Diagnostic Imaging and Assessment Using Angle Resolved Low Coherence

228 Pages·2012·7.36 MB·English

by  Hugh Crumley

Diagnostic Imaging and Assessment Using Angle Resolved Low Coherence
Interferometry
by
Michael G. Giacomelli
Department of Biomedical Engineering
Duke University

Date:_______________________
Approved:

___________________________
Adam Wax, Supervisor

___________________________
Joseph Izatt

___________________________
David Brady

___________________________
Tuan Vo- Dinh

___________________________
Sina Farsiu

Dissertation submitted in partial fulfillment of
the requirements for the degree of Doctor of Philosophy in the Department of
Biomedical Engineering in the Graduate School
of Duke University

2012
i
v
ABSTRACT
Diagnostic Imaging and Detection using Angle Resolved Low Coherence
Interferometry
by
Michael Giacomelli
Department of Biomedical Engineering
Duke University

Date:_______________________
Approved:

___________________________
Adam Wax, Supervisor

___________________________
Joseph Izatt

___________________________
David Brady

___________________________
Tuan Vo- Dinh

___________________________
Sina Farsiu

An abstract of a dissertation submitted in partial
fulfillment of the requirements for the degree
of Doctor of Philosophy in the Department of
Biomedical Engineering in the Graduate School
of Duke University

2012
Copyright by
Michael G. Giacomelli
2012
Abstract
The redistribution of incident light into scattered fields ultimately limits the
ability to image into biological media. However, these scattered fields also contain
information about the structure and distribution of protein complexes, organelles, cells
and whole tissues that can be used to assess the health of tissue or to enhance imaging
contrast by excluding confounding signals. The interpretation of scattered fields
depends on a detailed understanding of the scattering process as well as sophisticated
measurement systems. In this work, the development of new instruments based on low
coherence interferometry (LCI) is presented in order to perform precise, depth-resolved
measurements of scattered fields. Combined with LCI, the application of new light
scattering models based on both analytic and numerical methods is presented in order to
interpret scattered field measurements in terms of scatterer geometry and tissue health.
The first portion of this work discusses the application of a new light scattering
model to the measurement recorded with an existing technique, Angle Resolved Low
Coherence Interferometry (a/LCI). In the a/LCI technique, biological samples are
interrogated with collimated light and the energy per scattering angle at each depth in
the volume is recorded interferometrically. A light scattering model is then used to
invert the scattering measurements and measure the geometry of cell nuclei. A new
light scattering model is presented that can recover information about the size, refractive
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index, and for the first time, shape of cell nuclei. This model is validated and then
applied to the study of cell biology in a series of experiments measuring cell swelling,
cell deformation, and finally detecting the onset of apoptosis.
The second portion of this work introduces an improved version of a/LCI based
on two dimension angle-resolved measurement and Fourier domain low coherence
interferometry. A new system based on fiber scanning is presented for high speed and
polarization-resolved measurements of scattered fields. The combined system is
validated with phantoms and is shown to be able to uniquely determine the size and
shape of scattering particles using a single measurement. Finally, determination of the
orientation of scatterers relative to electric field is considered.
The third portion of this work develops the use of angle-resolved interferometry
for imaging through highly scattering media by exploiting the tendency of scatterers to
forward scatter light. A new interferometers is developed that can image through very
large numbers of scattering events with acceptable resolution. A computational model
capable of reproducing experimental measurements is developed and used to
understand the performance of the technique. Finally, theoretical arguments are
presented suggesting the feasibility of adapting the technique to Fourier domain
acquisition.
The final portion of the work develops a method for processing 2D angle
resolved measurements using optical autocorrelation. In this method, measurements
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over a range of angles are fused into a single depth scan that incorporates the
component of scattered light only from certain spatial scales. The utility of the technique
is demonstrated using a gene knockout model of retinal degeneration in mice. Optical
autocorrelation is shown to be a potentially useful biomarker of tissue disease.
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Contents

Abstract ......................................................................................................................................... iv
List of Tables ................................................................................................................................ xii
List of Figures ............................................................................................................................ xiii
Acknowledgements ................................................................................................................ xxiv
1. Introduction ............................................................................................................................... 1
1.1 Light and Matter ............................................................................................................... 1
1.2 Motivation ......................................................................................................................... 4
1.3 Organization ...................................................................................................................... 7
2. Background ................................................................................................................................ 8
2.1 Low Coherence Interferometry ...................................................................................... 8
2.1.1 Optical Coherence Tomography ............................................................................. 13
2.2 Modeling of Light and Matter Interactions ................................................................ 14
2.2.1 Mie Theory ................................................................................................................. 14
2.2.2 T-matrix ...................................................................................................................... 17
2.3 Light Scattering Techniques .......................................................................................... 18
2.3.1 Light Scattering Spectroscopy ................................................................................. 18
2.3.2 Fourier-Domain Low Coherence Interferometry .................................................. 19
2.3.3 Confocal Light Absorption and Scattering Spectroscopy (CLASS).................... 21
2.3.4 Two Dimension Angular Optical Spectroscopy ................................................... 22
2.3.5 4D Elastic Light Scattering Spectroscopy ............................................................... 22
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2.3.6 Angle-Resolved Low Coherence Interferometry .................................................. 23
2.3.7 Fourier Holographic Light Scattering Angular Spectroscopy ............................ 24
2.4 Angle-Resolved Low Coherence Interferometry Processing ................................... 25
2.4.1 Depth Extraction ........................................................................................................ 25
2.4.2 Correlation Filtering .................................................................................................. 25
2.4.3 χ2 Error Calculation ................................................................................................... 27
2.4.4 χ2 Database Preparation ........................................................................................... 28
2.5 Summary .......................................................................................................................... 28
3. Development of Advanced Light Scattering Models ......................................................... 30
3.1 Background ..................................................................................................................... 30
3.2 Scattering Coordinate System ....................................................................................... 34
3.3 Distributed Computing Software for Computation of T-matrix Databases .......... 36
3.3.1 MySQL Server ............................................................................................................ 38
3.3.2 DC Worker Software ................................................................................................. 40
3.3.3 T-matrix Software ...................................................................................................... 40
3.3.4 Client Software .......................................................................................................... 41
3.4 Validation of the T-matrix Using Non-spherical Phantoms ..................................... 42
3.4.1 Development of Spheroidal Phantoms .................................................................. 42
3.4.2 Determining Spheroid Size ...................................................................................... 44
3.5 Summary .......................................................................................................................... 47
4. Development of Angle Resolved Low Coherence Interferometry (a/LCI) using the T-
matrix method ............................................................................................................................. 48
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4.1 Previous Results.............................................................................................................. 48
4.2 Overview of Time-Domain a/LCI ................................................................................ 49
4.3 Validating Mie Theory based fitting Using T-matrix simulations .......................... 50
4.3.1 Analysis ...................................................................................................................... 51
4.3.2 Results ......................................................................................................................... 54
4.3.3 Summary .................................................................................................................... 56
4.4 Size and Shape Measurement of Cell Nuclei in Culture ........................................... 56
4.4.1 Results ......................................................................................................................... 58
4.5 Investigation of Cell Deformation by Nanotopological Cues .................................. 61
4.5.1 Methods ...................................................................................................................... 62
4.5.2 Results ......................................................................................................................... 64
4.5.3 Discussion ................................................................................................................... 68
4.6 Investigation of Chemotherapy Induced Apoptosis Using the Fractal Dimension
of Scatterers ........................................................................................................................... 69
4.6.1 Apoptosis .................................................................................................................... 69
4.6.2 Residual Analysis of a/LCI signals ......................................................................... 70
4.6.3 Calculating the Fractal Dimension .......................................................................... 71
4.6.4 Cell culture Methods ................................................................................................. 75
4.6.5 Results ......................................................................................................................... 75
4.6.6 Discussion ................................................................................................................... 81
4.7 Summary .......................................................................................................................... 83
5. Development of 2D Angle Resolved Low Coherence Interferometry (2D a/LCI) ......... 85
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5.1 Fiber-optic interferometric Two Dimensional Scattering (FITS) System ................ 87
5.2 Size and Shape determination using 2D Scattering ................................................... 96
5.2.1 T-matrix Database ..................................................................................................... 96
5.2.2 Image Registration .................................................................................................... 97
5.2.3 Database Fitting ......................................................................................................... 98
5.2.4 Fitting Results ............................................................................................................ 98
5.2.5 Discussion ................................................................................................................. 103
5.3 Scatterer Orientation .................................................................................................... 104
5.4 Summary ........................................................................................................................ 107
6. Development of Multiple Scattering Low Coherence Interferometry (MS/LCI) ......... 108
6.1 Motivation ..................................................................................................................... 109
6.2 MS/LCI Experimental Realization .............................................................................. 113
6.2.1 System Development .............................................................................................. 113
6.2.2 Imaging through 1 µm Bead Media ...................................................................... 117
6.2.3 Imaging through 11 µm Beads Media .................................................................. 120
6.2.4 Attenuation of Multiply Scattered Light .............................................................. 121
6.2.5 MS/LCI Resolution .................................................................................................. 123
6.2.6 Discussion ................................................................................................................. 124
6.3 Theoretical analysis and Computational Results ..................................................... 129
6.3.1 GPU Based Monte Carlo Model ............................................................................ 131
6.3.2 MC Model Validation ............................................................................................. 134
6.3.3 MC Model Resolution ............................................................................................. 136
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