1. Articles in category: Student Theses

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    1. Assessment and Diagnosis of Human Ovarian and Colorectal Cancer using Optical and Photoacoustic Imaging (Thesis)

      Assessment and Diagnosis of Human Ovarian and Colorectal Cancer using Optical and Photoacoustic Imaging (Thesis)

      Optical imaging modalities have the advantage of high resolution, label free, rapid, low cost imaging for both in vivo and ex vivo diagnosis of biological tissues. Optical scattering, which is the main contrast of optical coherence tomography (OCT), is related to elastic scattering components, mainly stromal collagen. Tissue elasticity has recently emerged as an important diagnostic parameter associated with tumor development and progression and is also related to the distribution of structural components such as tissue collagen. We have used an optical coherence tomography elastography (OCTE) system for characterizing the differences in the micro-mechanical properties of benign and malignant human ...

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    2. OPTICAL COHERENCE TOMOGRAPHY FOR CORONARY ARTERY DISEASE (Thesis)

      OPTICAL COHERENCE TOMOGRAPHY FOR CORONARY ARTERY DISEASE (Thesis)

      The aim of this thesis was to develop a software pipeline for tissue analysis in IVOCT by systematically addressing different open questions for analysis. In Chapter 2, we report on a first attempt to quantify the correlation between the position of the catheter with respect to the luminal wall and the image intensities. We implemented the Depth-Resolved (DR) model for IVOCT images in Chapter 3. In addition to the attenuation coefficient, we further extended the model to estimate a backscatter term, and proposed an algorithm to exclude the noisy region. For the first time, it was implemented in IVOCT images ...

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    3. Characterisation of textured surfaces under a laminar flow by Optical Coherence Tomography (Thesis)

      Characterisation of textured surfaces under a laminar flow by Optical Coherence Tomography (Thesis)

      Textured surfaces are present everywhere in nature and in our daily life, interacting constantly with a flow. In this report, we focus on how a textured surface with pillars responds to a laminar flow inside a confined channel. The study is mainly focused on the measurements of the bending of the pillars and of the velocity field, using optical coherence tomography. The potential of this technique, which is not very common in microfluidics, is explored here to characterise our system and its limits are discussed. The measurements of the bending and of the velocity field allow to get the value ...

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    4. Automated Segmentation of Retinal Optical Coherence Tomography Images (Thesis)

      Automated Segmentation of Retinal Optical Coherence Tomography Images (Thesis)

      Aim Optical Coherence Tomography (OCT) is a fast and non-invasive medical imaging technique which helps in the investigation of each individual retinal layer structure. For early detection of retinal diseases and the study of their progression, segmentation of the OCT images into the distinct layers of the retina plays a crucial role. However, segmentation done by the clinicians manually is extremely tedious, time-consuming and variable with respect to the expertise level. Hence, there is an utmost necessity to develop an automated segmentation algorithm for retinal OCT images which is fast, accurate, and eases clinical decision making. Methods Graph-theoretical methods have ...

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    5. Developing algorithms for the analysis of retinal Optical Coherence Tomography images (Thesis)

      Developing algorithms for the analysis of retinal Optical Coherence Tomography images (Thesis)

      Vision loss, with a prevalence loss greater than 42 million in the United States is one of the major challenges of today's health-care industry and medical science. Early detection of different retinal-related diseases will dramatically reduce the risk of vision loss. Optical Coherence Tomography (OCT) is a relatively new imaging technique which is of great importance in the identification of ocular and especially retinal diseases. Thus, the efficient analysis of OCT images provides several advantages. In this thesis, we propose a series of image processing and machine learning techniques for the automated analysis of OCT images. The proposed methodology ...

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    6. Automated Glaucoma Detection using Retinal Layers Segmentation and Optic Cup to Disc Ratio in OCT Images (Thesis)

      Automated Glaucoma Detection using Retinal Layers Segmentation and Optic Cup to Disc Ratio in OCT Images (Thesis)

      Glaucoma is an eye problem that affects the retina and weakens the nerve cells that assist in visual recognition. This disease can be the cause of blindness and visual impairments if not treated in time. Increase in Intraocular pressure (IOP) is the main cause for glaucoma presence and succession. The diameter of the optic cup within optic disc region is increased due to the excessive retinal pressure. Cup to disc ratio (CDR) is the mainly used clinical feature to diagnose glaucoma. The increment in CDR is the main factor to classify glaucoma patients. This causes the retina to be affected ...

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    7. 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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    8. 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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    9. 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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    10. 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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    11. 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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    12. 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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    13. 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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    14. 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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    15. 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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    16. 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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    17. 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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    18. 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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    19. 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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    20. 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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    21. 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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    22. 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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    23. 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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    24. 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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