Automated retinal layer segmentation and pre-apoptotic monitoring for three-dimensional optical coherence tomography

The aim of this PhD thesis was to develop segmentation algorithm adapted and optimized to retinal OCT data that will provide objective 3D layer thickness which might be used to improve diagnosis and monitoring of retinal pathologies. Additionally, a 3D stack registration method was produced by modifying an existing algorithm. A related project was to develop a pre-apoptotic retinal monitoring based on the changes in texture parameters of the OCT scans in order to enable treatment before the changes become irreversible; apoptosis refers to the programmed cell death that can occur in retinal tissue and lead to blindness. These issues can be critical for the examination of tissues within the central nervous system. A novel statistical model for segmentation has been created and successfully applied to a large data set. A broad range of future research possibilities into advanced pathologies has been created by the results obtained. A separate model has been created for choroid segmentation located deep in retina, as the appearance of choroid is very different from the top retinal layers. Choroid thickness and structure is an important index of various pathologies (diabetes etc.). As part of the pre-apoptotic monitoring project it was shown that an increase in proportion of apoptotic cells in vitro can be accurately quantified. Moreover, the data obtained indicates a similar increase in neuronal scatter in retinal explants following axotomy (removal of retinas from the eye), suggesting that UHR-OCT can be a novel non-invasive technique for the in vivo assessment of neuronal health. Additionally, an independent project within the computer science department in collaboration with the school of psychology has been successfully carried out, improving analysis of facial dynamics and behaviour transfer between individuals. Also, important improvements to a general signal processing algorithm, dynamic time warping (DTW), have been made, allowing potential application in a broad signal processing field.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Automated retinal layer segmentation and pre-apoptotic monitoring for three-dimensional optical coherence tomography

The aim of this PhD thesis was to develop segmentation algorithm adapted and optimized to retinal OCT data that will provide objective 3D layer thickness which might be used to improve diagnosis and monitoring of retinal pathologies. Additionally, a 3D stack registration method was produced by modifying an existing algorithm. A related project was to develop a pre-apoptotic retinal monitoring based on the changes in texture parameters of the OCT scans in order to enable treatment before the changes become irreversible; apoptosis refers to the programmed cell death that can occur in retinal tissue and lead to blindness. These issues can be critical for the examination of tissues within the central nervous system. A novel statistical model for segmentation has been created and successfully applied to a large data set. A broad range of future research possibilities into advanced pathologies has been created by the results obtained. A separate model has been created for choroid segmentation located deep in retina, as the appearance of choroid is very different from the top retinal layers. Choroid thickness and structure is an important index of various pathologies (diabetes etc.). As part of the pre-apoptotic monitoring project it was shown that an increase in proportion of apoptotic cells in vitro can be accurately quantified. Moreover, the data obtained indicates a similar increase in neuronal scatter in retinal explants following axotomy (removal of retinas from the eye), suggesting that UHR-OCT can be a novel non-invasive technique for the in vivo assessment of neuronal health. Additionally, an independent project within the computer science department in collaboration with the school of psychology has been successfully carried out, improving analysis of facial dynamics and behaviour transfer between individuals. Also, important improvements to a general signal processing algorithm, dynamic time warping (DTW), have been made, allowing potential application in a broad signal processing field

Surface Denoising based on The Variation of Normals and Retinal Shape Analysis

Through the development of this thesis, starting from the curvature tensor, we have been able to understand the variation of tangent vectors to define a shape analysis operator and also a relationship between the classical shape operator and the curvature tensor on a triangular surface. In continuation, the first part of the thesis analyzed the variation of surface normals and introduced a shape analysis operator, which is further used for mesh and point set denoising. In the second part of the thesis, mathematical modeling and shape quantification algorithms are introduced for retinal shape analysis. In the first half, this thesis followed the concept of the variation of surface normals, which is termed as the normal voting tensor and derived a relation between the shape operator and the normal voting tensor. The concept of the directional and the mean curvatures is extended on the dual representation of a triangulated surface. A normal voting tensor is defined on each triangle of a geometry and termed as the element-based normal voting tensor (ENVT). Later, a deformation tensor is extracted from the ENVT and it consists of the anisotropy of a surface and the mean curvature vector is defined based on the ENVT deformation tensor. The ENVT-based mesh denoising algorithm is introduced, where the ENVT is used as a shape operator. A binary optimization technique is applied on the spectral components of the ENVT that helps the algorithm to retain sharp features in the concerned geometry and improves the convergence rate of the algorithm. Later, a stochastic analysis of the effect of noise on the triangular mesh based on the minimum edge length of the elements in the geometry is explained. It gives an upper bound to the noise standard deviation to have minimum probability for flipped element normals. The ENVT-based mesh denoising concept is extended for a point set denoising, where noisy vertex normals are filtered using the vertex-based NVT and the binary optimization. For vertex update stage in point set denoising, we added different constraints to the quadratic error metric based on features (edges and corners) or non-feature (planar) points. This thesis also investigated a robust statistics framework for face normal bilateral filtering and proposed a robust and high fidelity two-stage mesh denoising method using Tukey’s bi-weight function as a robust estimator, which stops the diffusion at sharp features and produces smooth umbilical regions. This algorithm introduced a novel vertex update scheme, which uses a differential coordinate-based Laplace operator along with an edge-face normal orthogonality constraint to produce a high-quality mesh without face normal flips and it also makes the algorithm more robust against high-intensity noise. The second half of thesis focused on the application of the proposed geometric processing algorithms on the OCT (optical coherence tomography) scan data for quantification of the human retinal shape. The retina is a part of the central nervous system and comprises a similar cellular composition as the brain. Therefore, many neurological disorders affect the retinal shape and these neuroinflammatory conditions are known to cause modifications to two important regions of the retina: the fovea and the optical nerve head (ONH). This thesis consists of an accurate and robust shape modeling of these regions to diagnose several neurological disorders by detecting the shape changes. For the fovea, a parametric modeling algorithm is introduced using Cubic Bezier and this algorithm derives several 3D shape parameters, which quantify the foveal shape with high accuracy. For the ONH, a 3D shape analysis algorithm is introduced to measure the shape variation regarding different neurological disorders. The proposed algorithm uses triangulated manifold surfaces of two different layers of the retina to derive several 3D shape parameters. The experimental results of the fovea and the ONH morphometry confirmed that these algorithms can provide an aid to diagnose several neurological disorders

Topics in Adaptive Optics

Advances in adaptive optics technology and applications move forward at a rapid pace. The basic idea of wavefront compensation in real-time has been around since the mid 1970s. The first widely used application of adaptive optics was for compensating atmospheric turbulence effects in astronomical imaging and laser beam propagation. While some topics have been researched and reported for years, even decades, new applications and advances in the supporting technologies occur almost daily. This book brings together 11 original chapters related to adaptive optics, written by an international group of invited authors. Topics include atmospheric turbulence characterization, astronomy with large telescopes, image post-processing, high power laser distortion compensation, adaptive optics and the human eye, wavefront sensors, and deformable mirrors

Functional and structural organisation of the visual system in human albinism

Albinism is a developmental disorder which involves the misrouting of optic nerve projections, leading to an abnormally organised visual system. Despite the aberrant input, people with albinism have relatively normal vision and experience the world in much the same way as their peers. This thesis explores the functional and structural organisation of visual cortex in human albinism using magnetic resonance imaging (MRI) techniques. This thesis covers four main experiments. Experiment 1 deals with stimulus optimisation for population receptive field (pRF) mapping in healthy adults. pRF mapping is a functional MRI technique for estimating cortical receptive field characteristics non-invasively. In this experiment, a stimulus configuration optimized for short acquisition time requirements is presented and implemented in subsequent experiments. Experiment 2 combines the pRF approach for retinotopic localization with diffusion MRI tractography in healthy adults to show evidence for direct extrastriate connections of the human optic radiation. The optic radiation is the principal white matter pathway for relaying retinal input to visual cortex, and typically considered a projection to primary visual cortex. In this experiment, independent pathways of the optic radiation to visual areas V2 and V3 are identified, and functional-structural methodologies developed for Experiment 4. Experiment 3 investigates the functional organisation of visual cortex in participants with albinism. A pRF mapping approach was implemented, identifying abnormal retinotopic organisation and altered receptive field properties in extrastriate visual cortex. In addition, we explore evidence for and against a dual receptive field model of visual field representation in albinism. Experiment 4 examines the structural and functional connectivity of early visual system in human albinism. In particular, differences in white matter microstructure and inter- hemispheric visual map connectivity are found between participants with albinism and a cohort of healthy controls. This thesis highlights the capacity and limitations of developmental plasticity in human albinism

Object Recognition

Vision-based object recognition tasks are very familiar in our everyday activities, such as driving our car in the correct lane. We do these tasks effortlessly in real-time. In the last decades, with the advancement of computer technology, researchers and application developers are trying to mimic the human's capability of visually recognising. Such capability will allow machine to free human from boring or dangerous jobs

Visual Cortex

The neurosciences have experienced tremendous and wonderful progress in many areas, and the spectrum encompassing the neurosciences is expansive. Suffice it to mention a few classical fields: electrophysiology, genetics, physics, computer sciences, and more recently, social and marketing neurosciences. Of course, this large growth resulted in the production of many books. Perhaps the visual system and the visual cortex were in the vanguard because most animals do not produce their own light and offer thus the invaluable advantage of allowing investigators to conduct experiments in full control of the stimulus. In addition, the fascinating evolution of scientific techniques, the immense productivity of recent research, and the ensuing literature make it virtually impossible to publish in a single volume all worthwhile work accomplished throughout the scientific world. The days when a single individual, as Diderot, could undertake the production of an encyclopedia are gone forever. Indeed most approaches to studying the nervous system are valid and neuroscientists produce an almost astronomical number of interesting data accompanied by extremely worthy hypotheses which in turn generate new ventures in search of brain functions. Yet, it is fully justified to make an encore and to publish a book dedicated to visual cortex and beyond. Many reasons validate a book assembling chapters written by active researchers. Each has the opportunity to bind together data and explore original ideas whose fate will not fall into the hands of uncompromising reviewers of traditional journals. This book focuses on the cerebral cortex with a large emphasis on vision. Yet it offers the reader diverse approaches employed to investigate the brain, for instance, computer simulation, cellular responses, or rivalry between various targets and goal directed actions. This volume thus covers a large spectrum of research even though it is impossible to include all topics in the extremely diverse field of neurosciences

Quarterly literature review of the remote sensing of natural resources

The Technology Application Center reviewed abstracted literature sources, and selected document data and data gathering techniques which were performed or obtained remotely from space, aircraft or groundbased stations. All of the documentation was related to remote sensing sensors or the remote sensing of the natural resources. Sensors were primarily those operating within the 10 to the minus 8 power to 1 meter wavelength band. Included are NASA Tech Briefs, ARAC Industrial Applications Reports, U.S. Navy Technical Reports, U.S. Patent reports, and other technical articles and reports

Novel photoreceptor cells, pupillometry and electrodiagnosis in orbital, vitreo-retinal and refractive disorders

Imperial Users onl

Autocalibrating vision guided navigation of unmanned air vehicles via tactical monocular cameras in GPS denied environments

This thesis presents a novel robotic navigation strategy by using a conventional tactical monocular camera, proving the feasibility of using a monocular camera as the sole proximity sensing, object avoidance, mapping, and path-planning mechanism to fly and navigate small to medium scale unmanned rotary-wing aircraft in an autonomous manner. The range measurement strategy is scalable, self-calibrating, indoor-outdoor capable, and has been biologically inspired by the key adaptive mechanisms for depth perception and pattern recognition found in humans and intelligent animals (particularly bats), designed to assume operations in previously unknown, GPS-denied environments. It proposes novel electronics, aircraft, aircraft systems, systems, and procedures and algorithms that come together to form airborne systems which measure absolute ranges from a monocular camera via passive photometry, mimicking that of a human-pilot like judgement. The research is intended to bridge the gap between practical GPS coverage and precision localization and mapping problem in a small aircraft. In the context of this study, several robotic platforms, airborne and ground alike, have been developed, some of which have been integrated in real-life field trials, for experimental validation. Albeit the emphasis on miniature robotic aircraft this research has been tested and found compatible with tactical vests and helmets, and it can be used to augment the reliability of many other types of proximity sensors