1. Articles in category: Student Theses

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    1. ALGORITHMS FOR OPTICAL COHERENCE TOMOGRAPHY AND ITS CLINICAL APPLICATIONS (Thesis)

      ALGORITHMS FOR OPTICAL COHERENCE TOMOGRAPHY AND ITS CLINICAL APPLICATIONS (Thesis)

      Optical Coherence Tomography (OCT) is a clinically adapted, high resolution, non-invasive, non-contact imaging modality that gives a cross-sectional depth-resolved image of the biological sample. Several modifications in OCT instrumentation and development of new reconstruction algorithms have made OCT a potential diagnostic tool. This thesis discusses a free space experimental set-up and development of effective image reconstruction algorithm for Spectral Domain Optical Coherence Tomography (SD-OCT). This algorithm is initially validated on the in-house developed phantoms and later applied on the various biological samples. The same algorithm is implemented for oral tissue and stomach tissue analysis. Further, the OCT imaging was explored ...

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    2. Differences in optical coherence tomography assessment of radial peripapillary capillaries with axial length and optic nerve head morphology (Thesis)

      Differences in optical coherence tomography assessment of radial peripapillary capillaries with axial length and optic nerve head morphology (Thesis)

      INTRODUCTION: Optic nerve head morphological parameters and axial length have been shown to be associated with altered retinal perfusion and microvascular characteristics. The radial peripapillary capillaries (RPC) are a fine network of vessels embedded within the retinal nerve fiber layer which can be visualized using optical coherence tomography (OCT) angiography. RPC is susceptible to ocular hypertension, ischemia, trauma, or biomechanical stress. Since axially myopic eyes have greater propensity for developing glaucoma, assessing the relationship between morphological parameters and RPC characteristics may contribute to evidence important to understanding the pathophysiology of glaucoma and other optic neuropathies. PURPOSE: To investigate the association ...

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    3. Quantitative Optical Coherence Tomography Methods for Functional Microvascular Imaging (Thesis)

      Quantitative Optical Coherence Tomography Methods for Functional Microvascular Imaging (Thesis)

      In recent years, the importance of blood flow distribution has been highlighted in a wide range of diseases that involve the cerebral microvasculature. Specifically, microvascular heterogeneity, related to the non-uniform distribution of blood flow through the microvasculature, is an important parameter that is critical to the efficacy of oxygen extraction. As increased heterogeneity may lead to oxygen insufficiency, even with blood flow above ischemic levels, heterogeneity may be an important biomarker for understanding disease progression. However, current methods of quantifying microvascular heterogeneity over large microvascular networks that extend deep into biological tissue (such as the cerebral cortical microvasculature) are limited ...

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    4. High Resolution Wide Field-of-View Optical Coherence Tomography For 3D Imaging (Thesis)

      High Resolution Wide Field-of-View Optical Coherence Tomography For 3D Imaging (Thesis)

      Optical coherence tomography (OCT) is a noninvasive, cross-sectional, and three-dimensional (3D) tomographic imaging modality. It offers subsurface deeper penetration depth and larger scan area than confocal microscopy as well as higher resolution than ultrasound imaging, very suitable for 3D in vivo imaging of eyes, skins, blood vessels, and other non-biomedical samples. However, there is a trade-off problem among lateral resolution, lateral field of view (FOV), and axial imaging depth, limiting the performance of OCT systems. In this dissertation, we report our studies to solve these problems and to make the OCT a competitive tool for a variety of 3D imaging ...

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    5. Non-destructive biomechanical testing of tissues using a vibrational optical coherence tomography setup (Thesis)

      Non-destructive biomechanical testing of tissues using a vibrational optical coherence tomography setup (Thesis)

      The mechanical properties of tissues and implants contribute to their physiological functionality, and have been vast areas of research in fields such as Dermatology, Cardiology, Neurology, Ophthalmology, Orthopedics and Urology. Several tests and modalities have been used to measure the mechanical properties of tissues and implants including tensile, compressive, shear, and bending in one or more axial directions. However, majority of these tests are destructive, rendering the material unusable post-testing; whereas most of the non-destructive imaging modalities such as magnetic resonance imaging (MRI), nuclear magnetic resonance (NMR) and ultrasound are costly and have lower spatial resolution. Optical coherence tomography (OCT ...

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    6. Safeguarding ovarian tissue autotransplantation in cancer patients (Thesis)

      Safeguarding ovarian tissue autotransplantation in cancer patients (Thesis)

      Autotransplantation of ovarian tissue can be used to restore fertility in cancer patients following gonadotoxic treatment. Whether this procedure is safe remains unclear, as current tumor detection methods (e.g. PCR analysis, immunohistochemistry) render the ovarian tissue unsuitable for transplantation. As a result, the current tumor detection approach includes assessment of only one or two cortical ovarian fragments that are not transplanted, whereas cortical ovarian tissue fragments that are placed back remain unchecked. The studies described in this thesis focused on determining the risk of reintroducing malignant tumor cells following ovarian tissue autotransplantation using the current tumor detection approach, and ...

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    7. Structural and functional optical coherence tomography imaging of the colon (Thesis)

      Structural and functional optical coherence tomography imaging of the colon  (Thesis)

      Colorectal cancer (CRC) remains the second deadliest cancer in the United States, despite steady reduction in mortality rate over the last three decades. Colonoscopy is the gold-standard screening modality with high sensitivity and specificity to mature polyps. However, the miss rate for small (< 5 mm) lesions is estimated to be as high as 26%. Because the five-year survival rate for CRC detected at the local stage is 90%, there is a clear need for a screening procedure that is sensitive to these small lesions. Optical coherence tomography (OCT) has become a major biomedical imaging modality since its invention in 1991 ...

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    8. Polarization-maintaining fiber-based Optical Coherence Tomography and its applications (Thesis)

      Polarization-maintaining fiber-based Optical Coherence Tomography and its applications (Thesis)

      Recent advances in Optical Coherence Tomography (OCT) have enabled wide ranges of attractive applications, including characterization of biological tissues, morphological tracking, intravascular imaging, developmental biology and in functional spectroscopic aspects. Neural activity has been studied using optical methods in the past few decades. The use of light to probe neural activity allows outstanding resolution, and the possibility for simultaneous measurement from a range of targeted locations without physical contact with the tissue. Optically detectable signals, such as transient changes with phase and backscattered light intensity, are captured using spectral-domain OCT system. In this dissertation, a fundamental introduction to polarizationmaintaining fiber-based ...

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    9. REVISITING THE VASCULAR THEORY OF GLAUCOMA USING OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY (Thesis)

      REVISITING THE VASCULAR THEORY OF GLAUCOMA USING OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY (Thesis)

      Glaucoma is a chronic progressive opƟ c neuropathy resulƟ ng from the apoptosis of reƟ nal ganglion cells (RGC).1 It is characterized by typical opƟ c disc and reƟ nal nerve fi ber layer (RNFL) changes with or without visual fi eld (VF) changes. The standard tests used to assess the amount of structural (opƟ c disc and RNFL) changes in current day clinical pracƟ ce are opƟ c disc photography (Figure 1, upper panel) and opƟ cal coherence tomography (OCT, Figure 1, middle panel). OCT also images the inner reƟ nal layers at the macular region (nerve fi ...

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    10. Reflectometry and Optical Coherence Tomography for Noninvasive High Resolution Tear Film ...

      Reflectometry and Optical Coherence Tomography for Noninvasive High Resolution Tear Film ...

      The human eye is an organ that detects light from the environment and translates it into vision with the help of the brain. Eye health is critical to our daily life, such as working, reading, driving, sporting, and communicating with people. Malfunction of the eye can cause eye discomfort and clinical depressions, impair the patients’ independence, and compromise quality of life. For this reason, there is a broad range of interests in the field of eye research for better understanding of the eye that could help in early diagnosis and treatment of the prevalence eye diseases and benefit an increasing ...

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    11. Automatic optical coherence tomography imaging analysis for retinal disease screening (Thesis)

      Automatic optical coherence tomography imaging analysis for retinal disease screening (Thesis)

      The retina and the choroid are two important structures of the eye and on which the quality of eye sight depends. They have many tissue layers which are very important for monitoring the health and the progression of the eye disease from an early stage. These layers can be visualised using Optical Coherence Tomography (OCT) imaging. The abnormalities in these layers are indications of several eye diseases that can lead to blindness, such as Diabetic Macular Edema (DME), Age-related Macular Degeneration (AMD) and Glaucoma. If the retina and the choroid are damaged there is little chance to recover normal sight ...

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    12. High-speed phase-stable swept source optical coherence tomography: functional imaging and biomedical applications (Thesis)

      High-speed phase-stable swept source optical coherence tomography: functional imaging and biomedical applications (Thesis)

      In the past decades, the performance of swept source optical coherence tomography (SS-OCT) has experienced an unprecedented improvement which is mainly driven by the rapidly evolving laser technologies: the state-of-art SS-OCT is now tens of dB more sensitive, six orders of magnitude faster, and seeing ten times deeper than the original version of time domain OCT. Regardless of the abovementioned progress, the phase instability is always considered the biggest weakness of SS-OCT and the mainstream belief often states that the mechanical tuning mechanism of the swept source is to blame. In my study, I first developed a high-speed phase-stable SS-OCT ...

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    13. Ultrahigh resolution spectral domain optical coherence tomography and its functional extension for human myocardium and breast tissue imaging (Thesis)

      Ultrahigh resolution spectral domain optical coherence tomography and its functional extension for human myocardium and breast tissue imaging (Thesis)

      Over the past 25 years of development and innovation, optical coherence tomography (OCT) has successfully fills the gap between the ex vivo high-resolution optical microscopy technologies and in vivo low-resolution medical imaging modalities, including computed tomography (CT), magnetic resonance imaging (MRI), ultrasound (US). Ultrahigh resolution (UHR) OCT categorizes OCT systems with an axial resolution below 3 µm in tissue. With the improved resolution, UHR OCT may impart the knowledge of detailed structures of the tissues that are almost close to what histology may provide. This is how UHR OCT can act as a bridge between radiology and histology. This thesis ...

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    14. Biofouling investigation in membrane filtration systems using Optical Coherence Tomography (OCT) (Thesis)

      Biofouling investigation in membrane filtration systems using Optical Coherence Tomography (OCT)  (Thesis)

      Biofouling represents the main problem in membrane filtration systems. Biofouling arises when the biomass growth negatively impacts the membrane performance parameters (i.e. flux decrease and feed channel pressure drop). Most of the available techniques for characterization of biofouling involve membrane autopsies, providing information ex-situ destructively at the end of the process. OCT, is non-invasive imaging technique, able to acquire scans in-situ and non-destructively. The objective of this study was to evaluate the suitability of OCT as in-situ and non-destructive tool to gain a better understanding of biofouling behavior in membrane filtration systems. The OCT was employed to study the ...

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    15. Development of Optical Coherence Tomography Systems for Ophthalmic Imaging and Intrasurgical Guidance

      Development of Optical Coherence Tomography Systems for Ophthalmic Imaging and Intrasurgical Guidance

      Ophthalmic microsurgery is one of the most commonly performed surgical procedures in the world and it necessitates precise three-dimensional manipulation of tissue at submillimeter spatial scales. As a result, ophthalmic surgeons require an operating microscope to perform surgery and to asses alterations to the tissue. Unfortunately, modern operating microscopes provide a limited en face perspective of the three-dimensional surgical field, and surgeons must infer depth information using stereoscopy and cannot directly visualize subsurface anatomy. These limitations may compromise the surgeon’s ability to maneuver instruments axially and to comprehensively evaluate the three-dimensional tissue structure. Optical coherence tomography (OCT) is a ...

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    16. Design and Implementation of Full Field-Optical Coherence Tomography on an Olympus IX73 Microscope (Thesis)

      Design and Implementation of Full Field-Optical Coherence Tomography on an Olympus IX73 Microscope (Thesis)

      Optical Coherence Tomography (OCT) has established itself as an important imaging technology for biomedical and industrial applications. In this thesis, we describe the design and implementation of a novel Full-Field OCT optical module that is specifically designed to fit inside an Olympus IX73 inverted microscope. We describe the design, components, and implementation of this novel optical module in detail. The resulting FF-OCT setup (microscope and OCT optical module) can be used as either a Time-Domain system or a Fourier-Domain (swept-source) system, without the need for considerable changes to the OCT optical module. However, we used our FF-OCT setup to implement ...

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    17. Evaluation and Correlation of Morphological, Blood Flow and Physiological Retinal Changes in a Rat Model of Glaucoma with a Combined Optical Coherence Tomography and Electroretinography System (Thesis)

      Evaluation and Correlation of Morphological, Blood Flow and Physiological Retinal Changes in a Rat Model of Glaucoma with a Combined Optical Coherence Tomography and Electroretinography System (Thesis)

      Glaucoma is a chronic disease associated with progressive dysfunction of the retinal ganglion cells (RGC), reduction of the retinal blood flow, thinning of the retinal nerve fiber layer (RNFL) and deformation of the optical nerve head (ONH). It is the second leading cause of blindness worldwide, with an estimate of 64.3 million people between the ages of 40 to 80 years affected in 2013, 76.7 million by 2020, and 111.8 million by 2040. Currently, there is no cure for glaucoma and any clinically available pharmaceutical or surgical approaches to treating the disease can only slow its progression ...

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    18. Investigating Functional Extension of Optical Coherence Tomography for Spectroscopic Analysis of Blood Oxygen Saturation (Thesis)

      Investigating Functional Extension of Optical Coherence Tomography for Spectroscopic Analysis of Blood Oxygen Saturation (Thesis)

      Over the past two decades, optical coherence tomography (OCT) has been successfully applied to various fields of biomedical researching and clinical studies, including cardiology, urology, dermatology, dentistry, oncology, and most successfully, ophthalmology. This dissertation seeks to extend the current OCT practice, which is still largely morphology-based, into a new dimension, functional analysis of metabolic activities in vivo. More specifically, the investigation is focused on retrieving blood oxygen saturation (sO2) using intrinsic hemoglobin optical absorption contrast. Most mammalian cells rely on aerobic respiration to support cellular function, which means they consume oxygen to create adenosine triphosphate (ATP). Metabolic rate of oxygen ...

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    19. OPTICAL COHERENCE TOMOGRAPHY TO MEASURE EFFECTS OF AUTOLOGOUS MESENCHYMAL STEM CELL TRANSPLANT IN MULTIPLE SCLEROSIS PATIENTS (Thesis)

      OPTICAL COHERENCE TOMOGRAPHY TO MEASURE EFFECTS OF AUTOLOGOUS MESENCHYMAL STEM CELL TRANSPLANT IN MULTIPLE SCLEROSIS PATIENTS (Thesis)

      Anterior visual pathway disease affects >50% of multiple sclerosis (MS) patients. Optical coherence tomography (OCT) monitors MS-related retinal degeneration. Retinal nerve fiber layer (RNFL) and ganglion cell layer (GCL) thinning in MS correlates with clinical and visual disability, and brain atrophy. Mesenchymal stem cells (MSC) are immunomodulatory in MS animal models, targeting inflammatory CNS injury. A recent Cleveland Clinic phase 1 trial demonstrated feasibility/tolerability of autologous MSC transplant in MS patients. My study analyzed GCL and RNFL relationships with clinical, visual, and MRI measures, before and after MSC transplant. MSC transplant affected no differences from baseline to 6 months ...

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      Mentions: Cleveland Clinic
    20. Old and New Methods of Glaucoma Diagnosis Using Spectral-Domain Optical Coherence Tomography: Testing Limitations of Older Retinal Nerve Fiber Layer Thickness Measurements and Diagnostic Potential of Newer Retinal Volume Measurements (Thesis)

      Old and New Methods of Glaucoma Diagnosis Using Spectral-Domain Optical Coherence Tomography: Testing Limitations of Older Retinal Nerve Fiber Layer Thickness Measurements and Diagnostic Potential of Newer Retinal Volume Measurements (Thesis)

      Purpose: Optical coherence tomography (OCT) retinal nerve fiber layer (RNFL) thickness measurements are a reproducible and quantitative diagnostic modality widely used for glaucoma evaluations, but a high rate of testing artifacts limits its clinical utility. In Part I of this thesis, we aimed to characterize artifact types and assess artifact rates in two-dimensional (2D) RNFL thickness measurements obtained by the Spectralis OCT machine (Heidelberg Engineering, Heidelberg, Germany), as well as to determine patient factors and eye conditions associated with a higher artifact prevalence. In Part II of this thesis, we aimed to compare a new parameter, peripapillary retinal volume (RV ...

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    21. Development and translation of label-free functional microscopy based on optical coherence tomography (Thesis)

      Development and translation of label-free functional microscopy based on optical coherence tomography (Thesis)

      Optical coherence tomography (OCT), an imaging modality based on low coherence interferometry, can be extended to obtain various endogenous functional contrasts. This thesis focuses on the development and translation of angiographic and polarization sensitive (PS) OCT techniques for clinical and preclinical applications. This goal includes four specific aims. The first aim is to develop a clinical imaging system to image the anatomy and microvasculature of human skin. The second aim is to develop a high performance post-processing algorithm for angiographic OCT. Towards this aim, we developed a processing algorithm based on complex differential variance (CDV) and confirmed its performance by ...

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    22. Multiple Scattering Model for Optical Coherence Tomography with Rytov Approximation (Thesis)

      Multiple Scattering Model for Optical Coherence Tomography with Rytov Approximation (Thesis)

      Optical Coherence Tomography (OCT) is a coherence-gated, micrometer-resolution imaging technique that focuses a broadband near-infrared laser beam to penetrate into optical scattering media, e.g. biological tissues. The OCT resolution is split into two parts, with the axial resolution defined by half the coherence length, and the depth-dependent lateral resolution determined by the beam geometry, which is well described by a Gaussian beam model. The depth dependence of lateral resolution directly results in the defocusing effect outside the confocal region and restricts current OCT probes to small numerical aperture (NA) at the expense of lateral resolution near the focus. Another ...

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    23. Scalable Parallel Optimization of Digital Signal Processing in the Fourier Domain (Thesis)

      Scalable Parallel Optimization of Digital Signal Processing in the Fourier Domain (Thesis)

      The aim of the research presented in this thesis is to study different approaches to the parallel optimization of digital signal processing algorithms and optical coherence tomography methods. The parallel approaches are based on multithreading for multi-core and many-core architectures. The thesis follows the process of designing and implementing the parallel algorithms and programs and their integration into optical coherence tomography systems. Evaluations of the performance and the scalability of the proposed parallel solutions are presented. The digital signal processing considered in this thesis is divided into two groups. The first one includes generally employed algorithms operating with digital signals ...

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    24. Reflectometry and Optical Coherence Tomography for Non-invasive High Resolution Tear Film Thickness Evaluation and Ophthalmic Imaging (Thesis)

      Reflectometry and Optical Coherence Tomography for Non-invasive High Resolution Tear Film Thickness Evaluation and Ophthalmic Imaging (Thesis)

      Dry eye debilitates the patients physically, limit their ability to perform daily tasks, cause clinical depression, and compromise quality of life. Accurate diagnosis of the dry eye and the research on the pathological mechanism and treatment both depend largely on the available measurement techniques. The development of new measurement techniques helps better understanding of the disease and paves the way for accurate early diagnosis and better treatment. The purpose of this study was to develop additional tools in ophthalmic study for non-invasive high resolution tear film thickness evaluation and eye imaging. Optical coherence tomography (OCT) is a non-invasive imaging technology ...

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