Contour Based 3D Biological Image Reconstruction and Partial Retrieval

Image segmentation is one of the most difficult tasks in image processing. Segmentation algorithms are generally based on searching a region where pixels share similar gray level intensity and satisfy a set of defined criteria. However, the segmented region cannot be used directly for partial image retrieval. In this dissertation, a Contour Based Image Structure (CBIS) model is introduced. In this model, images are divided into several objects defined by their bounding contours. The bounding contour structure allows individual object extraction, and partial object matching and retrieval from a standard CBIS image structure. The CBIS model allows the representation of 3D objects by their bounding contours which is suitable for parallel implementation particularly when extracting contour features and matching them for 3D images require heavy computations. This computational burden becomes worse for images with high resolution and large contour density. In this essence we designed two parallel algorithms; Contour Parallelization Algorithm (CPA) and Partial Retrieval Parallelization Algorithm (PRPA). Both algorithms have considerably improved the performance of CBIS for both contour shape matching as well as partial image retrieval. To improve the effectiveness of CBIS in segmenting images with inhomogeneous backgrounds we used the phase congruency invariant features of Fourier transform components to highlight boundaries of objects prior to extracting their contours. The contour matching process has also been improved by constructing a fuzzy contour matching system that allows unbiased matching decisions. Further improvements have been achieved through the use of a contour tailored Fourier descriptor to make translation and rotation invariance. It is proved to be suitable for general contour shape matching where translation, rotation, and scaling invariance are required. For those images which are hard to be classified by object contours such as bacterial images, we define a multi-level cosine transform to extract their texture features for image classification. The low frequency Discrete Cosine Transform coefficients and Zenike moments derived from images are trained by Support Vector Machine (SVM) to generate multiple classifiers

Grounding semantics in robots for Visual Question Answering

In this thesis I describe an operational implementation of an object detection and description system that incorporates in an end-to-end Visual Question Answering system and evaluated it on two visual question answering datasets for compositional language and elementary visual reasoning

Methods for Analysing Endothelial Cell Shape and Behaviour in Relation to the Focal Nature of Atherosclerosis

The aim of this thesis is to develop automated methods for the analysis of the spatial patterns, and the functional behaviour of endothelial cells, viewed under microscopy, with applications to the understanding of atherosclerosis. Initially, a radial search approach to segmentation was attempted in order to trace the cell and nuclei boundaries using a maximum likelihood algorithm; it was found inadequate to detect the weak cell boundaries present in the available data. A parametric cell shape model was then introduced to fit an equivalent ellipse to the cell boundary by matching phase-invariant orientation fields of the image and a candidate cell shape. This approach succeeded on good quality images, but failed on images with weak cell boundaries. Finally, a support vector machines based method, relying on a rich set of visual features, and a small but high quality training dataset, was found to work well on large numbers of cells even in the presence of strong intensity variations and imaging noise. Using the segmentation results, several standard shear-stress dependent parameters of cell morphology were studied, and evidence for similar behaviour in some cell shape parameters was obtained in in-vivo cells and their nuclei. Nuclear and cell orientations around immature and mature aortas were broadly similar, suggesting that the pattern of flow direction near the wall stayed approximately constant with age. The relation was less strong for the cell and nuclear length-to-width ratios. Two novel shape analysis approaches were attempted to find other properties of cell shape which could be used to annotate or characterise patterns, since a wide variability in cell and nuclear shapes was observed which did not appear to fit the standard parameterisations. Although no firm conclusions can yet be drawn, the work lays the foundation for future studies of cell morphology. To draw inferences about patterns in the functional response of cells to flow, which may play a role in the progression of disease, single-cell analysis was performed using calcium sensitive florescence probes. Calcium transient rates were found to change with flow, but more importantly, local patterns of synchronisation in multi-cellular groups were discernable and appear to change with flow. The patterns suggest a new functional mechanism in flow-mediation of cell-cell calcium signalling

Weak lensing cosmology with convolutional neural networks on noisy data

Weak gravitational lensing is one of the most promising cosmological probes of the late universe. Several large ongoing (DES, KiDS, HSC) and planned (LSST, EUCLID, WFIRST) astronomical surveys attempt to collect even deeper and larger scale data on weak lensing. Due to gravitational collapse, the distribution of dark matter is non-Gaussian on small scales. However, observations are typically evaluated through the two-point correlation function of galaxy shear, which does not capture non-Gaussian features of the lensing maps. Previous studies attempted to extract non-Gaussian information from weak lensing observations through several higher-order statistics such as the three-point correlation function, peak counts or Minkowski-functionals. Deep convolutional neural networks (CNN) emerged in the field of computer vision with tremendous success, and they offer a new and very promising framework to extract information from 2 or 3-dimensional astronomical data sets, confirmed by recent studies on weak lensing. We show that a CNN is able to yield significantly stricter constraints of ($\sigma_8, \Omega_m$) cosmological parameters than the power spectrum using convergence maps generated by full N-body simulations and ray-tracing, at angular scales and shape noise levels relevant for future observations. In a scenario mimicking LSST or Euclid, the CNN yields 2.4-2.8 times smaller credible contours than the power spectrum, and 3.5-4.2 times smaller at noise levels corresponding to a deep space survey such as WFIRST. We also show that at shape noise levels achievable in future space surveys the CNN yields 1.4-2.1 times smaller contours than peak counts, a higher-order statistic capable of extracting non-Gaussian information from weak lensing maps

تمثيل الإطار الخارجي للكلمات العربية بكفاءة من خلال الدمج بين نموذج الكنتور النشط وتحديد ونقاط الزوايا

Graphical curves and surfaces fitting are hot areas of research studies and application, such as artistic applications, analysis applications and encoding purposes. Outline capture of digital word images is important in most of the desktop publishing systems. The shapes of the characters are stored in the computer memory in terms of their outlines, and the outlines are expressed as Bezier curves. Existing methods for Arabic font outline description suffer from low fitting accuracy and efficiency. In our research, we developed a new method for outlining shapes using Bezier curves with minimal set of curve points. A distinguishing characteristic of our method is that it combines the active contour method (snake) with corner detection to achieve an initial set of points that is as close to the shape's boundaries as possible. The method links these points (snake + corner) into a compound Bezier curve, and iteratively improves the fitting of the curve over the actual boundaries of the shape. We implemented and tested our method using MATLAB. Test cases included various levels of shape complexity varying from simple, moderate, and high complexity depending on factors, such as: boundary concavities, number of corners. Results show that our method achieved average 86% of accuracy when measured relative to true shape boundary. When compared to other similar methods (Masood & Sarfraz, 2009; Sarfraz & Khan, 2002; Ferdous A Sohel, Karmakar, Dooley, & Bennamoun, 2010), our method performed comparatively well. Keywords: Bezier curves, shape descriptor, curvature, corner points, control points, Active Contour Model.تعتبر المنحنيات والأسطح الرسومية موضوعاً هاماً في الدراسات البحثية وفي التطبيقات البرمجية مثل التطبيقات الفنية، وتطبيقات تحليل وترميز البيانات. ويعتبر تخطيط الحدود الخارجية للكلمات عملية أساسية في غالبية تطبيقات النشر المكتبي. في هذه التطبيقات تخزن أشكال الأحرف في الذاكرة من حيث خطوطها الخارجية، وتمثل الخطوط الخارجية على هيئة منحنيات Bezier. الطرق المستخدمة حالياً لتحديد الخطوط الخارجية للكلمات العربية تنقصها دقة وكفاءة الملاءمة ما بين الحدود الحقيقية والمنحنى الرسومي الذي تقوم بتشكيله. في هذا البحث قمنا بتطوير طريقة جديدة لتخطيط الحدود الخارجية للكلمات تعتمد على منحنيات Bezier بمجموعة أقل من المنحنيات الجزئية. تتميز طريقتنا بخاصية مميزة وهي الدمج بين آلية لاستشعار الزوايا مع آلية نموذج الكنتور النشط (الأفعى). يتم الدمج بين نقاط الزوايا ونقاط الأفعى لتشكيل مجموعة موحدة من النقاط المبدئية قريبة قدر الإمكان من الحدود الحقيقية للشكل المراد تحديده. يتشكل منحنى Bezier من هذه المجموعة المدمجة، وتتم عملية تدريجية على دورات لملاءمة المنحنى على الحدود الحقيقية للشكل. قام الباحث بتنفيذ وتجربة الطريقة الجديدة باستخدام برنامج MATLAB. وتم اختيار أشكال رسومية كعينات اختبار تتصف بمستويات متباينة من التعقيد تتراوح ما بين بسيط إلى متوسط إلى عالي التعقيد على أساس عوامل مثل تقعرات الحدود، عدد نقاط الزوايا، الفتحات الداخلية، إلخ. وقد أظهرت نتائج الاختبار أن طريقتنا الجديدة حققت دقة في الملائمة تصل نسبتها إلى 86% مقارنة بالحدود الحقيقية للشكل المستهدف. وكذلك فقد كان أداء طريقتنا جيداً بالمقارنة مع طرق أخرى مماثلة

CAD system for lung nodule analysis.

Lung cancer is the deadliest type of known cancer in the United States, claiming hundreds of thousands of lives each year. However, despite the high mortality rate, the 5-year survival rate after resection of Stage 1A non–small cell lung cancer is currently in the range of 62%– 82% and in recent studies even 90%. Patient survival is highly correlated with early detection. Computed Tomography (CT) technology services the early detection of lung cancer tremendously by offering a minimally invasive medical diagnostic tool. Some early types of lung cancer begin with a small mass of tissue within the lung, less than 3 cm in diameter, called a nodule. Most nodules found in a lung are benign, but a small population of them becomes malignant over time. Expert analysis of CT scans is the first step in determining whether a nodule presents a possibility for malignancy but, due to such low spatial support, many potentially harmful nodules go undetected until other symptoms motivate a more thorough search. Computer Vision and Pattern Recognition techniques can play a significant role in aiding the process of detecting and diagnosing lung nodules. This thesis outlines the development of a CAD system which, given an input CT scan, provides a functional and fast, second-opinion diagnosis to physicians. The entire process of lung nodule screening has been cast as a system, which can be enhanced by modern computing technology, with the hopes of providing a feasible diagnostic tool for clinical use. It should be noted that the proposed CAD system is presented as a tool for experts—not a replacement for them. The primary motivation of this thesis is the design of a system that could act as a catalyst for reducing the mortality rate associated with lung cancer

Visual region understanding: unsupervised extraction and abstraction

The ability to gain a conceptual understanding of the world in uncontrolled environments is the ultimate goal of vision-based computer systems. Technological societies today are heavily reliant on surveillance and security infrastructure, robotics, medical image analysis, visual data categorisation and search, and smart device user interaction, to name a few. Out of all the complex problems tackled by computer vision today in context of these technologies, that which lies closest to the original goals of the field is the subarea of unsupervised scene analysis or scene modelling. However, its common use of low level features does not provide a good balance between generality and discriminative ability, both a result and a symptom of the sensory and semantic gaps existing between low level computer representations and high level human descriptions. In this research we explore a general framework that addresses the fundamental problem of universal unsupervised extraction of semantically meaningful visual regions and their behaviours. For this purpose we address issues related to (i) spatial and spatiotemporal segmentation for region extraction, (ii) region shape modelling, and (iii) the online categorisation of visual object classes and the spatiotemporal analysis of their behaviours. Under this framework we propose (a) a unified region merging method and spatiotemporal region reduction, (b) shape representation by the optimisation and novel simplication of contour-based growing neural gases, and (c) a foundation for the analysis of visual object motion properties using a shape and appearance based nearest-centroid classification algorithm and trajectory plots for the obtained region classes. 1 Specifically, we formulate a region merging spatial segmentation mechanism that combines and adapts features shown previously to be individually useful, namely parallel region growing, the best merge criterion, a time adaptive threshold, and region reduction techniques. For spatiotemporal region refinement we consider both scalar intensity differences and vector optical flow. To model the shapes of the visual regions thus obtained, we adapt the growing neural gas for rapid region contour representation and propose a contour simplication technique. A fast unsupervised nearest-centroid online learning technique next groups observed region instances into classes, for which we are then able to analyse spatial presence and spatiotemporal trajectories. The analysis results show semantic correlations to real world object behaviour. Performance evaluation of all steps across standard metrics and datasets validate their performance

Automatic Image Based Time Varying 3D Feature Extraction and Tracking

3D time-varying data sets are complex. The intrinsics of those data cannot be readily comprehended by users solely based on visual investigation. Computational tools such as feature extraction and tracking are often necessary. Until now, most existing algorithms in this domain work effectively in the object space, relying on prior knowledge of the data. How to find a more flexible and efficient method which can perform automatically to implement extraction and tracking remains an attractive topic. This thesis presents a new image-based method that extracts and tracks the 3D time- varying volume data sets. The innovation of the proposed approach is two-fold. First, all analyses are performed in the image space on volume rendered images without accessing the actual volume data itself. The image-based processing will help to both save storage space in the memory and reduce computation burden. Secondly, the new approach does not require any prior knowledge of the user-defined “feature” or a built model. All the parameters used by the algorithms are automatically determined by the system itself, thus flexibility and efficiency can be achieved at the same time. The proposed image-based feature extraction and tracking system consists of four components: feature segmentation (or extraction), feature description (or shape analysis), classification, and feature tracking. Feature segmentation is to identify and label individual features from the image so that we can describe and track them separately. We combine both region-based and edge-based segmentation approaches to implement the extraction process. Feature description is to analyze each feature and derive a vector to describe the feature such that the subsequent tracking step does not have to rely on the entire feature extracted, but instead a much smaller and informative feature descriptor. Classification is to identify the corresponding features from two consecutive image frames along both the time and the spatial domain. Feature tracking is to study and model the evolution of features based on the correspondence computation result from classification stage. Experimental results show that the image-based feature extraction and tracking system provides high fidelity with great efficiency