Optical Coherence Tomography (OCT) is an optical tomography technique which provides high resolution non-invasive three-dimensional (3D) structural images of the sample based on coherent properties of light. The dissertation focuses on the use of OCT systems for detecting glaucoma, which is the second leading cause of blindness worldwide. First, as a prerequisite of analyzing ophthalmologic OCT images, a retinal sublayer segmentation algorithm is presented and implemented with GPU assisted computation. Then, a polarization-sensitive optical coherence tomography (PS-OCT) system was constructed for the study of glaucoma. Three closely related clinical and animal studies on early-stage glaucoma detection using either OCT or PS-OCT were performed. Statistical analysis of the study results indicates that the scattering property of retinal nerve fiber layer (RNFL) is the earliest indicator for glaucoma. Finally, to investigate the scattering properties of RNFL, a pathlength-multiplexed scattering-angle-diverse optical coherence tomography (PM-SAD-OCT) system was designed and built. PM-SAD-OCT images were collected from human and rodent retina as well as earthworm nerve cord. PM-SAD-OCT system shows promising potentials to detect neurodegenerative diseases including glaucoma. / text

Thesis (M.S.)--California Polytechnic State University, 2008. / Mode of access: Internet. Title from PDF title page, viewed on March 26, 2009. Major professor: Dennis Derickson, Ph.D. "Presented to the Electrical Engineering Department Faculty of California Polytechnic State University, San Luis Obispo." "In partial fulfillment of the requirements for the Master of Science degree in Electrical Engineering." "December 2008." Includes bibliographical references (p. 93-94). Will also be available on microfiche.

Thesis supervisor: Mona K. Garvin. Includes bibliographic references (p. 55-57).

In the medical field, the detection and diagnosis of diseases continue to improve. Developments in diagnostic techniques have helped to improve treatment in the early stages and avoid many risks to patients. One relatively new diagnostic technique is optical coherence tomography (OCT), which is used in many medical applications to perform internal microstructure imaging of the human body at high resolution (typically 10 micro metre), at high speed and in real time. OCT is non-invasive and can be used as a contact or non-contact technique to obtain an image. In medicine, there are many applications that involve OCT, such as in ophthalmology, gastroenterology, cardiology and oncology. This work demonstrates the design, development and implementation of a high resolution swept laser OCT system for the imaging and diagnosis of tissues in laboratory and clinical experiments. It reports an investigation to measure the thickness of the peritoneal membrane and the use of optical imaging contrast agents such as gold nanorods. There is also an account of the design of an endoscope-catheter fast scanning OCT system for biomedical studies of the gastrointestinal tract and gynaecological areas. These results were achieved by using a swept tuneable laser source with a very high tuning speed of 16 kHz over a wide range of wavelengths: 1260 nm to 1390 nm. The laser sweeps across 110 nm at a 16 kHz repetition rate. The real axial line speed is limited by the source that is used in the OCT system. The axial resolution of the system is 7 µm and its transverse resolution is 15 µm. The bandwidth of the source is up to DeltaGamma = 110 nm, centred at Gamma0 = 1325 nm, and the coherent length is 7 µm. On the sample arm of the interferometer, the swept laser OCT technique is combined with an optical probe and endoscope in order to develop a novel diagnostic imaging device to visualize tissue in vivo for animal and human experimental trials.

This thesis presents the development of new optical coherence tomography imaging systems and techniques to improve in vivo 3D microvascular imaging. Specifically these systems and techniques were proposed to address three main problems with 3D Doppler optical coherence tomography imaging: (a) Motion artefacts, (b) angle dependence of the signal, and (c) relatively high minimum detectable velocity of conventional color Doppler algorithms (~500 μm/s). In order to overcome these limitations a multi-pronged strategy was employed: (1) Construction of a retrospectively gated OCT system for the mitigation of periodic motion artefacts. Proof of principle in vivo B-mode imaging of Xenopus Laevis (embryo of African clawed frog) cardiovascular function up to 1000 frames per second (fps) from data acquired at 12 fps. Additionally, 4D imaging of the Xenopus Laevis heart at 45 volumes per second was demonstrated. (2) Construction of a Fourier domain mode locked laser for high speed swept source optical coherence tomography imaging. This laser was capable of reaching sweep rates of 67 kHz and was optimized to function in the SNR limited phase noise regimes upto approximately 55 dB structural SNR. (3) Development of a novel speckle variance image processing algorithm for velocity and angle independent 3D microvascular imaging. The velocity and angle independence of the technique was validated through phantom studies. iii In vivo demonstration of the speckle variance algorithm was performed by imaging the capillary network in the dorsal skin-fold window chamber model, with the results being validated using fluorescence confocal microscopy. In the final part of this thesis, these newly developed technologies were applied to the assessment of anti-vascular and anti-angiogenic therapies in preclinical models, specifically, photodynamic therapy and targeted degradation of HIF-α.

This thesis presents the development of new optical coherence tomography imaging systems and techniques to improve in vivo 3D microvascular imaging. Specifically these systems and techniques were proposed to address three main problems with 3D Doppler optical coherence tomography imaging: (a) Motion artefacts, (b) angle dependence of the signal, and (c) relatively high minimum detectable velocity of conventional color Doppler algorithms (~500 μm/s). In order to overcome these limitations a multi-pronged strategy was employed: (1) Construction of a retrospectively gated OCT system for the mitigation of periodic motion artefacts. Proof of principle in vivo B-mode imaging of Xenopus Laevis (embryo of African clawed frog) cardiovascular function up to 1000 frames per second (fps) from data acquired at 12 fps. Additionally, 4D imaging of the Xenopus Laevis heart at 45 volumes per second was demonstrated. (2) Construction of a Fourier domain mode locked laser for high speed swept source optical coherence tomography imaging. This laser was capable of reaching sweep rates of 67 kHz and was optimized to function in the SNR limited phase noise regimes upto approximately 55 dB structural SNR. (3) Development of a novel speckle variance image processing algorithm for velocity and angle independent 3D microvascular imaging. The velocity and angle independence of the technique was validated through phantom studies. iii In vivo demonstration of the speckle variance algorithm was performed by imaging the capillary network in the dorsal skin-fold window chamber model, with the results being validated using fluorescence confocal microscopy. In the final part of this thesis, these newly developed technologies were applied to the assessment of anti-vascular and anti-angiogenic therapies in preclinical models, specifically, photodynamic therapy and targeted degradation of HIF-α.

Optical coherence tomography (OCT) is an innovative modern biomedical imaging technology that allows in-vivo, non-invasive imaging of biological tissues. At present, some of the major challenges in OCT include the need for fast data acquisition system for probing fast developing biochemical processes in biological tissue, for image processing algorithms to reduce speckle noise and to remove motion artefacts, and for dispersion compensation to improve axial resolution and image contrast. To address the need for fast data acquisition, a novel, high speed (47,000 A-scans/s), ultrahigh axial resolution (3.3μm) Fourier Domain Optical Coherence Tomography (FD-OCT) system in the 1060nm wavelength region has been built at the University of Waterloo. The system provides 3.3μm image resolution in biological tissue and maximum sensitivity of 110 dB. Retinal tomograms acquired in-vivo from a human volunteer and a rat animal model show clear visualization of all intra-retinal layers and increased penetration into the choroid. OCT is based on low-coherence light interferometry. Thus, image quality is dependent on the spatial and temporal coherence properties of the optical waves back-scattered from the imaged object. Due to the coherent nature of light, OCT images are contaminated with speckle noise. Two novel speckle noise reduction algorithms based on interval type II fuzzy sets has been developed to improve the quality of the OCT images. One algorithm is a combination of anisotropic diffusion and interval type II fuzzy system while the other algorithm is based on soft thresholding wavelet coefficients using interval type II fuzzy system. Application of these novel algorithms to Cameraman test image corrupted with speckle noise (variance=0.1) resulted in a root mean square error (RMSE) of 0.07 for both fuzzy anisotropic diffusion and fuzzy wavelet algorithms. This value is less compared to the results obtained for Wiener (RMSE=0.09), adaptive Lee (RMSE=0.09), and median (RMSE=0.12) filters. Applying the algorithms to optical coherence tomograms acquired in-vivo from a human finger-tip show reduction in the speckle noise and image SNR improvement of ~13dB for fuzzy anisotropic diffusion and ~11db for fuzzy wavelet. Comparison with the Wiener (SNR improvement of ~3dB), adaptive Lee (SNR improvement of ~5dB) and median (SNR improvement of ~5dB) filters, applied to the same images, demonstrates the better performance of the fuzzy type II algorithms in terms of image metrics improvement. Micrometer scale OCT image resolution is obtained via use of broad bandwidth light sources. However, the large spectral bandwidth of the imaging beam results in broadening of the OCT interferogram because of the dispersive properties of the imaged objects. This broadening causes deterioration of the axial resolution and as well as loss of contrast in OCT images. A novel even-order dispersion cancellation interferometry via a linear, classical interferometer has been developed which can be further expanded to dispersion canceled OCT.

Optical coherence tomography (OCT) is an innovative modern biomedical imaging technology that allows in-vivo, non-invasive imaging of biological tissues. At present, some of the major challenges in OCT include the need for fast data acquisition system for probing fast developing biochemical processes in biological tissue, for image processing algorithms to reduce speckle noise and to remove motion artefacts, and for dispersion compensation to improve axial resolution and image contrast. To address the need for fast data acquisition, a novel, high speed (47,000 A-scans/s), ultrahigh axial resolution (3.3μm) Fourier Domain Optical Coherence Tomography (FD-OCT) system in the 1060nm wavelength region has been built at the University of Waterloo. The system provides 3.3μm image resolution in biological tissue and maximum sensitivity of 110 dB. Retinal tomograms acquired in-vivo from a human volunteer and a rat animal model show clear visualization of all intra-retinal layers and increased penetration into the choroid. OCT is based on low-coherence light interferometry. Thus, image quality is dependent on the spatial and temporal coherence properties of the optical waves back-scattered from the imaged object. Due to the coherent nature of light, OCT images are contaminated with speckle noise. Two novel speckle noise reduction algorithms based on interval type II fuzzy sets has been developed to improve the quality of the OCT images. One algorithm is a combination of anisotropic diffusion and interval type II fuzzy system while the other algorithm is based on soft thresholding wavelet coefficients using interval type II fuzzy system. Application of these novel algorithms to Cameraman test image corrupted with speckle noise (variance=0.1) resulted in a root mean square error (RMSE) of 0.07 for both fuzzy anisotropic diffusion and fuzzy wavelet algorithms. This value is less compared to the results obtained for Wiener (RMSE=0.09), adaptive Lee (RMSE=0.09), and median (RMSE=0.12) filters. Applying the algorithms to optical coherence tomograms acquired in-vivo from a human finger-tip show reduction in the speckle noise and image SNR improvement of ~13dB for fuzzy anisotropic diffusion and ~11db for fuzzy wavelet. Comparison with the Wiener (SNR improvement of ~3dB), adaptive Lee (SNR improvement of ~5dB) and median (SNR improvement of ~5dB) filters, applied to the same images, demonstrates the better performance of the fuzzy type II algorithms in terms of image metrics improvement. Micrometer scale OCT image resolution is obtained via use of broad bandwidth light sources. However, the large spectral bandwidth of the imaging beam results in broadening of the OCT interferogram because of the dispersive properties of the imaged objects. This broadening causes deterioration of the axial resolution and as well as loss of contrast in OCT images. A novel even-order dispersion cancellation interferometry via a linear, classical interferometer has been developed which can be further expanded to dispersion canceled OCT.

Purpose To examine soft contact lens fitting characteristics using anterior segment imaging techniques and comfort. The specific aims of each chapter are as follows: Chapter 2: To calibrate the new ZEISS VisanteTM anterior segment optical coherence tomographer (OCT) using references with known physical thickness and refractive index equal to the human cornea and to compare the Visante measures to those from a previous generation OCT (Zeiss-Humphrey OCT II). Chapter 3: The first purpose of this study was to measure the repeatability of the Visante TM OCT in a normal sample. The second was to compare corneal thickness measured with the Visante TM OCT to the Zeiss-Humphrey OCT II (model II, Carl Zeiss Meditec, Jena Germany) adapted for anterior segment imaging and to the Orbscan II TM (Bausch and Lomb, Rochester New York). Chapter 4: Conjunctival displacement observed with the edges of the contact lens, when imaged may be real or may be an artefact of all OCT imagers. A continuous surface appears displaced when the refractive index of the leading medium changes at the edge of a contact lens. To examine this effect, edges of the contact lenses were imaged on a continuous surface using the UHR-OCT. Contact lens edges on the human conjunctival tissue were also imaged to see if the lens indentation on the conjunctival tissue is real or an artefact at the edge of the lens. Chapter 5: The main purpose of this study was to determine if we can predict end of the day discomfort and dryness using clinical predictive variables. The second purpose of the study was to determine if there was any relationship between lens fitting characteristics and clinical complications and especially to the superior cornea and conjunctiva with a dispensing clinical trial. Methods Chapter 2: Twenty two semi-rigid lenses of specified thicknesses were manufactured using a material with refractive index of 1.376. Central thickness of these lenses was measured using VisanteTM OCT and Zeiss-Humphrey OCT II (Zeiss, Germany). Two data sets consisting of nominal measures (with a standard pachymeter of the lenses and one obtained using a digital micrometer) were used as references. Regression equations between the physical and optical (OCT) measures were derived to calibrate the devices. Chapter 3: Fifteen healthy participants were recruited. At the Day 1 visit the epithelial and total corneal thickness, across the central 10mm of the horizontal meridian were measured using the OCT II and the Visante TM OCT. Only total corneal thickness across the central 10mm of the horizontal meridian was measured using the Orbscan II. The order of these measurements was randomized. These measurements were repeated on Day 2. Each individual measurement was repeated three times and averaged to give a single result. Chapter 4: (2-D) Images of the edges of marketed silicone hydrogel and hydrogel lenses with refractive indices (n) ranging from 1.41-1.51 were taken placing them concave side down on a continuous surface. Five images for each lens were taken using a UHR-OCT system, operating at 1060 nm with ~3.2um (axial) and 10μm (lateral) resolution at the rate of 75,000 A-scans/s. The displacement of the glass slide beneath the lens edge was measured using Image J. Chapter 5: Thirty participants (neophytes) were included in the study and the four lenses (Acuvue Advance 8.3, Acuvue Advance 8.7, Pure Vision 8.3, and Pure Vision 8.6) were randomly assigned for each eye. The lenses were worn for a period of two weeks on a daily wear basis for 8 to 10hrs per day. Lens performance was monitored over the 2week period. Assessment of subjective comfort was made using visual analogue scales. Total corneal and epithelium thickness was measured using the Visante OCT, the lens edge profiles of the contact lenses were observed using the ultra-high resolution OCT and the conjunctival epithelial thinning was measured using the RTVue OCT. Conjunctival blood velocity was measured at the baseline and 2 week visit using a high magnification camera. Results Chapter 2: Before calibration, repeated measures ANOVA showed that there were significant differences between the mean lens thicknesses from each of the measurement methods (p<0.05), where Visante measurements were significantly different from the other three (OCT II, MG and OP) methods (p<0.05). Visante thickness was significantly higher than the microgauge measures (453±37.6 µm compared to 445.1±38.2 µm) and the OCT II was significantly lower (424.5±36.1 µm both, p<0.05). After calibration using the regression equations between the physical and optical measurements, there were no differences between OCT II and Visante OCT (p<0.05). Chapter 3: Mean central corneal and epithelial thickness using the Visante™ OCT after calibration at the apex of the cornea was 536± 27 µm (range, 563-509 µm) and 55± 2.3 µm (range, 57.3-52.7 µm), respectively. The mean corneal and epithelial thickness using OCT II at the apex was 520±25µm and 56±4.9 µm, respectively. The mean of total corneal thickness measured with the Orbscan II was 609±29µm. Visante OCT was the most repeatable for test-retest at the apex, nasal and temporal quadrants of the cornea compared to OCT II and Orbscan II. COR’s of Visante OCT ranged from ±7.71µm to ±8.98µm for total corneal thickness and ± 8.72 µm to ± 9.92 µm for epithelial thickness. CCC’s with Visante OCT were high for total corneal thickness for test-retest differences ranging from 0.97 to 0.99, CCC’s for epithelial thickness showed moderate concordance for both the instruments. Chapter 4: Results showed that artefactual displacement of the contact lens edge was observed when the lenses were imaged on the glass reference sphere, custom made rigid contact lenses (1.376) and on the conjunctival tissue. The displacement measured on the conjunctival tissue ranged from 7.0±0.86 µm for the Air Optix Night and Day to 17.4±0.22 µm for the Acuvue Advance contact lenses. The range of displacement with the soft lens edges imaged on the rigid contact lens was from 5.51±0.03 µm to 9.72±0.12 µm. Chapter 5: The lenses with the steepest sag (Acuvue Advance 8.3, Pure Vision 8.3) resulted not only with the tightest fit, but with compromise to the superior conjunctiva. This was especially seen with the Acuvue Advance lenses. The steeper lenses caused more total corneal swelling, superior epithelial thinning, mechanical compression of conjunctiva, conjunctival staining, bulbar hyperemia, conjunctival indentation and reduced blood flow at the lens edge. Not many associations were observed between baseline clinical and 2 weeks sensory variables. However, significant associations were observed when comparing the baseline clinical variables to end of the day sensory variables. Baseline clinical variables compared to 2 week clinical variables also showed significant correlations. Conclusions Chapter 2: Using reference lenses with refractive index of the cornea (1.376) allows rapid and simple calibration and cross calibration of instruments for measuring the corneal thickness. The Visante and OCT II do not produce measurements that are equal to physical references with refractive index equal to the human cornea. Chapter 3: There is good repeatability of corneal and epithelial thickness using each OCT for test-retest differences compared to the between instruments repeatability. Measurements of epithelial thickness are less repeatable compared to the total corneal thickness for the instruments used in the study. Chapter 4: When contact lenses are imaged in-situ using UHR-OCT the conjunctival tissue appeared displaced. This experiment indicates that this displacement is an artefact of all OCT imagers since a continuous surface (glass slide) was optically displaced indicating that the displacement that is observed is a function of the refractive index change and also the thickness of the contact lens edges. Chapter 5: Discomfort is a complex issue to resolve since it appears to be related to ocular factors such as the corneal and conjunctival topography and sagittal depth; to lens factors that is 1) how the sag depth of the lenses relate to the corneal/conjunctival shape and depth and therefore how well it moves on the eye. 2) Also with the lens material; whether they are high or low modulus, low or high water content, dehydration properties, wetting agents used and its resistance to deposits, lens edge profile and thickness and its interaction with the upper eyelid.

A polarization sensitive optical coherence tomography (PS-OCT) instrument is presented for the study of glaucoma. Glaucoma is the second leading cause of blindness worldwide and causes irreversible damage to the retina. This PS-OCT system was built to perform retinal imaging with a swept source laser providing a 28 kHz A-scan repetition rate. Thickness, phase retardation, birefringence and reflectance index measurements were taken from the primate eyes on a weekly or semi-weekly basis through the course of a 30 week study. Statistical analysis of these measurements indicates that the reflectance index is the earliest measured indicator of glaucomatous changes and a potential marker for early glaucoma diagnosis. / text