Detection of Ulcerative Colitis Severity and Enhancement of Informative Frame Filtering Using Texture Analysis in Colonoscopy Videos

There are several types of disorders that affect our colon’s ability to function properly such as colorectal cancer, ulcerative colitis, diverticulitis, irritable bowel syndrome and colonic polyps. Automatic detection of these diseases would inform the endoscopist of possible sub-optimal inspection during the colonoscopy procedure as well as save time during post-procedure evaluation. But existing systems only detects few of those disorders like colonic polyps. In this dissertation, we address the automatic detection of another important disorder called ulcerative colitis. We propose a novel texture feature extraction technique to detect the severity of ulcerative colitis in block, image, and video levels. We also enhance the current informative frame filtering methods by detecting water and bubble frames using our proposed technique. Our feature extraction algorithm based on accumulation of pixel value difference provides better accuracy at faster speed than the existing methods making it highly suitable for real-time systems. We also propose a hybrid approach in which our feature method is combined with existing feature method(s) to provide even better accuracy. We extend the block and image level detection method to video level severity score calculation and shot segmentation. Also, the proposed novel feature extraction method can detect water and bubble frames in colonoscopy videos with very high accuracy in significantly less processing time even when clustering is used to reduce the training size by 10 times

Vision-based retargeting for endoscopic navigation

Endoscopy is a standard procedure for visualising the human gastrointestinal tract. With the advances in biophotonics, imaging techniques such as narrow band imaging, confocal laser endomicroscopy, and optical coherence tomography can be combined with normal endoscopy for assisting the early diagnosis of diseases, such as cancer. In the past decade, optical biopsy has emerged to be an effective tool for tissue analysis, allowing in vivo and in situ assessment of pathological sites with real-time feature-enhanced microscopic images. However, the non-invasive nature of optical biopsy leads to an intra-examination retargeting problem, which is associated with the difficulty of re-localising a biopsied site consistently throughout the whole examination. In addition to intra-examination retargeting, retargeting of a pathological site is even more challenging across examinations, due to tissue deformation and changing tissue morphologies and appearances. The purpose of this thesis is to address both the intra- and inter-examination retargeting problems associated with optical biopsy. We propose a novel vision-based framework for intra-examination retargeting. The proposed framework is based on combining visual tracking and detection with online learning of the appearance of the biopsied site. Furthermore, a novel cascaded detection approach based on random forests and structured support vector machines is developed to achieve efficient retargeting. To cater for reliable inter-examination retargeting, the solution provided in this thesis is achieved by solving an image retrieval problem, for which an online scene association approach is proposed to summarise an endoscopic video collected in the first examination into distinctive scenes. A hashing-based approach is then used to learn the intrinsic representations of these scenes, such that retargeting can be achieved in subsequent examinations by retrieving the relevant images using the learnt representations. For performance evaluation of the proposed frameworks, extensive phantom, ex vivo and in vivo experiments have been conducted, with results demonstrating the robustness and potential clinical values of the methods proposed.Open Acces

Computer-aided detection of polyps in CT colonography

Master'sMASTER OF ENGINEERIN

Classification of Gastric Lesions Using Gabor Block Local Binary Patterns

The identification of cancer tissues in Gastroenterology imaging poses novel challenges to the computer vision community in designing generic decision support systems. This generic nature demands the image descriptors to be invariant to illumination gradients, scaling, homogeneous illumination, and rotation. In this article, we devise a novel feature extraction methodology, which explores the effectiveness of Gabor filters coupled with Block Local Binary Patterns in designing such descriptors. We effectively exploit the illumination invariance properties of Block Local Binary Patterns and the inherent capability of convolutional neural networks to construct novel rotation, scale and illumination invariant features. The invariance characteristics of the proposed Gabor Block Local Binary Patterns (GBLBP) are demonstrated using a publicly available texture dataset. We use the proposed feature extraction methodology to extract texture features from Chromoendoscopy (CH) images for the classification of cancer lesions. The proposed feature set is later used in conjuncture with convolutional neural networks to classify the CH images. The proposed convolutional neural network is a shallow network comprising of fewer parameters in contrast to other state-of-the-art networks exhibiting millions of parameters required for effective training. The obtained results reveal that the proposed GBLBP performs favorably to several other state-of-the-art methods including both hand crafted and convolutional neural networks-based features

Geodesic tractography segmentation for directional medical image analysis

Acknowledgements page removed per author's request, 01/06/2014.Geodesic Tractography Segmentation is the two component approach presented in this thesis for the analysis of imagery in oriented domains, with emphasis on the application to diffusion-weighted magnetic resonance imagery (DW-MRI). The computeraided analysis of DW-MRI data presents a new set of problems and opportunities for the application of mathematical and computer vision techniques. The goal is to develop a set of tools that enable clinicians to better understand DW-MRI data and ultimately shed new light on biological processes. This thesis presents a few techniques and tools which may be used to automatically find and segment major neural fiber bundles from DW-MRI data. For each technique, we provide a brief overview of the advantages and limitations of our approach relative to other available approaches.Ph.D.Committee Chair: Tannenbaum, Allen; Committee Member: Barnes, Christopher F.; Committee Member: Niethammer, Marc; Committee Member: Shamma, Jeff; Committee Member: Vela, Patrici

Novel Image Representations and Learning Tasks

abstract: Computer Vision as a eld has gone through signicant changes in the last decade. The eld has seen tremendous success in designing learning systems with hand-crafted features and in using representation learning to extract better features. In this dissertation some novel approaches to representation learning and task learning are studied. Multiple-instance learning which is generalization of supervised learning, is one example of task learning that is discussed. In particular, a novel non-parametric k- NN-based multiple-instance learning is proposed, which is shown to outperform other existing approaches. This solution is applied to a diabetic retinopathy pathology detection problem eectively. In cases of representation learning, generality of neural features are investigated rst. This investigation leads to some critical understanding and results in feature generality among datasets. The possibility of learning from a mentor network instead of from labels is then investigated. Distillation of dark knowledge is used to eciently mentor a small network from a pre-trained large mentor network. These studies help in understanding representation learning with smaller and compressed networks.Dissertation/ThesisDoctoral Dissertation Computer Science 201