1. Articles in category: Student Theses

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    1. Evaluation of Transfer Learning for Classification of: (1) Diabetic Retinopathy by Digital Fundus Photography and (2) Diabetic Macular Edema, Choroidal Neovascularization and Drusen by Optical Coherence Tomography (Thesis)

      Evaluation of Transfer Learning for Classification of: (1) Diabetic Retinopathy by Digital Fundus Photography and (2) Diabetic Macular Edema, Choroidal Neovascularization and Drusen by Optical Coherence Tomography (Thesis)

      Deep learning has been successfully applied to a variety of image classification tasks. In the last few years, starting with the ground-breaking results of AlexNet at the ImageNet Large Scale Visual Recognition Challenge (ILSVRC), there has been tremendous and rapid growth in deep learning and its potential applications. There has been keen interest to apply deep learning in the medical domain, particularly specialties that heavily utilize imaging, such as dermatology, pathology, radiology, and ophthalmology. One issue that may hinder application of deep learning to the medical domain is the vast amount of data necessary to train deep neural networks (DNNs ...

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    2. Share your OCT Thesis on OCT News

      Share your OCT Thesis on OCT News

      OCT News is seeking links to bachelors, masters, and PhD theses in the area of "Optical Coherence Tomography". Traditionally student theses contain a great wealth of information but are rarely accessible to the OCT community. If you or someone you know wrote an OCT thesis and would like to share it with the community please submit a link or PDF using the "Contact OCT News" tab in the main menu bar or the feedback link in the footer and we will include it here: Student Theses. Thesis will only be included if the link is free of charge to users.

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    3. Software Implementation of a Combined Fluorescence and Swept Source Optical Coherence Tomography Imaging System (Thesis)

      Software Implementation of a Combined Fluorescence and Swept Source Optical Coherence Tomography Imaging System (Thesis)

      This paper serves as a detailed overview of the software developed for the Falloposcope endoscope being developed by the Jennifer Barton Optics Tissue Laboratory. The Falloposcope is designed for a screening procedure for early detection of ovarian cancer in the fallopian tubes. The software controls a charge-coupled device (CCD) camera to perform reflectance and fluorescence imaging, which serves to navigate the endoscope to the fallopian tubes and surveil suspicious tissue regions. It also controls a swept source optical coherence tomography (SS-OCT) imaging system to provide high resolution, cross-sectional tomographic images of these tissue regions. CCD imaging is performed using a ...

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    4. Development of Multimodal Optical System Guided by Optical Coherence Tomography (Thesis)

      Development of Multimodal Optical System Guided by Optical Coherence Tomography (Thesis)

      The goal of this dissertation is to develop multimodal light scattering techniques using optical coherence tomography (OCT) to improve clinical diagnosis. OCT is a noninvasive optical imaging technique that utilizes low coherence interferometry to detect reflected and scattered light from a sample to produce depth resolved images. OCT is an emerging technology for a wide range of biomedical applications, with its largest impact in the field of ophthalmology to assess retinal morphology and abnormalities. Due to its excellent axial resolution, OCT has been often jointly used with a variety of other optical techniques in multimodal platforms for enhanced characterization of ...

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      Mentions: Duke University
    5. Optical Coherence Tomography of the Retina in Schizophrenia: Relationships with Visual and Perceptual Function (Thesis)

      Optical Coherence Tomography of the Retina in Schizophrenia: Relationships with Visual and Perceptual Function (Thesis)

      Background: Visual perceptual impairments are well established in schizophrenia, ranging from deficits in basic visual discrimination to abnormalities in higher-level visual integration. Recent research has identified thinning o f retinal layers in individuals with schizophrenia, which may contribute to visual dysfunction. This study utilized optical coherence tomography to examine retinal integrity in individuals with schizophrenia, and investigated the contributions of retinal structure to low- and higher-level visual functions in schizophrenia. Methods: Participants were 12. individuals with schizophrenia-spectrum disorders and 12 age-matched healthy controls. Optical coherence tomography was utilized to obtain measurements for the retinal nerve fiber layer (RNFL), ganglion cell ...

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    6. Development of cellular resolution optical coherence tomography (Thesis)

      Development of cellular resolution optical coherence tomography (Thesis)

      Diagnosis of most mucosal diseases including epithelial cancers relies on white-light endoscopy/visual inspection followed by random biopsy and histologic examination. These current standard-of-care tools are associated with many issues such as sampling errors, tissue destruction, and processing artifacts. In addition, it is too traumatic to take a biopsy from tissues like eyes and coronary arteries. Being high resolution, high speed, and non-invasive, optical coherence tomography (OCT) has emerged as an endoscopic and intravascular imaging tool that provides valuable anatomic information complementary to the standard-of-care techniques. However, it has a typical resolution of 10 μm, which is too coarse to ...

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    7. Supercontinuum in the practice of Optical Coherence Tomography with emphasis on noise effects (Thesis)

      Supercontinuum in the practice of Optical Coherence Tomography with emphasis on noise effects (Thesis)

      Optical Coherence Tomography (OCT) is an imaging modality which has proven, since the early 1990s, its incredible potential. Nowadays, numerous fields of medical investigation, such as Ophthalmology, Dermatology or Cardiovascular imaging, would not be the same without the diagnostic tools bring by OCT. This tremendous development has been supported by industry support through improvement of dedicated components such as lasers, cameras and optics. A great example of this development is the evolution of Supercontinuum (SC) sources. Due to the extremely broad spectrum cover by SC sources, their high power density and high spatial coherence, it seems obvious to use them ...

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    8. Hyperspectral Imaging Using Visible-Light Optical Coherence Tomography (HIS-OCT) for Retina Imaging and Oximetry (Thesis)

      Hyperspectral Imaging Using Visible-Light Optical Coherence Tomography (HIS-OCT) for Retina Imaging and Oximetry (Thesis)

      Optical coherence tomography (OCT) is a diverse imaging modality that has been used to image the retina and diagnose various eye related disease due to its high resolution, fast acquisition speeds, and non-invasive properties [1] [2] [3] [4]. OCT has been increasingly used in a clinical setting since it was first introduced in 1991 [2] [5]; since that time, OCT has been able to improve how we diagnose and view eye maladies such as macular holes and macular pucker [5] [6], macular edema [7], age related macular degeneration [8], glaucoma [9], vitreous traction [10], and diabetic retinopathy (DR) [11]. Throughout ...

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      Mentions: UC Riverside
    9. From sample structure to optical properties and back : A theoretical framework for quantitative OCT and its clinical application (Thesis)

      From sample structure to optical properties and back : A theoretical framework for quantitative OCT and its clinical application (Thesis)

      The aim of this thesis is to provide a methodology to extract quantitative parameters from optical coherence tomography (OCT) images and to relate these parameters to sample properties such as structure, organization and flow. OCT uses near-infrared light to acquire 3D images of biological tissue, with a resolution around 5-15 μm and an imaging depth of approximately 2 mm. OCT can be a useful clinical tool for minimally-invasive, high-resolution imaging of tissue structures and morphology. In addition to morphological imaging, quantification of scattering properties from OCT images is a potential complementary source of information on microscopic tissue properties, which can ...

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    10. Investigating the reliability and clinical utility of minimally invasive portable electroretinography and optical coherence tomography techniques in children undergoing vigabatrin therapy (Thesis)

      Investigating the reliability and clinical utility of minimally invasive portable electroretinography and optical coherence tomography techniques in children undergoing vigabatrin therapy (Thesis)

      The antiepileptic drug for Infantile Spasms – vigabatrin, has been associated with retinal toxicity in over one third of children treated. Young and non-verbal children cannot cooperate with conventional adult-oriented monitoring devices, therefore a safe and reliable technique to monitor for vigabatrin retinal toxicity is missing. This study evaluated the tolerability, reliability and clinical feasibility of two alternative, handheld systems for assessment of retinal function: the RETeval ERG and Envisu OCT. We found that non-sedated children showed poor tolerability on the RETeval ERG. Under sedation the same children showed high tolerability on the handheld OCT. Responses from both techniques demonstrated good ...

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    11. A flow cytometric and optical coherence analysis of the role of microparticles as determinants of plaque instability in acute coronary syndrome (FOAM study) (Thesis)

      A flow cytometric and optical coherence analysis of the role of microparticles as determinants of plaque instability in acute coronary syndrome (FOAM study) (Thesis)

      Introduction: Microparticles (MPs) are implicated in the pathogenesis of coronary artery disease (CAD). / Aims: To determine whether circulating MPs correlate with high-risk coronary atherosclerotic plaque phenotype. / Methods: 25 patients with CAD undergoing percutaneous coronary intervention (PCI) were recruited; 13 were diagnosed to have acute coronary syndrome (ACS) & 12 with stable angina (SA). We characterized and compared coronary atherosclerotic plaque burden and vulnerable plaque phenotype by three-vessel optical coherence tomography (OCT) between ACS and SA groups. Endothelial (EMPs), platelet (PMPs), Neutrophil (NMPs), tissue factor (TFMPs) and smooth muscle (SMMPs) were quantified by flow cytometry, compared between groups pre PCI, post PCI ...

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    12. Fast simulation of finite-beam optical coherence tomography of inhomogeneous turbid media (Thesis)

      Fast simulation of finite-beam optical coherence tomography of inhomogeneous turbid media (Thesis)

      We developed a fast simulator of finite-beam optical coherence tomography (OCT) of inhomogeneous turbid media. Our Sequential Monte Carlo (MC) based finite beam OCT simulator can reach more than a hundred times faster than one that represents a finite OCT’s incident beam as a superposition of infinitely thin beams, i.e., a superposition-based MC simulator. In this thesis, first, we highlight the lesser-known correspondence between the commonly used MC simulation of light in turbid media, and Sequential MC based solution of the Radiative Transfer Equation (RTE). Second, we describe the implementation of our simulator of finite-beam OCT as a ...

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    13. Clinical Applications of Angiographic Optical Coherence Tomography (Thesis)

      Clinical Applications of Angiographic Optical Coherence Tomography (Thesis)

      Angiographic optical coherence tomography (OCTA) has rapidly found utility within many facets of medical research. Here OCTA algorithms are enabled on a commercial OCT system and verified through correlation with intra-vital light microscopy (IVM). While the vast majority of vessels were accurately measured, smaller vessels (<30µm) have a tendency to appear dilated in comparison to IVM. The technique was also expanded upon to facilitate the imaging of subcutaneous murine fibrosarcoma tumours, negating the requirement for an intra-vital window. It was found that vessel measurement sensitivity was sufficiently high such that the morphologies of vessels within tumours expressing unique vascular ...

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    14. Fusion of X-ray angiography and optical coherence tomography for coronary flow simulation

      Fusion of X-ray angiography and optical coherence tomography for coronary flow simulation

      In conclusion, this thesis proposes a new approach for reconstruction of coronary artery and the implanted BRS by fusion of OCT and X-ray angiography to analyze intracoronary ESS in vivo. The studies conducted in this thesis demonstrate the feasibility of the proposed approach to analyze the detailed local coronary hemodynamics in patients, including the SS patterns after BRS implantation in coronary bifurcations. We observed that in vivo assessment of ESS was closely related to: (1) reconstruction of the side branches; (2) reconstruction of the BRS; (3) patient-specific flow; (4) post-processing portion size in which ESS was calculated. Based on these ...

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    15. 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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    16. 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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    17. 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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    18. 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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    19. 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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    20. 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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    21. 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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    22. 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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    23. 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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    24. 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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