller Formalism
Since 1852, when George G. Stokes gave his formalism to describe the polarization state of light
or in general of an electromagnetic radiation, several calculus have been developed, including
those based on Jones matrix, coherency matrix, Mueller matrix and other matrices
1
. Of these
methods, the Mueller calculus is most generally suited for describing intensity-measuring instru-
ments, including most polarimeters, radiometers, and spectrometers, and is used exclusively in
this thesis.
In the Mueller calculus, developed by Hans Mueller in 1943, the Stokes vector S is used
to describe the polarization state of a light beam, and the Mueller matrix M to describe the
polarization-altering characteristics of a sample. This sample may be a surface, a polarization
element, an optical system, or some other light-matter interaction which produces a reected,
refracted, diracted, or scattered light beam. The Stokes vector is dened relative to the fol-
lowing six intensity measurements I performed with ideal polarizers in front of a photo-diode,
spectrometer or a CCD [17]:
I
H
Intensity of horizontally polarized component (0

).
I
V
Intensity of vertically polarized component (90

).
I
P
Intensity of +45

polarized component.
I
M
Intensity of 45

polarized component.
I
L
Intensity of left circularly polarized component.
I
R
Intensity of right circularly polarized component.
The stokes vector is dened as [17, 13, 21],
S =
_
_
_
_
s
0
s
1
s
2
s
3
_
_
_
_
=
_
_
_
_
I
H
+I
V
I
H
I
V
I
P
I
M
I
L
I
R
_
_
_
_
(2.1)
1
Shurcli, 1962; Gerrard and Burch, 1975; Theocaris and Gdoutos, 1979; Azzam and Bashara, 1987; Coulson,
1988; Egan, 1992
13
where s
0
, s
1
, s
2
and s
3
are Stokes vector elements. s
0
gives the total intensity. The Stokes
vector does not need to be measured by these six ideal measurements; what is required is that
other methods reproduce the Stokes vector dened in this manner. Ideal polarizers are not
required. Further, the Stokes vector is a function of wavelength, position on the object, and the
lights direction of emission or scatter.
From the Stokes vector, the following polarization parameters are determined [17],
Degree of Polarization: describes the portion of an electromagnetic wave which is
polarized be it linear, cicular or elliptical.
DOP =
_
s
2
1
+s
2
2
+s
2
3
s
0
(2.2)
Degree of Linear Polarization: describes the portion of an electromagnetic wave which
is linearly polarized.
DOLP =
_
s
2
1
+s
2
2
s
0
(2.3)
Degree of Circular Polarization: describes portion of an electromagnetic wave which
is circularly polarized.
DOCP =
s
3
s
0
(2.4)
Note: Degree of polarization (DOP) for a unpolarized light is zero whereas for partially polar-
ized light is less than unity.
The Mueller matrix M for a polarization-altering device is dened as the matrix which
transforms an incident Stokes vector S into the exiting (reected, transmitted, or scattered)
Stokes vector S

,
S

=
_
_
_
_
s

0
s

1
s

2
s

3
_
_
_
_
= MS =
_
_
_
_
m
11
m
12
m
13
m
14
m
21
m
22
m
23
m
24
m
31
m
32
m
33
m
34
m
41
m
42
m
43
m
44
_
_
_
_
_
_
_
_
s
0
s
1
s
2
s
3
_
_
_
_
(2.5)
The Mueller matrix is a 44 matrix with real valued elements. The Mueller matrix M(k, ) for
a device is always a function of the direction of propagation k and wavelength . The Mueller
matrix is an appropriate formalism for characterizing polarization measurements because it
contains within its elements all of the polarization properties: diattenuation, retardance, de-
polarization, and their form, either linear, circular, or elliptical. When the Mueller matrix is
known, then the exiting polarization state is known for an arbitrary incident polarization state.
Table 2.1 is a compilation of Mueller matrices for common polarization elements, together with
the corresponding transmitted Stokes vector.
2.2 Commonly used measurement approaches
There are a number of Mueller matrix measurement approaches that researchers have proposed
in years. As technology improves more of such approaches and strategies are expected to come.
In this section two of such approaches that have been widely accepted by scientists and are in use
namely modulation based and direct measurement approaches are briey described highlighting
their advantages and major drawbacks.
14
Table 2.1: Mueller matrices for some of the common optical elements along with the corre-
sponding transmitted Stokes vector.
Nonpolarizing element
_

_
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
_

_
_

_
s
1
s
2
s
3
s
4
_

_
=
_

_
s
1
s
2
s
3
s
4
_

_
An absorber
_

_
a 0 0 0
0 a 0 0
0 0 a 0
0 0 0 a
_

_
_

_
s
1
s
2
s
3
s
4
_

_
=
_

_
as
1
as
2
as
3
as
4
_

_
A linear polarizer, transmission axis 0

_
1 1 0 0
1 1 0 0
0 0 0 0
0 0 0 0
_

_
_

_
s
1
s
2
s
3
s
4
_

_
=
_

_
s
1
+s
2
s
1
+s
2
0
0
_

_
A linear diattenuator, axis

, intensity transmittances, q, r
_

_
q +r (q r) cos 2 (q r) sin 2 0
(q r) cos 2 (q +r) cos
2
2 + 2

qr sin
2
2 (q +r 2

qr) sin 2 cos 2 0

(q r) sin 2 (q +r 2

qr) sin 2 cos 2 (q +r) cos

2
2 + 2

qr sin
2
2 0
0 0 0 2

qr
_

_
Linear retarder, fast axis , retardance
_

_
1 0 0 0
0 cos
2
2 + sin
2
2 cos sin 2 cos 2(1 cos ) sin 2 sin
0 sin 2 cos 2(1 cos ) cos
2
2 + sin
2
2 cos cos 2 sin
0 sin 2 sin cos 2 sin cos
_

_
2.2.1 Modulation based approaches
Modulation based approaches make use of photo-elastic [22], electro-optic or magneto-optics
modulators to rapidly change the polarization states and a lock-in based point detection with a
photo-diode to measure the intensity of these rapidly changing polarization states. One of the
main advantages of these strategies is that due to the use of modulated polarization and lock-in
based detection the measurements are very accurate and precise. Even a single measurement
made using this approach is sucient to determine all sixteen elements of the Mueller matrix.
Such experimental setups are capable of extracting even a weak polarized component of light
from the strong depolarization background noise.
On the other hand one of the major drawback of such strategies is that they can not be used
for neither imaging nor spectral measurements. This is essentially because of the limitation
imposed by the use of lock-in with a photo-diode which is capable of only a point measurement.
And secondly the functioning of the photo-elastic modulators also depend on the wavelength
and can not be used for spectral measurements.
15
2.2.2 Direct measurements
Direct measurement strategies refers to the calculation of the Mueller matrix directly from
the intensity measurements corresponding to dierent incident and analyzed polarization states
generated by rotating polarizers or wave retarders [23] or both. This measurement strategy is
best suited for imaging and spectral Mueller matrix measurements and since does not reqiure
any extra measurements, if automated could give very quick results. Although is not very
accurate and is prone to huge elemental errors. In order to get a more acurate result one has
to increase the number of measurements which might not always be possible. Moreover taking
36 or 49 measurements in order to nd the sixteen unknown elements of a 4 4 Mueller matrix
is a shear wastage of resources and time.
16
Chapter 3
Our MM Measurement Strategy
3.1 Dual rotating retarder approach
The dual rotating retarder approach refers to the two rotating retarders (here quarter wave-
plates) used along with two xed linear polarizers to generate sixteen elliptically polarized states
so as to determine the sixteen unknown elements of the 4 4 Mueller matrix. A schematic of
the experimental setup is shown in Fig. 3.2.
3.1.1 Polarization State Generator (PSG)
Polarization state generator (PSG) consists of a xed linear polarizer (P
1
) with the choice of
orienting its polarization axis at any arbitrary orientation angle followed by a rotatable retarder
(Q
1
) (quarter waveplate here), orientation of the fast axis is with respect to the polarizer P
1
.
If both, polarizer and retarder are allowed to change their orientations, PSG in principal can
be used to generate any polarization state of light. As mentioned in the section 2.1 Mueller
matrix of an optical element essentially describes how the polarization of the incident light is
transformed by that optical element. The un-polarized light or in terms of Stokes formalism
the Stokes vector S
0
= (1 0 0 0)
T
for un-polarized light is incident on the polarization state
generator which is then transformed to some other polarization state or Stokes vector depending
upon the conguration of the elements in PSG. For some orientation angle lets say
1
of the
retarder the output stokes vector W

1
can be calculated from the Mueller matrices for the
retarder and polarizer as follows,
W

1
=
_
_
_
_
1 0 0 0
0 C
2

1
+S
2

1
C

1
C

1
(1 C

) S

1
S

0 S

1
C

1
(1 C

) S
2

1
+C
2

1
C

1
S

0 S

1
S

1
S

_
_
_
_
. .
M
Retarder

_
_
_
_
1 1 0 0
1 1 0 0
0 0 0 0
0 0 0 0
_
_
_
_
. .
M
Pol
at Horizontal

_
_
_
_
1
0
0
0
_
_
_
_
. .
Unpol.
(3.1)
W

1
=
_
_
_
_
1
C
2

1
+S
2

1
C

1
S

1
(1 C

)
S

1
S

_
_
_
_
(3.2)
where, C

= cos , S

= sin , C

i
= cos 2
i
and S

i
= sin 2
i
,
i
s being orientation angles
of the fast axis of retarder (Q
1
) with respect to the polarizer P
1
and being its retardance
( = /2 radians for a quarter waveplate). For measuring complete Mueller matrix i.e. all
sixteen elements we need to generate and analyze four dierent polarization states. In this
strategy four input polarization states are generated by rotating the retarder in PSG to four
dierent orientation angles (
1
,
2
,
3
&
4
). The corresponding output stokes vectors for these
17
four orientations of retarder are clubbed together to get the 4 4 W or PSG matrix such that
each column of W represents an incident Stokes vector or incident polarization state (incident
at the sample) as shown below.
W =
_
_
_
_
1 1 1 1
C
2

1
+S
2

1
C

C
2

2
+S
2

2
C

C
2

3
+S
2

3
C

C
2

4
+S
2

4
C

1
S

1
(1 C

) C

2
S

2
(1 C

) C

3
S

3
(1 C

) C

4
S

4
(1 C

)
S

1
S

2
S

3
S

4
S

_
_
_
_
(3.3)
3.1.2 Polarization State Analyzer (PSA)
The construction of polarization state analyser (PSA) is very similar to that of the generator
and comprises of a rotatable quarter waveplate (Q
2
), fast axis again oriented with respect to
polarizer P
1
, followed by a xed linear polarizer (P
2
) crossed with P
1
. Again if both retarder
and polarizer are allowed to change PSA can be used to measure any unknown incident Stokes
vector or polarization state. Here since the order with respect to the incident light of retarder
and polarizer is reversed the corresponding Mueller matrices also get reversed in the construc-
tion of the PSA matrix. For some orientation of the quarter wave plate Q
2
lets say
1
, the
transformation matrix would be given by,
A

1
=
_
_
_
_
1 1 0 0
1 1 0 0
0 0 0 0
0 0 0 0
_
_
_
_
. .
M
Pol
at Vertical

_
_
_
_
1 0 0 0
0 C
2

1
+S
2

1
C

1
C

1
(1 C

) S

1
S

0 S

1
C

1
(1 C

) S
2

1
+C
2

1
C

1
S

0 S

1
S

1
S

_
_
_
_
. .
M
Retarder
(3.4)
(symbols have the same meaning as dened earlier). As in most polarimeters as well as here
polarization state analyzer is followed by an intensity based detector, which just records the
total intensity falling on it, given by the rst element or row of the output Stokes vector, and
since,
S
out
= A

1
S
in
only rst row of A

1
is required for determination of the rst element of S
out
, given by,
A

1
=
_
1 C
2

1
S
2

1
C

1
C

1
(1 C

) S

1
S

_
(3.5)
Just as in PSG we generated four input polarization states here we need to analyze four polar-
ization states resulting in 16 measurements of each generated state (total four in number) with
all congurations of the analyzer. Clubbing the four congurations of the polarization state
analyzer for four orientation angles (lets say
1
,
2
,
3
&
4
) of the retarder (Q
2
) we have,
A =
_
_
_
_
1 C
2

1
S
2

1
C

1
C

1
(1 C

) S

1
S

1 C
2

2
S
2

2
C

2
C

2
(1 C

) S

2
S

1 C
2

3
S
2

3
C

3
C

3
(1 C

) S

3
S

1 C
2

4
S
2

4
C

4
C

4
(1 C

) S

4
S

_
_
_
_
(3.6)
The construction of the polarization state generator (W) and analyzer (A) matrices is now
complete. The exact congurations of both, though needs optimization so as to yield best
possible outcomes. From W (PSG) and A (PSA) matrices, Mueller matrix for the unknown
sample M
s
is calculated as follows. We know that,
M = AM
s
W
where, M is a matrix formed by the intensity measurements for the sample S with Mueller
matrix M
s
. Hence, if we dene,
Q
1616
= A
44
W
T
44
(3.7)
18
= (M
s
)
161
= Q
1
1616
M
161
(3.8)
(M
s
)
161
is then reshaped back to the 4 4 matrix.
3.2 Optimization of Generator and Aanalyzer
As has been shown in the above sections the constructions of the polarization state generator and
analyzer is very crucial in this measurement strategy. To determine their exact congurations
we need to choose four polarization states for PSG and four for PSA by xing the orientation
angles of the two rotatable retarders (quarter waveplates here) (Q
1
and Q
2
). Choosing the angles
of the retarder Q
1
belonging to PSG would essentially x the four Stokes vectors, elliptically
polarized in this case, incident on the sample. Similarly for four angles of Q
2
the elliptically
polarized states that would be detected (only total intensity is recorded which corresponds
to the rst element S
0
of the Stokes vector) get xed. One basic criteria for choosing these
polarization states could be to maximize the determinant of the 16 16 matrix Q dened by
equation 3.7 and to make certain that it is strictly positive, since matrix Q has to be invertible
otherwise the samples Mueller matrix M
s
could not be calculated using 3.8. And since, here the
measurements are done over a spectral range, = 400 800 nm, the optics constituting PSG
and PSA is very likely to change its polarization characteristics with the wavelength. The 633
nm quarter waveplate does not behave like a quarter waveplate at other wavelengths as is shown
in Fig. 5.9. To be on the safer side the determinant of the matrix Q is maximized because Q
may change with wavelength for a particular conguration of the PSG and PSA matrices such
that its determinant approaches zero at certain other wavelength and this dependency of the
matrix Q or of PSG and PSA matrices is not known a-priori.
The orientation angles for the two quarter waveplates chosen by maximizing the determinant
of the matrix Q were 35

, 70

, 105

and 140

. For simplicity these angles for the two quarter

waveplates were kept same and close to the round gure.
The above chosen angles were also veried using a more rigorous approach of singular value
decomposition and a quantity named condition number was dened as follows,
Condition No. =
min {singular values}
max {singular values}
(3.9)
These singular values must be positive otherwise the resulting Mueller matrix from these cal-
culations will not be physically realisable [24, 17, 25]. The variation of condition number with
wavelength for the chosen conguration of PSG and PSA matrices is shown in Fig. 5.3. The
freedom that the group of four Stokes vectors constituting PSG and PSA can be rotated so as
to cover or span all the points on the Poincare sphere because of the fact that any polarization
state or conguration of the polarizer P
1
can be arbitrarily chosen and called Horizontal and
orientations of rest of the optics (P
2
, Q
1
and Q
2
) is with respect to this polarizer P
1
. This
enable the rotation of these stokes vectors together on the Poincare sphere. For illustration
these Stokes vectors are shown in Fig. 3.1 on the Poincare sphere.
19
x y
z
1
Figure 3.1: Poincare sphere showing Stokes vectors constituting PSG (red) and PSA (blue)
matrices assuming the ideal nature of both of them. x, y and z axis are the three elements S
1
,
S
2
and S
3
of the Stokes vector respectively as dened in section 2.1.
3.3 Experimental Setup
A schematic of the experimental setup is as shown in Fig. 3.2. It consists of a 50 W Ocean
Optics Xenon lamp, two wide-band linear polarizers P
1
and P
2
; P
1
s polarization axis is xed
at any arbitrary orientation angle and P
2
is crossed with P
1
, two 633 nm Thorlabs quarter
waveplates (Q1 & Q
2
) mounted on computer controlled rotational stages and an Ocean Optics
USB4000 bre-optic spectrometer used as a detector for the spectral measurements. The whole
setup rests on a goniometer which can be used for studies based on angular dependence of
scattering [2].
Figure 3.2: Schematic of the experimental setup for elastic scattering based Mueller matrix
measurements. Key: L
1
: Lens, A: Aperture, P
1
: Fixed linear polarizers with polarization
axis oriented at any arbitrary angle (calling this polarization state as H), Q
1
& Q
2
: Rotatable
quarter waveplates (orientation angles are with respect to P
1
), S: Sample with unknown Mueller
matrix, P
2
: Fixed linear polarizer (acting as analyzer), polarization axis crossed with polarizer
P
1
.
The sample S is mounted in between the polarization state generator and analyzer arrange-
ment and for calibration purposes a wide-band Glan Thompson linear polarizer and a single
wavelength quarter wave retarder was used. The setup was completely automated using Lab-
view with the aid of the VIs and SDKs provided by the manufacturers of these instruments.
The front panel and block diagram for the automation VI are shown in appendix C. Obtained
results are presented in the following chapters.
20
3.4 Advantages of this strategy
Following are some of the main advantages of this measurement strategy over other commonly
used approaches listed in section 2.2:
1. Independent of source and detector polarization responses: Even if the source does not emit
completely un-polarized light and detectors like spectrometer uses a grating to separate
various wavelengths of the light falling on it, it may have some intrinsic polarization
response which need not be corrected separately in this measurement strategy, since the
two linear polarizers P
1
and P
2
are always xed at horizontal and vertical polarization
states respectively. The polarizer P
1
will pass the horizontally polarized component of
light which will always have the same intensity even if the source is not ideal.
2. Simultaneous spectral and imaging measurements: It is capable of recording spectral and
spatial mapping or imaging simultaneously by using liquid crystal variable lters together
with a charge coupled device (CCD). The ability to generate PSG and PSA matrices
through Eigenvalue calibration method described in section 4.1 for the entire spectral range
makes it very ecient in terms of accuracy for spectral Mueller matrix measurements. The
elemental error in the measured Mueller matrices is 0.01 over the entire spectral range
as shown in Fig. 5.6.
3. Is completely automated: Since the measurement system is completely automated, it is
very precise and take a very little time (about a few minutes) for recording all sixteen
spectral measurements. This also reduces chances of human errors.
21
Chapter 4
Calibration and Decomposition
4.1 Eigenvalue Calibration
The Eigenvalue Calibration Method is the rst which uses the matrix formalism for the global
experimental setup to be calibrated [26]. It is capable of determining the polarization state
generator (PSG) and analyzer (PSA) matrices over the entire spectral range thus automatically
correcting for the non-ideal behaviour and wavelength dependence of the optics comprising
generator and analyzer [27, 28, 29]. The only requirement of this method is to take a few extra
measurements for the chosen reference or calibration samples. The form of the Mueller matrices
for these reference samples must be known a-priori. Its wavelength dependence may or may not
be known. A brief description [26] of this method follows.
4.1.1 Mathematical Formulation
Let us choose our calibration (or reference) sample to be a diattenuating retarder just for the
purpose of illustration, in a more general case any optical element whose form of the Mueller
matrix is known can be used for calibration purpose, and call the set of measurements (refers to
the matrix formed by the sixteen intensity-based measurements for dierent polarization states)
as B. The eigenvalue calibration method requires another set of measurements for blank (no
specic sample, hence its Mueller matrix is a 4 4 identity matrix), and let us denote it by B
0
.
These measurements can be expressed in terms of polarization state generator (PSG) matrix
(W), polarization state analyzer (PSA) matrix (A) (both unknown at this point) and Mueller
matrix of the sample (M), whose form is only known (its spectral variation need not be known)
as follows.
B
0
= AW, B = AMW (4.1)
since Mueller matrix for blank is identity. Another set of matrices C and C

is constructed such
that one of them is independent of the PSA matrix A and other is independent of PSG matrix
W.
C = B
1
0
B = W
1
MW, C

= BB
1
0
= AMA
1
(4.2)
Clearly, matrices C, M and C

form a group of similar matrices and thus have same eigenvalues.

The eigenvalues of the matrix C (calculated from measurements B and B
0
) are computed and
are equated to the eigenvalues of the Mueller matrix of the calibration sample M. This can
always be done since the form of the Mueller matrix for the calibration sample is known (one
of the requirements of this method). Here, a diattenuating retarder is chosen as one of the
reference samples whose Mueller matrix is known to have the following form,
M =
_

_
1 cos 2 0 0
cos 2 1 0 0
0 0 sin 2 cos sin 2 sin
0 0 sin 2 sin sin 2 cos
_

_
(4.3)
22
where, and are the ellipsometric parameters for the diattenuating retarder and is its
transmittance. Matrix M has four eigenvalues, two of which are real (
R
1
,
R
2
) and two
complex (
C
1
,
C
2
).

R
1
= 2 cos
2

R
2
= 2 sin
2

C
1
= sin 2e
i

C
2
= sin 2e
i
(4.4)
Solving for the parameters, , , and , we have,
=

R
1
+
R
2
2
, = tan
1

R
1

R
2
, = log

C
2

C
1
(4.5)
From these measured values of the ellipsometric parameters Mueller matrix M for the reference
sample (diattenuating retarder) is constructed using (4.3). If more than one reference sam-
ples are taken for calibration their individual Mueller matrices for various wavelengths can be
constructed like this.
Consider the following matrix equations,
MX XC = 0, MX

= 0 (4.6)
After calculating C, C

and M from the measurements as described above, (4.6) with solutions:

X = W and X

= A since, (4.2) can be solved using the least square method[26] as described
below. The PSG matrix W
44
is written as a vector W
161
= {w
n
}
n=1...16
in a basis set
{G
n
}
n=1...16
such that,
W
44
=
16

n=1
w
n
G
n
(4.7)
W
44
=
_
_
_
_
w
1
w
2
w
3
w
4
w
5
w
6
w
7
w
8
w
9
w
10
w
11
w
12
w
13
w
14
w
15
w
16
_
_
_
_
=
16

n=1
w
n
G
n
(4.8)
where,
G =
_

_
_
_
_
_
1 0 0 0
0 0 0 0
0 0 0 0
0 0 0 0
_
_
_
_
,
_
_
_
_
0 1 0 0
0 0 0 0
0 0 0 0
0 0 0 0
_
_
_
_
,
_
_
_
_
0 0 1 0
0 0 0 0
0 0 0 0
0 0 0 0
_
_
_
_
, ,
_
_
_
_
0 0 0 0
0 0 0 0
0 0 0 0
0 0 0 1
_
_
_
_
_

_
T
(4.9)
In this basis the mapping H(X) = MXXC, hence H(W) = 0 acts on vectors with 16 elements,
and is represented by a 16 16 real matrix H, so that the following applies:
H(W
161
) = 0 (4.10)
The matrix H is calculated in the following way:
(H
1616
)
ij
=
_
(H(G
i
))
F
_
j
(4.11)
where F denotes the attening operation,
_
_
_
_
1 2 3 4
5 6 7 8
9 10 11 12
13 14 15 16
_
_
_
_
F
=
_
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
_
(4.12)
23
The least-squares solution of equation 4.10 is given by the relation:
KW
161
= 0
where,
K = H
T
H
The 16 16 matrix K is diagonizable, and because W
161
is the only solution of HW
161
= 0,
W
161
is the unique eigenvector associated with the null eigenvalue. In practice H(W) is not
exactly zero because of experimental errors, but still the following applies to the eigenvalues ()
of K:
0
1
<<
2
<
3
<
4
< . . . <
16
It should be noted here that an unknown misalignment of the various reference samples causes
an increase of
1
/
16
. The minimum value of this ratio corresponds to the case that the applied
Mueller matrices of the reference samples are exactly the Mueller matrices of the used reference
samples. It follows now that W
161
is the eigenvector associated with the smallest eigenvalue
of K. The vector W
161
is written back as a 4 4 matrix W in accordance with equation 4.12.
From W, A is calculated as A = B
0
W
1
where, B
0
is the measurement matrix for blank.
The results for PSG (W) and PSA (A) matrices for the entire concerned spectral range
( = 500 700 nm) are shown in Figs. 5.1 and 5.2 respectively.
4.1.2 Limitations and Advantages
The Eigenvalue calibration method described in above few sections plays a major role in the
proposed measurement strategy. For most calibration methods the choice of a proper calibration
sample is very crucial since most of the results depend on a few extra measurements recorded
for these calibration samples. However, for eigenvalue calibration method this choice is very
easy to make. The only requirement of this procedure is that the form of the Mueller matrix
for the chosen reference sample(s) must be know a-priori. Its wavelength dependence may or
may not be known. Through this calibration technique one can automatically correct for the
errors [30, 31, 32] due to non-ideal behaviour of the optics over the spectral range constituting
polarization state generator (PSG) and analyzer (PSA) arrangements. Small deviations or
misalignments in the orientations or congurations of the chosen reference samples are also
taken care o by the Eigenvalue calibration method since these values are calculated from the
measurments using the eigenvalues of the matrix C or C

before reconstructing the Mueller

matrix for these reference samples and are not assumed to be those set by hand.
4.2 Polar Decomposition
In polar decomposition method, a given 4 4 Mueller matrix M for a medium is decomposed
or written as a product of three 4 4 matrices [33],
M = M

M
R
M
D
(4.13)
where the depolarizer matrix M

denotes the depolarization eects both linear and circular of

the medium/sample, retardance matrix M
R
takes care of linear and circular (or optical rotation)
retardance eects and M
D
called the diattenuation matrix includes the diattenuation eects.
For optically clear media, the validity of this method was rst given by Lu and Chipman
[33]. Some basic polarization properties of the medium/sample, namely, diattenuation (d)
(dierential attenuation of orthogonal polarizations, both linear and circular), depolarization
coecients (, linear and circular), linear retardance () (dierence in phase between the two
orthogonal linear polarizations), and circular retardance () (dierence in phase between right
and left circularly polarized light) are then derived from these decomposed matrices [4] as
described in the following section.
24
4.2.1 Mathematical Formulation
The diattenuation matrix M
D
is dened as [33, 4],
M
D
=
_
1

d
T

d m
D
_
(4.14)
where m
D
is a 3 3 sub-matrix with the standard form,
m
D
=
_
(a d
2
)I + (1
_
1 d
2
)

d
T
here, I is a 3 3 identity matrix,

d is the diattenuation vector with

d its unit vector dened as,

d =
1
M
11
_
M
12
M
13
M
14

T
and

d =

d
|

d|
The magnitude of the diattenuation vector is given by,
|

d| =
1
M
11
_
M
2
12
+M
2
13
+M
2
14
The coecients M
12
and M
13
represents the linear diattenuation along horizontal (vertical) and
+45 (45) linear polarizations respectively and M
14
represents circular diattenuation. Now,
from (4.13) we have,
M

M
R
= MM
1
D
= M

(4.15)
The matrices M
R
, M

and M

have the following form,

M

=
_
1

0
T
P

_
, M
R
=
_
1

0
T

0 m
R
_
and M

=
_
1

0
T
P

_
(4.16)
where,
P

P m

d
1 d
2
and polarization vector,

P =
1
M
11
_
M
21
M
31
M
41

T
and m

is a 3 3 submatrix of M

, which can be written as,

m

= m

m
R
(4.17)
The depolarization can be calculated from the M

matrix as [33, 4],

=
1
3
|Tr (M

) 1| (4.18)
And, now from (4.17) we have,
m
R
= m
1

From (4.16) retardance matrix M

R
can be calculated and the value of total retardance is given
by the following,
R = cos
1
_
Tr(M
R
)
2
1
_
(4.19)
The values for optical rotation and linear retardance can also be determined from the matrix
M
R
as follows,
= cos
1
_
_
[(M
R
)
22
+ (M
R
)
33
]
2
+ [(M
R
)
32
(M
R
)
23
]
2
1
_
(4.20)
25
= tan
1
_
(M
R
)
32
(M
R
)
23
(M
R
)
22
+ (M
R
)
33
_
(4.21)
Due to the non-commuting nature of matrix multiplication, six dierent combinations for de-
composition of the Mueller matrix are possible. It has been shown that among these six decom-
position permutations, the one given by (4.13) or its reverse order (M = M
D
M
R
M

) always
produces physically realizable matrices [34].
26
Chapter 5
Results and Discussion
Some of the important results including those of eigenvalue calibration method and Mueller
matrix measurements are shown in the following sections.
5.1 Calibration Results
As mentioned earlier in section 4.1 that the optical elements comprising the polarization state
generator and analyzer do not behave ideally and also depend on the wavelength of light. To
incorporate this behaviour of polarizers and quarter waveplates the setup was calibrated using
the Eigenvalue calibration method. From a few extra measurements using this calibration
Figure 5.1: Variation of individual elements of Polarization State Generator Matrix (W) as a
function of wavelength ().
procedure the actual PSA and PSG matrices could be determined for the entire spectral range
( = 500 700 nm). Fig 5.1 shows the variation of individual elements of the polarization
state generator (or W matrix) with wavelength. Each column of this matrix represents a Stokes
vector corresponding to the optimized orientation angles of the quarter waveplate Q
1
which are
27
35

, 70

, 105

and 140

. For example rst column represents the normalized Stokes vector as

constructed in subsection 3.1.1 for
1
= 35

and so on.
In Fig. 5.2 individual elements of polarization state analyzer (A) matrix are shown as a
function of wavelength () from 500 700 nm. Here as constructed in subsection 3.1.2 each
row represent the top row of the combined Mueller matrix of the optical elements forming PSA.
Please note that unlike PSG rows or columns of PSA can not be called the Stokes vectors
directly. Rows when multiplied by the incident Stokes vector on the PSA setup gives the total
intensity i.e. rst element of the output Stokes vector.
Figure 5.2: Variation of individual elements of Polarization State Analyzer Matrix (A) as a
function of wavelength ().
Figure 5.3: Condition number for polarization state generator matrix (W) and polarization
state analyzer matrix (A) calculated for the spectral region ( = 500 700 nm).
Condition number dened by equation 3.9 is plotted in Fig. 5.3 for both polarization state
generator and analyzer matrices as a function of wavelength ( = 500 700 nm). It should be
28
noted that the value of condition number for both PSA and PSG over the entire spectral range
is strictly positive (greater than 0.25). This ensures that the chosen PSA and PSG matrices
for the entire spectral range would yield physically realizable Mueller matrices for the chosen
sample.
Figure 5.4: An estimate of the error in determination of the PSG and PSA matrices for the
same spectral region.
Fig. 5.4 shows an estimate of the error in determination of the PSG and PSA matrices using
the Eigenvalue calibration method which may have incurred due to a possible misalignment of
various reference samples. As stated earlier in subsection 4.1.1 a small value of the ratio of
the smallest to the largest eigenvalue of the matrix K
1616
corresponds to the case when the
applied (assumed for calculation) Mueller matrices of the reference samples are exactly the
Mueller matrices of the used reference samples. The observed value of this ratio for the entire
spectral range is plotted in Fig. 5.4 and is of the order of 10
3
. It is very well known that the
Figure 5.5: Variation of the individual elements of Mueller matrix for blank (no sample) over
the spectral region ( = 500 700 nm). Ideally Mueller matrix for blank should be identity.
29
Mueller matrix for a nonpolarizing element is a 4 4 identity matrix. So for blank, where the
sample is absent the Mueller matrix should ideally be an identity. Fig. 5.5 shows individual
elements of the Mueller matrix for blank obtained using the proposed strategy for the spectral
range 500 700 nm. Diagonal elements are close to unity and rest are close to zero.
Figure 5.6: Null (zero) elements of the Mueller matrix for a quarter waveplate, fast axis oriented
at an angle of 23

for the spectral range = 500 700 nm. Clearly the elemental error in the
measure Mueller matrices is of the order of 0.01.
One of the best ways to see how accurate these measurements are in determining the Mueller
matrices for various optical elements is to plot the null (or zero) elements for that particular
element. Fig. 5.6 shows the null elements of the Mueller matrix for a quarter wave retarder,
fast axis oriented at an angle of 23

from the horizontal of polarizer P

1
over the spectral range.
From Table 2.1 it can be seen that M
12
, M
13
, M
14
, M
21
, M
31
and M
41
are the null elements
for all retarders in general and are shown.
30
5.2 Polar Decomposition Results
Figure 5.7: Polar decomposition derived polarization parameters namely depolarization (),
diattenuation (d) and retardance (R) for blank Mueller matrix over the spectral region ( =
500 700 nm). Expected values of all three parameters for blank was zero.
The measured Mueller matrices for dierent samples were decomposed using Polar decom-
position method described in section 4.2 to get the basic polarization parameters namely depo-
larization , diattenuation d, and retardance R along with their linear and circular components.
Fig. 5.7 shows the values of these parameters for the blank Mueller matrix (Fig. 5.5). Ideally
for blank all these parameters should be zero. Polar decomposition derived diattenuation for
Figure 5.8: Polar decomposition derived diattenuation (d) for a wide-band Glan-Thompson
linear polarizer with polarization axis oriented at an angle of 28

over the spectral region

( = 500 700 nm). Expected value of diattenuation (d) was one.
a wide-band Glan Thompson linear polarizer with polarization axis aligned at an angle of 28

with respect to horizontal of polarizer P

1
in the spectral range = 500 700 nm is shown
in Fig. 5.8. Since an ideal linear polarizer acts like a perfect diattenuator its diattenuation is
31
expected to be close to unity. Fig. 5.9 shows polar decomposition derived linear retardance ()
Figure 5.9: Polar decomposition derived linear retardance () for a 632.8 nm quarter waveplate
with fast-axis oriented at an angle of 23

over the spectral region ( = 500700 nm). Expected

value of linear retardance was /2 or 1.57 radians at = 632.8 nm.
for a single wavelength quarter wave retarder with fast axis oriented at an angle of 23

with
respect to horizontal of polarizer P
1
in the spectral range = 500 700 nm. Since this is a 633
nm quarter waveplate we would expect that at = 633 nm the value of the linear retardance
should be close to /2 radians. The observed value at = 632.8 nm is 1.54 radians. Also the
need for calibration specially in spectral measurements is quite clear from this gure.
32
Chapter 6
Applications towards Tissue
Characterization
6.1 Introduction
Several studies conducted in the past decade have established the potential of laser induced
uorescence technique for diagnosis of cancer [12]. However, the use of polarized uorescence
spectroscopy for cancer diagnosis has only been explored recently [35]. These studies demon-
strated that polarized uorescence spectroscopic measurements have important advantages over
unpolarized uorescence measurement for cancer diagnosis [36, 35]. For example, a complica-
tion often encountered in using static autouorescence spectra from tissue for cancer diagnosis
is the large site to site variability in both intensity and line-shape of the uorescence spec-
tra of sites belonging to the same class (normal or cancerous). Moreover, for epithelial tissue
the contrast in autouorescence from cancerous and non-cancerous sites is known to strongly
depend on the dierences in depth distribution of endogenous uorophores in the supercial
epithelial and the underlying connective tissue layer. Studies have demonstrated that that the
use of polarized uorescence instead of conventional unpolarized uorescence can address both
these issues. It was observed that the eect of wavelength dependent absorption in tissue (for
example by blood) is reduced in polarized uorescence spectra thereby leading to reduced site-
to-site variability in intensity and line shape as compared to the unpolarized uorescence. This
follows because the polarized fraction of the total uorescence comes only from a few transport
scattering lengths and therefore bears minimal signature of absorption and scattering properties
of tissue. For the same reason, uorescence emitted from deeper layers of tissue is expected
to get more depolarized due to multiple scattering as compared to that emitted from super-
cial layers. Measurement of uorescence polarized at varying angles with respect to excitation
linear polarization was therefore used to accomplish depth resolved uorescence measurements
in tissue. As compared to the polarimetric technique used in these studies, measurement of
Mueller matrix of uorescence emitted from tissue would allow one to obtain more complete
information on polarization properties of uorescence. This therefore might turn out to be an
ecient approach to fully exploit the advantages of polarized uorescence measurements and
design the optimal polarization scheme for quantitative tissue diagnosis.
6.2 Experimental Setup
A schematic of the experimental setup for in-elastic (uorescence) scattering with simultane-
ous imaging and spectroscipic Mueller matrix measurements designed especially for biomedical
applications is as shown in Fig. 6.1. The three light sources, 405 nm & 473 nm lasers for ex-
citing the uorophores in tissues and other samples and a Xenon lamp required for Eigenvalue
33
Figure 6.1: Schematic of the experimental setup for in-elastic (uorescence) scattering with
simultaneous imaging and spectroscopic Mueller matrix measurements. Key: L: Lens, A:
Aperture, BS: Beam splitter, NDF: Neutral density lter, GT: Wide-band Glan Thompson
linear polarizer, QWP: Quarter waveplate, MO: Mounting optics, F: Filter, LCV F: Liquid
crystal variable lter.
calibration of the setup. The laser soucres can be changed according to the requirements of the
experiment. A 450 nm lter F is used with 405 nm laser after the collecting lens L
4
to cut
o the incident 405 nm radiations reected from the tissue or glass slide surface and only the
uorescence signal was recorded using an Andor CCD spectrograph. The PSG and PSA have
similar arrangement as was for the elastic scattering Mueller matrix measurement setup Fig.
3.2.
6.3 Preliminary Results
As mentioned earlier we are mainly interested in probing one of the endogenous uorophores in
tissues namely, Collagen which has been found to undergo structural and biochemical changes
during the progression of a disease like Cancer. But since the absoption and emission spectra
of Collagen overlaps to a huge extent with that of NADH it was not always possible distinguish
the cancerous tissues from healthy one by just looking at the uorescence spectra or yield. In
the uorescence spectra thus we expect to see two close emission peaks corresponding to these
uorophores.
In Fig. 6.2 rst element (M
11
) of the uorescence Mueller matrix for human cervical cancer
tissue biopsy slide (tissue thickness few m) over the entire spectral range ( = 450 800
nm) is shown. Clearly two broad convoluted emission peaks can be seen which correspond to
the emission spectrum of Collagen and NADH as is indicated in the gure.
Individual elements of the uorescence Mueller matrix (normalized with respect to M
11
)
34
Figure 6.2: First element of uorescence Mueller matrix M
11
(un-normalized) for human cervical
cancer tissue biopsy slide (thickness few m) over the spectral region ( = 450 800 nm).
A bandpass lter (450 900 nm) was used to cut o the incident wavelength 405 nm used
of exciting the tissue sample. The uorescence emission peaks of Collagen and NADH are
indicated.
for the same human cervical tissue biopsy slide are shown in Fig. 6.3 for the spectral region
( = 475 800 nm).
Fig. 6.4 shows the behaviour of diattenuation obtained from the measured uorescence
Mueller matrix for the human cervical cancer biopsy slides a few microns thick over the indicated
spectral range for two dierent grades (stages) of cancer. This gradation was done on the basis
of the histo-pathology report. Grade 1 indicates the onset of cancer while Grade 3 refers to
a more severe stage. It should be noted here that diattenuation peaks at a wavelength which
coincides with the peak of the emission spectra of Collagen indicated in Fig. 6.2. Collagen
due to its brous structure is expected to give higher diattenuation as compared to that due to
NADH with an isotropic structure.
It should be noted that the results shown in this section are based on just initial studies
and shows that such polarization based uorescence Mueller matrix polarimetry has potential
to be used for tissue characterization and diagnostic applications.
35
Figure 6.3: Individual elements of uorescence Mueller matrix for human cervical cancer tissue
biopsy slide (thickness few m) over the spectral region ( = 475 800 nm).
Figure 6.4: Polar decomposition derived diattenuation (d) for human cervical cancer tissue
biopsy slide (thickness few m) over the spectral region ( = 450 800 nm) for two dierent
grades (stages) of cancer determined from histo-pathology report of the sample.
36
Chapter 7
Applications towards
Nanoplasmonics
7.1 Introduction
Studies on optical properties of noble metal nanoparticles and nanostructures are of considerable
current interest both from the point of fundamental understanding and potential applications
[13, 37, 38]. These attribute to their unique optical properties which are governed by the col-
lective oscillations of the free (conduction) electrons, the so-called surface plasmon polaritons,
in resonance with the incident electromagnetic (EM) eld, known as surface plasmon resonance
[13]. The surface plasmon can either be propagating, for instance at planar metal-dielectric in-
terfaces, or localized as in the case of metal nanoparticles. In both cases, this leads to strongly
enhanced and highly localized electromagnetic elds. The surface plasmon resonance in metal
nanoparticles and nanostructures are being pursued for numerous practical applications in var-
ious branches of science and technology. Ultra-high sensitive chemical and biomedical sensing,
bio-molecular manipulation, labeling, detection, contrast enhancement in biomedical imaging,
surface enhanced spectroscopy (Raman and uorescence), development of new generation opti-
cal devices including plasmonic wave guiding nano-devices, optical information processing and
data storage, are just a smattering of its diversied uses [37, 39, 40, 41, 42]. In addition to the
potential applications, basic studies on various optical properties of the metal nanoparticles are
also important in context to fundamental understanding of light-matter interaction.
Although extinction, absorption and scattering are still the primary optical properties of in-
terest, various other approaches are also brought to bear on these metal nanoparticles, including
Surface Enhanced Raman Scattering (SERS), a variety of non-linear scattering measurements
(hyper Rayleigh, hyper Raman and second harmonic generation etc.) and time resolved mea-
surements [39, 40, 43, 44, 45]. In context to the investigation and applications of the above-
mentioned optical properties, synthesis and characterization of metal nanoparticles having dif-
ferent controllable size and shapes, have drawn considerable attention [46, 47]. This follows
because control of the size and shapes of these nanoparticles facilitates tuning of the plasmon
resonance bands to desirable wavelengths for specic applications [46]. Moreover, such control
over size and shapes can also enhance and optimize other potentially applicable optical eects
such as the local eld enhancement, giant non-linear responses, wave guiding properties etc. [47].
The measurement on the resulting optical properties of the nanoparticles (or nano-structures)
are conventionally done using a variety of experimental tools, Rayleigh scattering measurements
in dark eld microscope, confocal microscopic imaging (and spectroscopy), near eld scanning
optical microscopy (NSOM), are to name a few [48, 49]. These techniques have been used
to conduct both spectroscopic and imaging studies on nano-structures, single nanoparticles to
ensemble of particles. Analogously, the EM interaction of light with such nanoparticles and
structures have been modeled using various numerical methods, such as the discrete dipole ap-
37
proximation (DDA), the T-matrix method, nite dierence time domain (FDTD) simulations,
nite element calculations, the multiple multipole method etc. [50, 51].
The polarization properties of light play an important role in the interaction of light with
such non-spherical metal nanoparticles [52]. Thus, knowledge on the polarization properties of
the incident and scattered light and their spectral (wavelength dependent) characteristics are
crucial for both fundamental understanding of the interactions and for optimizing experimental
parameters for many practical applications. Indeed, recent experimental studies have suggested
that recording the changes in the polarization emission pattern (spectral and angular) are useful
for instance, in in-situ monitoring and controlling of size and shape of nanoparticles during
synthesis, improving schemes for plasmonic sensing, single molecule detection and importantly
for enhancing contrast in biomedical imaging [47, 52, 53, 54].
As noted previously, specially engineered non-spherical metal nanoparticles are actively be-
ing pursued as contrast agents in in-vitro and in-vivo biomedical imaging (diagnosis and therapy)
employing optical imaging techniques such as optical coherence tomography (OCT), photo-
acoustic tomography, non-linear microscopy (two photon and second harmonic generation) and
dark-eld microscopy etc. [55, 56]. A major diculty encountered in such nanoparticle-based
biomedical imaging is the fact that the strong scattering from the biological (tissue or cell) dielec-
tric structures often swamps the scattering from the nanoparticles, thus limiting detectability of
nanoparticles in such media. Polarization control may play an important role in this regard for
isolating scattering of plasmonic nanoparticles from the background Rayleigh / Mie scattering
of biological dielectric structures and thereby enhancing contrast in nanoparticle-based biomed-
ical imaging. In previous studies exploring this possibility, the polarization information has
usually been measured or modelled in terms of the conventionally dened degree of polarization
of light (or polarization anisotropy) [52, 53, 54]. The polarization information is obtained either
by performing measurements of co-polarized and crossed-polarized light intensity with respect
to a given input polarization state of incident light, or by recording selected Stokes vector ele-
ments (4 1 intensity vector describing the polarization state of light [13, 21]. Note however,
that for scattering medium (or particles) exhibiting simultaneous several polarization eects
(as should be the case for complex nano-bio composites where the most common polarimetry
events are depolarization, retardance and diattenuation, arising from both the metal nanopar-
ticles and the biological background; these are dened afterwards), the constituent scattering
and the polarization eects contribute in a complex interrelated way to the measured degree of
polarization or the selected Stokes vector elements of light [4, 5, 8]. These therefore represent
several lumped eects. Scattering from even optically inactive scatterers can exhibit complex
scattering-induced diattenuation and retardance eects, in addition to depolarization [5, 8]. Ex-
traction, quantication and unique interpretation of the individual, intrinsic polarimetry eects
of the non-spherical metal nanoparticles (or nano-structures) are thus expected to provide bet-
ter insight into the polarizing interaction of light with such nanoparticles, which in turn can be
exploited for contrast enhancement in nanoparticle-based biomedical imaging. Polar decompo-
sition of Mueller matrix (a 44 matrix that describes the transfer function of any medium in its
interaction with polarized light, and contains complete information about all the polarization
properties of a medium [13, 21] is one such approach that facilitates extraction and quanti-
cation of the individual intrinsic polarimetry characteristics from any complex system [33, 5].
To the best of our knowledge, use of such inverse polarimetry analysis methods on scattering
Mueller matrices from plasmon resonant metal nanoparticles, have not been investigated before.
We have thus theoretically investigated possibility (and plausible advantages) of such quanti-
tative plasmon polarimetry by employing polar decomposition method on scattering Mueller
matrices from non-spherical (as representative of non-sphericity, we have chosen the spheroidal
shape) metal (silver) nanoparticles. The scattering Mueller matrices for the spheroidal silver
nanoparticles in their surface plasmon resonance bands were generated using T-matrix method
for light scattering [14, 57] and these were subjected to the polar decomposition approach for
38
quantitative polarimetry analysis. The analysis indeed revealed interesting spectral (wavelength
dependent) and angular behaviour of the constituent polarimetry characteristics of the metal
nanoparticles, which were distinctly dierent from similar dielectric particles. The details of
these results are presented in the following sections and their implications for contrast enhance-
ment in nanoparticle-based biomedical imaging are discussed.
7.2 Theory
Mie theory provides the exact solution of scattering of electromagnetic plane wave by a spherical
scatterer [13]. In the framework of Mie theory, the Stokes vector of the incident (S
i
) and the
scattered (S
o
) light can be related through the so-called scattering matrix (M()) as,
S
o
= M()S
i
(7.1)
where is the scattering angle, the Stokes vectors (S
i
, S
o
) and M() are dened in the scattering
plane (plane containing the incident and the scattered light). For spherically symmetric particle,
the scattering matrix has a very simple block diagonal structure with only four independent
elements [13, 14],
M() =
_

_
M
11
M
12
0 0
M
12
M
11
0 0
0 0 M
33
M
34
0 0 M
34
M
33
_

_
(7.2)
These elements for known spherical scatterers (with known radius r, and refractive index n
s
)
can be computed using Mie theory embedded inside a surrounding medium (refractive index
n
m
) [13].
For non-spherical scatterers having arbitrary shapes, the form of scattering Mueller matrix
M() is however, far more complex, essentially having non-zero values for all the matrix el-
ements [13, 57, 14]. As noted previously, there do exist several methods for computing light
scattering from such non-spherical particles [14]. Among these, the T-matrix approach is one of
the most powerful and widely used tools [57, 58, 59]. This approach, based on directly solving
Maxwells equations, provides accurate expressions of the scattering parameters for both single
and composite non-spherical particles. Although the method is potentially applicable to any
particle shapes, most practical implementations of this technique pertain to particles having
rotationally symmetric shapes [57, 58]. Thus T-matrix code developed by Mishchenko et al.
[58] were used to compute the scattering Mueller matrices M() for spheroidal nanoparticles
(both preferentially and randomly oriented) investigated in this study. Note that for any axi-
ally symmetric non-spherical particle, the co-ordinates of the particle reference frame and the
laboratory reference frame may not coincide in general. However, for conceptual and practical
reasons (discussed later), the spheroids were preferentially oriented such that the particle refer-
ence frame coincides with the laboratory reference frame. In this case, the computed scattering
matrix (for any scattering angle ) relates the Stokes vector of scattered light to that of the
incident light dened with respect to the scattering plane (as in (7.1)). For computing the
scattering matrix for randomly oriented spheroidal particles, orientation averaging was carried
out as described in reference [58].
The scattering matrices for both randomly and preferentially oriented spheroidal nanoparti-
cles were generated for varying sizes and shapes. The sizes and the shapes of the spheroids were
specied by the radius of equal surface area sphere (r) and aspect ratio () respectively [57, 58].
Note that values of > 1 and < 1 correspond to oblate and prolate spheroids respectively.
Computation of the scattering matrices [M(, ), is the wavelength] were performed for sliver
nanoparticles in their surface plasmon resonance spectral region ( = 325 525 nm). The
optical properties of silver (real and imaginary part of refractive index; n
s
and k
s
) are avail-
able in literature [60]. The refractive index of the surrounding medium was kept n
m
= 1.33.
39
The scattering matrices over the same spectral region were generated for spheroidal dielectric
nanoparticles also, for varying sizes and shapes. The refractive indices of the dielectric particles
were assumed to be constant over the spectral region (n
s
= 1.59 and k
s
= 0).
7.3 Results and Discussion
The scattering Mueller matrix computed for randomly oriented spheroidal nanoparticles using
T-matrix method (as discussed in section 7.2) for both silver nanoparticles, in their plasmon
resonance spectral region ( = 325 525 nm) and for dielectric particles having identical size
and shape were decomposed using Polar decomposition method described in section 4.2 to yield
individual polarimetry characteristics. The matrices were computed for varying radius (r) and
aspect ratios () of the spheroidal nanoparticles at varying scattering angles ( = 0

180

).
Table 7.1 gives an example of the decomposition of the scattering matrix (M) for randomly
oriented spheroidal silver nanoparticles having radius (of equal surface area sphere) of r = 20 nm
and aspect ratio of = 1.5 ( > 1, oblate spheroid) to get the individual polarization parameters;
diattenuation (d), net depolarization coecient () and linear retardance () are listed in the
bottom part of the table. The wavelength was chosen to be 400 nm and the scattering angle was
= 45

. The reason for choosing this wavelength is discussed subsequently. Individual values for
the linear and circular depolarization coecients (
L
and
C
) are also listed. For comparision
the decomposition-derived polarization parameters for spheroidal dielectric nanoparticles having
identical size and shape are also included in the table. As is apparent from the table, the
scattering matrix for the silver nanoparticles resembles a diattenuating depolarizer Mueller
matrix [33]. A perfect depolarizing Mueller matrix has diagonal form, with its diagonal elements
representing linear and circular depolarization. Additionally, the non-zero value for the M
12
element indicates presence of horizontal (vertical) diattenuation eect. Most importantly, for
this scattering angle ( = 45

), the net depolarization coecient for the silver nanoparticles

is signicantly higher than the corresponding value for the similar dielectric particles (for which
depolarization is negligible). Similar trend was observed for all other scattering angles (although
at around = 90

, the value of for the dielectric particles was also considerably high), some
of which are presented subsequently. It can also be noted that for the metal nanoparticles,
the circular depolarization coecient is higher compared to the linear depolarization coecient
(
C
>
L
). This is in agreement with the fact that for Rayleigh scatterers (having sizes much
smaller compared to the wavelength, r << ), depolarization of incident circular polarization is
stronger compared to the depolarization of incident linear polarization [61, 62]. This dierence
in relative rate of depolarization of linearly and circularly polarized light can be attributed to
the dierent mechanism of depolarization of the two. While randomization of the incident eld
vectors direction (here as a consequence of scattering from randomly oriented non-spherical
particles) is solely responsible for the depolarization of incident linear polarization state, the
depolarization of circular polarization state is additionally inuenced by the randomization of
the helicity (handed-ness) [61, 62]. Since for Rayleigh scatterers, the latter eect is predominant,
depolarization of circularly polarized light is more pronounced for such scatterers [61, 62].
In Fig. 7.1, the variation of the decomposition-derived net depolarization coecient ()
as a function wavelength ( = 325 525 nm) for the randomly oriented silver nanoparticles
with radius r = 20 nm is shown for varying aspect ratios of the oblate spheroids ( = 1 2)
and the scattering angle was once again chosen to be = 45

. As expected, due to spherical

symmetry, there is no depolarization ( 0) for shperical particles and the value of increases
with increasing aspect ratio of the spheroidal nanoparticles. Interestingly, the depolarization
characteristics show distinct spectral features with a peak around 380 410 nm. The peak
of the depolarization curve is also observed to show slight shift towards shorter wavelengths with
increasing . Although the magnitude of the decomposition-derived depolarization coecients
were dierent at other scattering angles, the observed trends were qualitatively similar to that
40
Table 7.1: Top: The T-matrix computed scattering matrix (M) for randomly oriented spheroidal
silver nanoparticles having radius of r = 20 nm and aspect ratio of = 1.5. The wavelength
was 400 nm and the scattering angle was = 45

. The constituent basis matrices obtained

via decomposition (section 4.2) are shown in the 2nd row. Bottom: The values for the polar-
ization parameters (diattenuation (d), net depolarization coecient () and linear retardance
()) extracted from the decomposed matrices. Individual values for the linear and circular de-
polarization coecients (
L
and
C
) are also listed. The decomposition-derived polarization
parameters of randomly oriented spheroidal dielectric nanoparticles having identical size and
shape (3rd column).

1.00 0.16 0 0
0.16 0.48 0 0
0 0 0.45 0.01
0 0 0.01 0.08

1.00 0 0 0
0.08 0.47 0 0
0 0 0.46 0
0 0 0 0.09

1.00 0 0 0
0 1.00 0 0
0 0 1.00 0.02
0 0 0.02 1.00

M
R

1.00 0.16 0 0
0.16 1.0 0 0
0 0 0.99 0
0 0 0 0.99

M
D
Parameters
Estimated values for the polarization parameters
Spheroidal metal Spheroidal dielectric
nanoparticle nanoparticle
d 0.161 0.3315
0.662 0.01

L
0.536 0.01

C
0.914 0.01
(rad.) 0.021 0
for = 45

.
In order to understand the origin of the observed spectral characteristics of the depolariza-
tion coecients, in Fig. 7.2, we show the computed scattering eciency (Q
sca
) as a function
of wavelength for the spheroidal silver nanoparticles of varying aspect ratios ( = 1.25 2.0)
and having a xed radius of 20 nm. The observed two distinct peaks in the scattering spec-
tra are known to be due to the plasmon resonances corresponding to the longitudinal and the
transverse dipolar polarizabilities [37, 46]. The weaker peak at around 365 nm and the stronger
peak at around 440 nm (e.g., for = 1.5) can be identied due to the surface plasmon reso-
nance along the short axis (transverse) and the long axis (longitudinal) of the oblate spheroids
respectively. The relative intensities of the two bands and their spectral positions are controlled
by the relative strength of the two orthogonal dipolar plasmon polarizabilities. Since these are
determined by the aspect ratio, with increasing , the two resonance peaks start moving apart
(the transverse and the longitudinal one gets blue and red shifted respectively) [37, 13, 46]. The
two peaks however, coalesce to a single peak (at 410 nm) for a sphere. Comparing the spec-
tral characteristics of the depolarization coecient (Fig. 7.1) to that of the plasmon resonance
bands (Fig. 7.2), it is evident that the magnitude of peaks around the overlap spectral region
of the two dipolar plasmon bands. In what follows, the reason for such intriguing depolarization
characteristics is investigated by performing polar scattering matrix decomposition analysis on
preferentially oriented spheroidal nanoparticles.
In Table 7.2, the results of the polar decomposition of the scattering matrix for preferen-
tially oriented spheroidal silver nanoparticles having r = 20 nm and = 1.5 are shown. The
wavelength was chosen to be 400 nm and the scattering angle was = 45

. Several interest-
ing features can be noted from the elements of the scattering matrix M. Even at the forward
41
Figure 7.1: The variation of the decomposition-derived net depolarization coecient () as a
function wavelength ( = 325 525 nm) for randomly oriented silver nanoparticles with radius
r = 20 nm. The results are shown for varying aspect ratios of the oblate spheroids ( = 1 2)
and the scattering angle was chosen to be = 45

.
scattering angle ( = 45

), the matrix elements M

33
and M
44
show negative values which corre-
spond to phase reversal. Moreover, the matrix elements M
34
and M
43
show considerably high
values corresponding to strong retardation eects [13, 62, 63]. It is well known that for dielectric
Rayleigh particles, the phase reversal (the so-called ipping of helicity of circularly polarized
light) occurs beyond a scattering angle of > 90

[13, 63, 61, 62]. Further, for such Rayleigh

particles, the elements M
34
and M
43
are always zero [63, 61, 62]. However, for these metal
nanoparticles, strong phase retardation eects are evident in the forward scattering angles as
well. Indeed the decomposition analysis yields a value of linear retardance of = 1.99 radians
for this scatterer ( > /2 radian corresponds to phase reversal or helicity ipping). As is ap-
parent from the decomposition-derived polarization parameters listed in the table (bottom part
of Table 7.2), no such scattering-induced retardation eects ( 0) are observed for similar
dielectric particles or for spherical silver nanoparticles. Analogous to the diattenuation eect,
the scattering-induced linear retardance arises due to the dierence in phase between the scat-
tered light polarized parallel and perpendicular to the scattering plane [5, 8]. This eect may
occur (even in the forward scattering angle) for larger sized Mie scatterers (sizes comparable
or larger than wavelength) due to the contribution of higher order multi-poles in the scattering
[37, 13, 46, 47]. However, for these metal nanoparticles, the contribution of the higher order
multi-poles (including the quadrupole) is not expected to be signicant. This can also be con-
rmed from the scattering spectra shown in Fig. 7.2; the contribution of quadrupole plasmon
polarizability is usually associated with appearance of additional resonance peak at shorter
wavelengths [46, 47], which is clearly absent here. The additional scattering-induced linear
retardance thus appears to originate due to the inherent phase retardation between the two
orthogonal dipolar plasmon polarizabilities (the longitudinal and the transverse dipolar plasmon
polarizabilities oscillating with a phase dierence between them). In addition to the observed
linear retardance, the decomposition process also yields signicant values for scattering-induced
diattenuation (d) for all the nanoparticles (spheroidal metal and dielectric nanoparticles and
spherical metal nanoparticles). In contrast to the results observed for the randomly oriented
spheroidal nanoparticles, for these preferentially oriented nanoparticles, the magnitude of d is
however, higher for the metal nanoparticles compared to its dielectric counter parts. Further, as
42
Figure 7.2: The T-matrix computed scattering eciency (Q
sca
) as a function of wavelength for
the spheroidal silver nanoparticles of varying aspect ratios ( = 1.25 2.0) and having a xed
radius of 20 nm.
expected, none of these preferentially oriented spheroidal nanoparticles (metal and the dielec-
tric nanoparticles) and the spherical metal nanoparticles are observed to exhibit depolarization
eects ( = 0).
Figure 7.3: The spectral variation of the decomposition-derived linear retardance () for pref-
erentially oriented (see text for details on orientation) spheroidal silver nanoparticles with radius
r = 20 nm and varying aspect ratio = 1.0 2.0. The scattering angle was = 45

.
The decomposition analysis was performed at various wavelengths covering the surface plas-
mon band ( = 325 525 nm) of the preferentially oriented spheroidal nanoparticles. The
spectral variation of the decomposition-derived () for spheroidal silver nanoparticles with
r = 20 nm and varying = 1.0 2.0 (for = 45

), are shown in Fig. 7.3. The magnitude

of () is observed to increase with increasing aspect ratio of the spheroids. Importantly, the
spectral variations of () for these preferentially oriented spheroidal metal nanoparticles are
observed to be qualitatively similar to the corresponding variations of the depolarization coef-
cient () for the randomly oriented nanoparticles (Fig. 7.1). As for the case of (), the
magnitude of peaks around the overlap spectral region of the two dipolar plasmon bands. The
43
Table 7.2: Top: the T-matrix computed scattering matrix (M) for preferentially oriented
spheroidal silver nanoparticle having radius of r = 20 nm and aspect ratio of = 1.5. The
wavelength was 400 nm and the scattering angle = 45

. The constituent basis matrices

obtained via polar decomposition are shown in the 2nd row. Bottom: the values for the polar-
ization parameters (d, and ) extracted from the decomposed matrices (2nd column). The
decomposition-derived polarization parameters of preferentially oriented spheroidal dielectric
nanoparticle having identical size and shape (3rd column) and spherical silver nanoparticle
having radius r = 20 nm (4th column).

1.00 0.43 0 0
0.43 1.00 0 0
0 0 0.37 0.82
0 0 0.82 0.37

1.00 0 0 0
0 1.00 0 0
0 0 1.00 0
0 0 0 1.00

1.00 0 0 0
0 1.00 0 0
0 0 0.42 0.91
0 0 0.82 0.42

M
R

1.00 0.43 0 0
0.43 1.00 0 0
0 0 0.90 0
0 0 0 0.90

M
D
Parameters
Estimated values for the polarization parameters
Spheroidal metal Spheroidal dielectric Spherical metal
nanoparticle nanoparticle nanoparticle
d 0.435 0.388 0.333
0 0 0
(rad.) 1.99 0 0.011
spectral variations of exhibit long tails spanning the entire longitudinal and the transverse
plasmon resonance bands (as was also observed for ()).
The above analysis performed on preferentially oriented spheroidal nanoparticles reveals
that the observed enhanced depolarization (and its intriguing spectral characteristics) for ran-
domly oriented spheroidal metal nanoparticles originates from the presence of strong linear
retardance eect in the individual oriented nanoparticles (due to the inherent phase dierences
between the longitudinal and the transverse plasmon polarizabilities). This follows because the
scattering Mueller matrix from randomly oriented particles can be thought of being due to the
averaging (over all possible orientation) of the individual Mueller matrices from preferentially
oriented particles. Since incoherent addition of pure retarder Mueller matrices (from preferen-
tially oriented nanoparticles) having random orientation of retardation axes leads to the Mueller
matrix corresponding to a pure depolarizer [4, 33], this manifests as strong depolarization ()
of light for randomly oriented spheroidal metal nanoparticles. The spectral characteristics of
() for the randomly oriented particles are thus determined by the corresponding spectral
characteristics of () for the preferentially oriented ones.
In order to investigate this intriguing polarization characteristics further, in Fig. 7.4, we
show the scattering angle () dependence of the decomposition-derived value of linear retardance
for preferentially oriented spheroidal silver nanoparticles with r = 20 nm and = 1.5. The
results are shown for three dierent wavelengths; 365 nm, 440 nm (corresponding to the peaks of
the transverse and the longitudinal plasmon resonances respectively) and 400 nm (corresponding
to the peak of () and ()). The corresponding variation of the similar dielectric particle
is shown by solid line in the gure ( = 400 nm). As discussed previously, the variation of
() for the dielectric particle resemble the usual behaviour for Rayleigh particle [63, 61, 62],
where one observes a phase reversal ( > /2 rad.) beyond a scattering angle of > 90

, and
the magnitude of (for any value of ) is either close to zero or . In contrast, the trend is
reversed for the metal nanoparticles at 400 nm, where is greater than /2 rad. (indicating
44
Figure 7.4: The scattering angle () dependence of the decomposition-derived value of linear
retardance for preferentially oriented spheroidal silver nanoparticle with r = 20 nm and
= 1.5. The results are shown for three dierent wavelengths: 365 nm, 440 nm (corresponding
to the peaks of the transverse and the longitudinal plasmon resonances respectively) and 400
nm (corresponding to the peak of () and ()). The corresponding variation of the similar
dielectric particle is shown by solid circle in the gure ( = 400 nm).
phase reversal) in the forward scattering angles ( < 90

) and no phase reversal is observed in

the backscattering ( < /2 rad. for > 90

). Moreover, there is appreciable retardance in the

entire angular region ( is signicantly dierent from zero or ). The corresponding variations
of () for 365 nm and 440 nm are dierent from that of 400 nm in that, here the phase reversal
is not observed in the forward scattering angles. Never-the-less at either of these wavelengths
appreciable value of linear retardance is apparent.
The results presented above demonstrate that the polarization behaviour of scattered light
from spheroidal metal nanoparticles in their surface plasmon resonance spectral region is sig-
nicantly dierent from similar dielectric nanoparticles. It might be useful to relate these
results to the experimentally observed enhanced depolarization of light from metal nanoparti-
cles [54, 53]. Indeed recent experimental studies have shown that the depolarization of light
from colloidal metal nanoparticles (silver and gold) in their surface plasmon resonance bands are
signicantly higher as compared to that observed from colloidal solutions of similar dielectric
particles [54, 53]. The combined T-matrix and polar matrix decomposition analysis presented
above reveals that the presence of two dipolar plasmon resonances having a dierence in phase
between them manifests as additional linear retardance for preferentially oriented individual
spheroidal metal nanoparticles and that for randomly oriented nanoparticles, orientation aver-
aging of such linear retardance lead to the observed strong depolarization eects in the latter
case. It is also pertinent to note here that the results of the combined T-matrix and polar
matrix decomposition analysis presented above are for oblate spheroids (aspect ratio > 1).
45
Chapter 8
Conclusions and Future directions
8.1 Conclusions
A highly sensitive and fully automated spectral Mueller matrix polarimeter for both elastic and
inelastic scattering (uorescence) has been developed. It is capable of recording Mueller matrices
with an elemental error of the order of 0.01 over the whole spectral range ( = 500 700 nm)
within a few minutes time. It uses two rotating wave retarders and two xed linear polarizers
to generate sixteen elliptically polarized states which are then recorded using a spectrometer.
It has been shown that these wave retarders and polarizers may or may not function ideally
for all wavelengths never-the-less their actual values can be calculated using the Eigenvalue
calibration (EVC) procedure proposed by E. Compain et. al. [26] for the entire spectral range.
The method of calculating the unknown 4 4 Mueller matrix for any sample in general from
these sixteen spectral measurements has been developed and discussed in detail in section 3.1.
The correctness of this method has also been veried by the checking for the desired results
of the estimated polarization parameters and Mueller matrics for the known standard optical
elements like blank, polarizer, quarter waveplate etc.
Similar strategy was applied for measurement of the complete spectral Mueller matrix for
inelastic scattering (uorescence basically) and had initially been used to characterize human
cervical cancer tissues on the basis of subtle morphological and physiological changes and shows
promising aspects. Since Mueller matrix stores all the polarization characteristics of the sample
such complete spectral Mueller matrix measurements strategies may have important biomedical
applications especially for cancer diagnosis or for detecting any abnormalities in tissues in
general.
This uorescence based spectral Mueller matrix measurement technique also showed promis-
ing aspects in the eld of material characterization (mainly for uorescent materials). The
uorescence Mueller matrices for some of the uorescent dyes like Coumarin 102 and Coumarin
152 were recorded with the aim to study their polarization characteristics and some interesting
results were obtained, though not reported in this thesis since the study could not be completed
due to the constraint of time.
Derivation, quantication and understanding of the intrinsic plasmon polarization charac-
teristics aided by the Mueller matrix decomposition method may have important implications
in metal nanoparticles-based biomedical imaging. The polarization characteristics of scattered
light from spheroidal metal (silver) nanoparticles in their surface plasmon resonance spectral
region were investigated using polar decomposition of scattering Mueller matrices. The de-
composition analysis on the scattering matrices (computed using T-matrix approach) from
preferentially oriented nanoparticles revealed the presence of strong linear retardance eects
in the surface plasmon spectral band of the spheroidal metal nanoparticles. Moreover, the
derived linear retardance () for these preferentially oriented spheroidal metal nanoparticles
showed distinct spectral characteristics, the magnitude of peaking around the spectral overlap
46
region of the transverse and the longitudinal dipolar plasmon resonance bands. Interestingly,
the helicity ipping of circularly polarized (or phase reversal) shows anomalous behavior for
the spheroidal metal nanoparticles at wavelengths corresponding to the overlap region of the
transverse and the longitudinal dipolar plasmon resonance bands. In contrast to usual Rayleigh
particles, phase reversal is exhibited in the forward scattering angles ( > /2 at < 90

),
whereas no phase reversal is observed in the backscattering ( < /2 radian for > 90

).
The observed linear retardance eects were attributed to the inherent dierences in phases,
of the two orthogonal (longitudinal and the transverse) dipolar plasmon polarizabilities of the
spheroidal metal nanoparticles. The analysis also revealed that when averaged over all possi-
ble orientations of the particles (for randomly oriented spheroids), addition of the retardance
matrices having random orientation of axes manifests as stronger depolarization () of light
in spheroidal metal nanoparticles as compared to their dielectric counterparts (as observed in
recent experimental studies [53, 54]). Consequently, the spectral variations of () for the
randomly oriented nanoparticles resemble that for the variation of () for the preferentially
oriented ones.
Since the spectral behaviour of the constituent polarimetry characteristics of the non-
spherical metal nanoparticles are distinctly dierent from dielectric particles, these can be
exploited to develop polarization-controlled novel schemes for enhancing contrast in plasmon
resonant nanoparticle-based biomedical imaging [55, 56].
8.2 Future Directions
As noted above that the spectral behaviour of the constituent polarimetry characteristics of
the non-spherical metal nanoparticles are distinctly dierent from dielectric particles and thus
can be exploited to develop novel schemes for contrast enhancement in biomedical imaging.
For example, co- and crossed circular polarization imaging scheme (with proper choice of wave-
length of light) can be adopted to discriminate (thus enhance contrast) plasmonic scattering
from the background Rayleigh/Mie scattering of biological (tissue or cell) dielectric structures
in single particle microscopic imaging. This follows because the scattered light from spheroidal
metal nanoparticles will have opposite helicity of circular polarization as compared to the
Rayleigh/Mie scattered light from background dielectric structures. Similarly, co- and crossed
linear polarization detection scheme can be used (exploiting the much stronger depolarization
eect and its unique spectral characteristics) to distinguish plasmonic scattering from back-
ground dielectric medium for imaging ensemble of particles [54]. One should however, note that
the nanoparticle-based biomedical imaging applications would additionally be confounded by
strong multiple scattering eects (specically in biological tissues, multiple scattering causes
extensive depolarization) and by other simultaneously occurring complex tissue polarimetry
events (these include linear birefringence due to anisotropic tissue structures and optical rota-
tion due to optically active (chiral) molecules and structures) [64]. Moreover, in applications
involving ensemble of nanoparticles, one would expect additional depolarization eects caused
by multiple scattering within the ensemble of nanoparticles also. With regard to the rst issue,
it is pertinent to note that the intrinsic polarization characteristics (linear retardance and de-
polarization) of the non-spherical (spheroidal, in this study) metal nanoparticles exhibit very
distinct spectral characteristics (which is known a-priori and can be controlled by varying the
aspect ratio of the spheroids) and is expected to be dierent from the spectral polarimetry ef-
fects of background biological (tissue) dielectric structures. This therefore oers the possibility
of exploiting multi-spectral polarimetric imaging (whereby polarimetric imaging is performed
at multiple selected wavelengths) for discriminating against background polarization character-
istics of biological tissues/cells. For example, polarization images (either full Mueller matrix
image or selected combination of linear and circular polarization state images) captured at
wavelength corresponding to the peak of the depolarization or linear retardance of the metal
47
nanoparticles and similar images captured at slightly dierent wavelength may be combined
to minimize background polarization eects from tissue dielectric structures. In general, full
Mueller matrix imaging with appropriate combination of wavelengths and the matrix elements
(either directly from the measured Mueller matrix or the constituent basis matrices obtained
via the decomposition analysis) or the derived polarization parameters, may thus facilitate a
robust approach for contrast enhancement in nanoparticle-based imaging. The eects of multi-
ple scattering on quantitative polarimetry characteristics of ensemble of spherical/non-spherical
metal nanoparticles also need to be studied.
In addition to biomedical diagnostics and imaging, the derived polarization parameters (and
their unique spectral characteristics) may also be exploited for monitoring and controlling of size
and shape of metal nanoparticles during synthesis. Moreover, such quantitative polarimetry may
also have useful applications in optimizing/enhancing the sensitivity of the metal nanoparticles
(or nanostructures)-based plasmonic sensors, as well as in other important areas related to
nano-plasmonics.
48
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53
Appendix A
Eigenvalue Calibration - MATLAB
Script
The Eigenvalue calibration was done for each wavelength (w) so as to get PSG (W) and PSA
(A) matrices at all wavelengths. bo and b are measurement vectors for blank and reference
samples respectively. Following is the matlab script that was used for implementing eigenvalue
calibration method. The credits for developing this script goes to Harshit Lakhotia, Jalpa Soni
and myself.
1 function[Evals, W, A]=programcalibration(w,b,bo)
2 Bo = reshape(bo(:,w,2),4,4);
3 B1 = reshape(b(1,:,w,2),4,4);
4 B2 = reshape(b(2,:,w,2),4,4);
5 B3 = reshape(b(3,:,w,2),4,4);
6 B4 = reshape(b(4,:,w,2),4,4);
7 C1 = (inv(Bo))*B1;
8 C2 = (inv(Bo))*B2;
9 C3 = (inv(Bo))*B3;
10 C4 = (inv(Bo))*B4;
11 lambda1=eig(C1);
12 lambda2=eig(C2);
13 lambda3=eig(C3);
14 lambda4=eig(C4);
15 taup = real(lambda2(1));
16 taur = (lambda3(3) + lambda3(4))/2;
17 r = (angle(lambda3(2)/lambda3(1)))/2;
18 if r>0
19 r = pi - r;
20 else
21 r = -r;
22 end
23 psih = pi/4;
24 M1 = (taup/2)*[1,0.56,0.83,0;
25 0.56,0.31,0.46,0;
26 0.83,0.46,0.69,0;
27 0,0,0,0];
28 M2 = (taup/2)*[1, -0.83, 0.56, 0;
29 -0.83, 0.69, -0.46, 0;
30 0.56, -0.46, 0.31, 0;
54
31 0, 0, 0, 0];
32 cq = cos(2*psih);
33 sq = sin(2*psih);
34 cd = cos(r);
35 sd = sin(r);
36 M3 = taur*[1,-0.69*cq,-0.72*cq,0;
37 -0.69*cq,(0.48+(0.52*cd*sq)),(0.50-(0.50*cd*sq)),-0.72*sd*sq;
38 -0.72*cq,(0.50-(0.50*cd*sq)),(0.52+(0.48*cd*sq)),0.69*sd*sq;
39 0,0.72*sd*sq,-0.69*sd*sq,cd*sq];
40 M4 = taur*[1,0.72*cq,-0.69*cq,0;
41 0.72*cq,(0.52+(0.48*cd*sq)),(-0.5+(0.5*cd*sq)),-0.69*sd*sq;
42 -0.69*cq,(-0.5+(0.5*cd*sq)),(0.48+(0.52*cd*sq)),-0.72*sd*sq;
43 0,0.69*sd*sq,0.72*sd*sq,cd*sq];
44 U1 = [1,0,0,0;0,0,0,0;0,0,0,0;0,0,0,0];
45 U2 = [0,1,0,0;0,0,0,0;0,0,0,0;0,0,0,0];
46 U3 = [0,0,1,0;0,0,0,0;0,0,0,0;0,0,0,0];
47 U4 = [0,0,0,1;0,0,0,0;0,0,0,0;0,0,0,0];
48 U5 = [0,0,0,0;1,0,0,0;0,0,0,0;0,0,0,0];
49 U6 = [0,0,0,0;0,1,0,0;0,0,0,0;0,0,0,0];
50 U7 = [0,0,0,0;0,0,1,0;0,0,0,0;0,0,0,0];
51 U8 = [0,0,0,0;0,0,0,1;0,0,0,0;0,0,0,0];
52 U9 = [0,0,0,0;0,0,0,0;1,0,0,0;0,0,0,0];
53 U10 = [0,0,0,0;0,0,0,0;0,1,0,0;0,0,0,0];
54 U11 = [0,0,0,0;0,0,0,0;0,0,1,0;0,0,0,0];
55 U12 = [0,0,0,0;0,0,0,0;0,0,0,1;0,0,0,0];
56 U13 = [0,0,0,0;0,0,0,0;0,0,0,0;1,0,0,0];
57 U14 = [0,0,0,0;0,0,0,0;0,0,0,0;0,1,0,0];
58 U15 = [0,0,0,0;0,0,0,0;0,0,0,0;0,0,1,0];
59 U16 = [0,0,0,0;0,0,0,0;0,0,0,0;0,0,0,1];
60 G1G1 = M1*U1 - U1*C1;
61 G1G2 = M1*U2 - U2*C1;
62 G1G3 = M1*U3 - U3*C1;
63 G1G4 = M1*U4 - U4*C1;
64 G1G5 = M1*U5 - U5*C1;
65 G1G6 = M1*U6 - U6*C1;
66 G1G7 = M1*U7 - U7*C1;
67 G1G8 = M1*U8 - U8*C1;
68 G1G9 = M1*U9 - U9*C1;
69 G1G10 = M1*U10 - U10*C1;
70 G1G11 = M1*U11 - U11*C1;
71 G1G12 = M1*U12 - U12*C1;
72 G1G13 = M1*U13 - U13*C1;
73 G1G14 = M1*U14 - U14*C1;
74 G1G15 = M1*U15 - U15*C1;
75 G1G16 = M1*U16 - U16*C1;
76 G2G1 = M2*U1 - U1*C2;
77 G2G2 = M2*U2 - U2*C2;
78 G2G3 = M2*U3 - U3*C2;
79 G2G4 = M2*U4 - U4*C2;
80 G2G5 = M2*U5 - U5*C2;
81 G2G6 = M2*U6 - U6*C2;
55
82 G2G7 = M2*U7 - U7*C2;
83 G2G8 = M2*U8 - U8*C2;
84 G2G9 = M2*U9 - U9*C2;
85 G2G10 = M2*U10 - U10*C2;
86 G2G11 = M2*U11 - U11*C2;
87 G2G12 = M2*U12 - U12*C2;
88 G2G13 = M2*U13 - U13*C2;
89 G2G14 = M2*U14 - U14*C2;
90 G2G15 = M2*U15 - U15*C2;
91 G2G16 = M2*U16 - U16*C2;
92 G3G1 = M3*U1 - U1*C3;
93 G3G2 = M3*U2 - U2*C3;
94 G3G3 = M3*U3 - U3*C3;
95 G3G4 = M3*U4 - U4*C3;
96 G3G5 = M3*U5 - U5*C3;
97 G3G6 = M3*U6 - U6*C3;
98 G3G7 = M3*U7 - U7*C3;
99 G3G8 = M3*U8 - U8*C3;
100 G3G9 = M3*U9 - U9*C3;
101 G3G10 = M3*U10 - U10*C3;
102 G3G11 = M3*U11 - U11*C3;
103 G3G12 = M3*U12 - U12*C3;
104 G3G13 = M3*U13 - U13*C3;
105 G3G14 = M3*U14 - U14*C3;
106 G3G15 = M3*U15 - U15*C3;
107 G3G16 = M3*U16 - U16*C3;
108 G4G1 = M4*U1 - U1*C4;
109 G4G2 = M4*U2 - U2*C4;
110 G4G3 = M4*U3 - U3*C4;
111 G4G4 = M4*U4 - U4*C4;
112 G4G5 = M4*U5 - U5*C4;
113 G4G6 = M4*U6 - U6*C4;
114 G4G7 = M4*U7 - U7*C4;
115 G4G8 = M4*U8 - U8*C4;
116 G4G9 = M4*U9 - U9*C4;
117 G4G10 = M4*U10 - U10*C4;
118 G4G11 = M4*U11 - U11*C4;
119 G4G12 = M4*U12 - U12*C4;
120 G4G13 = M4*U13 - U13*C4;
121 G4G14 = M4*U14 - U14*C4;
122 G4G15 = M4*U15 - U15*C4;
123 G4G16 = M4*U16 - U16*C4;
124 g1=reshape(G1G1,16,1);
125 g2=reshape(G1G2,16,1);
126 g3=reshape(G1G3,16,1);
127 g4=reshape(G1G4,16,1);
128 g5=reshape(G1G5,16,1);
129 g6=reshape(G1G6,16,1);
130 g7=reshape(G1G7,16,1);
131 g8=reshape(G1G8,16,1);
132 g9=reshape(G1G9,16,1);
56
133 g10=reshape(G1G10,16,1);
134 g11=reshape(G1G11,16,1);
135 g12=reshape(G1G12,16,1);
136 g13=reshape(G1G13,16,1);
137 g14=reshape(G1G14,16,1);
138 g15=reshape(G1G15,16,1);
139 g16=reshape(G1G16,16,1);
140 H1 = [g1,g2,g3,g4,g5,g6,g7,g8,g9,g10,g11,g12,g13,g14,g15,g16];
141 g1=reshape(G2G1,16,1);
142 g2=reshape(G2G2,16,1);
143 g3=reshape(G2G3,16,1);
144 g4=reshape(G2G4,16,1);
145 g5=reshape(G2G5,16,1);
146 g6=reshape(G2G6,16,1);
147 g7=reshape(G2G7,16,1);
148 g8=reshape(G2G8,16,1);
149 g9=reshape(G2G9,16,1);
150 g10=reshape(G2G10,16,1);
151 g11=reshape(G2G11,16,1);
152 g12=reshape(G2G12,16,1);
153 g13=reshape(G2G13,16,1);
154 g14=reshape(G2G14,16,1);
155 g15=reshape(G2G15,16,1);
156 g16=reshape(G2G16,16,1);
157 H2 = [g1,g2,g3,g4,g5,g6,g7,g8,g9,g10,g11,g12,g13,g14,g15,g16];
158 g1=reshape(G3G1,16,1);
159 g2=reshape(G3G2,16,1);
160 g3=reshape(G3G3,16,1);
161 g4=reshape(G3G4,16,1);
162 g5=reshape(G3G5,16,1);
163 g6=reshape(G3G6,16,1);
164 g7=reshape(G3G7,16,1);
165 g8=reshape(G3G8,16,1);
166 g9=reshape(G3G9,16,1);
167 g10=reshape(G3G10,16,1);
168 g11=reshape(G3G11,16,1);
169 g12=reshape(G3G12,16,1);
170 g13=reshape(G3G13,16,1);
171 g14=reshape(G3G14,16,1);
172 g15=reshape(G3G15,16,1);
173 g16=reshape(G3G16,16,1);
174 H3 = [g1,g2,g3,g4,g5,g6,g7,g8,g9,g10,g11,g12,g13,g14,g15,g16];
175 g1=reshape(G4G1,16,1);
176 g2=reshape(G4G2,16,1);
177 g3=reshape(G4G3,16,1);
178 g4=reshape(G4G4,16,1);
179 g5=reshape(G4G5,16,1);
180 g6=reshape(G4G6,16,1);
181 g7=reshape(G4G7,16,1);
182 g8=reshape(G4G8,16,1);
183 g9=reshape(G4G9,16,1);
57
184 g10=reshape(G4G10,16,1);
185 g11=reshape(G4G11,16,1);
186 g12=reshape(G4G12,16,1);
187 g13=reshape(G4G13,16,1);
188 g14=reshape(G4G14,16,1);
189 g15=reshape(G4G15,16,1);
190 g16=reshape(G4G16,16,1);
191 H4 = [g1,g2,g3,g4,g5,g6,g7,g8,g9,g10,g11,g12,g13,g14,g15,g16];
192 K = (H1*H1 + H2*H2+ H3*H3 +H4*H4);
193 [V,LAMBDAK] = eig(K);
194 W16 = V(:,1);
195 Evals = LAMBDAK;
196 for pp=1:16
197 temp(pp)=Evals(pp,pp);
198 end
199 clear Evals;
200 Evals=temp;
201 clear temp;
202 W=reshape(W16,4,4);
203 for i = 1:4
204 W(:,i) = W(:,i)/W(1,i);
205 end
206 a = Bo*inv(W);
207 A=reshape(a,4,4);
208 for i = 1:4
209 A(i,:) = A(i,:)/A(i,1);
210 end
58
Appendix B
Polar Decomposition - MATLAB
Script
The obtained Mueller matrices (muel) were decomposed using Polar decomposition to get the
basic polarization properties, net depolatization (depol), diattenuation (D), total retardance
(R), optical rotation (rotation) and linear retardance (lin reta) for all wavelengths. Following
is the matlab script that was used for implementing this method. The credits for developing
this script goes to Dr. Nirmalya Ghosh and Jalpa Soni.
1 function[rvec,dvec,R,D,depol,rotation,lin reta]=polardecomposition paper(muel)
2 format long
3 I=[1 0 0;
4 0 1 0;
5 0 0 1];
6 pvec=[muel(2,1),muel(3,1),muel(4,1)]*(1/muel(1,1));
7 dvec=[muel(1,2),muel(1,3),muel(1,4)]*(1/muel(1,1));
8 D=((muel(1,2)^2+muel(1,3)^2+muel(1,4)^2)^0.5)*(1/muel(1,1));
9 m=(1/muel(1,1))*[muel(2,2),muel(2,3),muel(2,4);
10 muel(3,2),muel(3,3),muel(3,4);
11 muel(4,2),muel(4,3),muel(4,4)];
12 D1=(1-D^2)^0.5;
13 if D==0
14 muel 0=muel/muel(1,1);
15 else
16 mD=D1*I+(1-D1)*dvec*dvec/D^2;
17 MD=muel(1,1)*[1,dvec;
18 dvec,mD];
19 diattenuation = ((MD(1,2)^2+MD(1,3)^2+MD(1,4)^2)^0.5)*(1/MD(1,1));
20 muel 0=muel*inv(MD);
21 end
22 m 1=[muel 0(2,2) muel 0(2,3) muel 0(2,4);
23 muel 0(3,2) muel 0(3,3) muel 0(3,4);
24 muel 0(4,2) muel 0(4,3) muel 0(4,4)];
25 l 0=eig(m 1*m 1);
26 m 0=inv(m 1*m 1+((l 0(1)*l 0(2))^0.5+(l 0(2)*l 0(3))^0.5+(l 0(3)*l 0(1))^0.5)*I);
27 m 00=(l 0(1)^0.5+l 0(2)^0.5+l 0(3)^0.5)*m 1*m 1+I*(l 0(1)*l 0(2)*l 0(3))^0.5;
28 if det(m 1)>=0
29 mdelta=m 0*m 00;
30 else
59
31 mdelta=-m 0*m 00;
32 end
33 [v,mdeltaf] = eig(mdelta);
34 depol=1-(abs(mdelta(1,1))+abs(mdelta(2,2))+abs(mdelta(3,3)))/3;
35 depol1 =1-(abs(mdeltaf(1,1))+abs(mdeltaf(2,2))+abs(mdeltaf(3,3)))/3;
36 nul=(pvec-m*dvec)/D1^2;
37 Mdelta=[1 0 0 0;
38 nul mdelta];
39 Mdeltaf =[1 0 0 0;
40 nul mdeltaf];
41 Mdinv=inv(Mdelta);
42 MR=Mdinv*muel 0;
43 trmR=(MR(2,2)+MR(3,3)+MR(4,4))/2;
44 argu=trmR-1/2;
45 if abs(argu)>1
46 if argu>0
47 R=acos(1);
48 else
49 R=acos(-1);
50 end
51 else
52 R=acos(argu);
53 end
54 cssq 10=(MR(2,2)+MR(3,3))^2+(MR(3,2)-MR(2,3))^2;
55 tan rot=(MR(3,2)-MR(2,3))/((MR(2,2))+(MR(3,3)));
56 de=cssq 10^0.5-1;
57 if de>0.999999999999
58 de=1;
59 end
60 if de<-0.99999999999
61 de=-1;
62 end
63 lin reta=acos(de);
64 rotation=atan(tan rot);
65 if tan rot<0.000000001
66 rotation=rotation+pi;
67 end
68 rotation=rotation/2;
69 if (MR(3,2)-MR(2,3))<0.0
70 if (MR(2,2)+MR(3,3))<0.0
71 rotation=rotation+pi/2;
72 end
73 end
74 if (MR(3,2)-MR(2,3))<0.0
75 if (MR(2,2)+MR(3,3))>0.0
76 rotation=rotation+pi/2;
77 end
78 end
79 if abs(MR(3,2)-MR(2,3))<=0.000000001 && abs(MR(2,2)+MR(3,3))>0.0000000001
80 rotation=0;
81 end
60
82 if abs(sin(R))<=0.000000001
83 a3=((1+cos(lin reta))/2)^0.5;
84 a1=(MR(3,4)+MR(4,3))/(4*a3);
85 a2=(MR(4,2)+MR(2,4))/(4*a3);
86 else
87 D2=1/(2*sin(R));
88 a1=D2*(MR(3,4)-MR(4,3));
89 a2=D2*(MR(4,2)-MR(2,4));
90 a3=D2*(MR(2,3)-MR(3,2));
91 end
92 rvec=[1,a1,a2,a3];
93 if abs(cos(R))>=0.9999999999
94 C1=MR(2,2)+MR(3,3);
95 C2=MR(2,3)-MR(3,2);
96 if abs(C1)<0.0000000001
97 MR=MR*[1 0 0 0; 0 1 0 0; 0 0 -1 0; 0 0 0 -1];
98 rotation=0.5*acos((MR(2,2)+MR(3,3))/2);
99 lin reta=pi;
100 end
101 if C1<1.999999999
102 if abs(C2)<0.0000000001
103 MR=MR*[1 0 0 0; 0 -1 0 0; 0 0 -1 0; 0 0 0 1];
104 dum=MR(2,2)+MR(3,3)-1;
105 lin reta=acos(dum);
106 if dum>=1
107 lin reta=0;
108 end
109 if dum<=-1
110 lin reta=pi;
111 end
112 rotation=pi/2;
113 end
114 end
115 end
116 orientation = 0.5*atan(rvec(3)/rvec(2));
117 mr1=MR*inv(rota(rotation));
118 a1a=(mr1(3,4)-mr1(4,3));
119 a2a=(mr1(4,2)-mr1(2,4));
120 a3a=(mr1(2,3)-mr1(3,2));
121 rveca=[1,a1a,a2a,a3a];
122 orientationa = 0.5*atan(rveca(3)/rveca(2));
123 mr2=inv(rota(rotation))*MR;
124 a1b=(mr2(3,4)-mr2(4,3));
125 a2b=(mr2(4,2)-mr2(2,4));
126 a3b=(mr2(2,3)-mr2(3,2));
127 rvecb=[1,a1b,a2b,a3b];
128 orientationb = 0.5*atan(rvecb(3)/rvecb(2));
129 orientationc = 0.5*acos(MR(3,4)/sin(lin reta));
130 return
61
Appendix C
Labview Automation Code
Figure C.1: Front Panel of the automation VI.
The automation of the spectral Mueller matrix polarimeter was done using Labview. Fig.
C.1 is a snapshot of the front panel of the Labview code used for automation. The code was
designed by myself using the virtual instruments (VIs), software development kits (SDKs) and
other drivers provided along with each instrument.
The block diagram behind the above control is shown in Fig. C.2. Please note that this VI
consists of several other sub VIs which are not shown here. These were either supplied by the
manufacturers or were designed by me.
62
Figure C.2: Block Diagram of the automation VI.
63