Automatic Classification of Human Epithelial Type 2 Cell Indirect Immunofluorescence Images using Cell Pyramid Matching

This paper describes a novel system for automatic classification of images obtained from Anti-Nuclear Antibody (ANA) pathology tests on Human Epithelial type 2 (HEp-2) cells using the Indirect Immunofluorescence (IIF) protocol. The IIF protocol on HEp-2 cells has been the hallmark method to identify the presence of ANAs, due to its high sensitivity and the large range of antigens that can be detected. However, it suffers from numerous shortcomings, such as being subjective as well as time and labour intensive. Computer Aided Diagnostic (CAD) systems have been developed to address these problems, which automatically classify a HEp-2 cell image into one of its known patterns (eg. speckled, homogeneous). Most of the existing CAD systems use handpicked features to represent a HEp-2 cell image, which may only work in limited scenarios. We propose a novel automatic cell image classification method termed Cell Pyramid Matching (CPM), which is comprised of regional histograms of visual words coupled with the Multiple Kernel Learning framework. We present a study of several variations of generating histograms and show the efficacy of the system on two publicly available datasets: the ICPR HEp-2 cell classification contest dataset and the SNPHEp-2 dataset.Comment: arXiv admin note: substantial text overlap with arXiv:1304.126

Content-prioritised video coding for British Sign Language communication.

Video communication of British Sign Language (BSL) is important for remote interpersonal communication and for the equal provision of services for deaf people. However, the use of video telephony and video conferencing applications for BSL communication is limited by inadequate video quality. BSL is a highly structured, linguistically complete, natural language system that expresses vocabulary and grammar visually and spatially using a complex combination of facial expressions (such as eyebrow movements, eye blinks and mouth/lip shapes), hand gestures, body movements and finger-spelling that change in space and time. Accurate natural BSL communication places specific demands on visual media applications which must compress video image data for efficient transmission. Current video compression schemes apply methods to reduce statistical redundancy and perceptual irrelevance in video image data based on a general model of Human Visual System (HVS) sensitivities. This thesis presents novel video image coding methods developed to achieve the conflicting requirements for high image quality and efficient coding. Novel methods of prioritising visually important video image content for optimised video coding are developed to exploit the HVS spatial and temporal response mechanisms of BSL users (determined by Eye Movement Tracking) and the characteristics of BSL video image content. The methods implement an accurate model of HVS foveation, applied in the spatial and temporal domains, at the pre-processing stage of a current standard-based system (H.264). Comparison of the performance of the developed and standard coding systems, using methods of video quality evaluation developed for this thesis, demonstrates improved perceived quality at low bit rates. BSL users, broadcasters and service providers benefit from the perception of high quality video over a range of available transmission bandwidths. The research community benefits from a new approach to video coding optimisation and better understanding of the communication needs of deaf people

Energy efficient enabling technologies for semantic video processing on mobile devices

Semantic object-based processing will play an increasingly important role in future multimedia systems due to the ubiquity of digital multimedia capture/playback technologies and increasing storage capacity. Although the object based paradigm has many undeniable benefits, numerous technical challenges remain before the applications becomes pervasive, particularly on computational constrained mobile devices. A fundamental issue is the ill-posed problem of semantic object segmentation. Furthermore, on battery powered mobile computing devices, the additional algorithmic complexity of semantic object based processing compared to conventional video processing is highly undesirable both from a real-time operation and battery life perspective. This thesis attempts to tackle these issues by firstly constraining the solution space and focusing on the human face as a primary semantic concept of use to users of mobile devices. A novel face detection algorithm is proposed, which from the outset was designed to be amenable to be offloaded from the host microprocessor to dedicated hardware, thereby providing real-time performance and reducing power consumption. The algorithm uses an Artificial Neural Network (ANN), whose topology and weights are evolved via a genetic algorithm (GA). The computational burden of the ANN evaluation is offloaded to a dedicated hardware accelerator, which is capable of processing any evolved network topology. Efficient arithmetic circuitry, which leverages modified Booth recoding, column compressors and carry save adders, is adopted throughout the design. To tackle the increased computational costs associated with object tracking or object based shape encoding, a novel energy efficient binary motion estimation architecture is proposed. Energy is reduced in the proposed motion estimation architecture by minimising the redundant operations inherent in the binary data. Both architectures are shown to compare favourable with the relevant prior art

Log-Euclidean Bag of Words for Human Action Recognition

Representing videos by densely extracted local space-time features has recently become a popular approach for analysing actions. In this paper, we tackle the problem of categorising human actions by devising Bag of Words (BoW) models based on covariance matrices of spatio-temporal features, with the features formed from histograms of optical flow. Since covariance matrices form a special type of Riemannian manifold, the space of Symmetric Positive Definite (SPD) matrices, non-Euclidean geometry should be taken into account while discriminating between covariance matrices. To this end, we propose to embed SPD manifolds to Euclidean spaces via a diffeomorphism and extend the BoW approach to its Riemannian version. The proposed BoW approach takes into account the manifold geometry of SPD matrices during the generation of the codebook and histograms. Experiments on challenging human action datasets show that the proposed method obtains notable improvements in discrimination accuracy, in comparison to several state-of-the-art methods

3D Medical Image Lossless Compressor Using Deep Learning Approaches

The ever-increasing importance of accelerated information processing, communica-tion, and storing are major requirements within the big-data era revolution. With the extensive rise in data availability, handy information acquisition, and growing data rate, a critical challenge emerges in efficient handling. Even with advanced technical hardware developments and multiple Graphics Processing Units (GPUs) availability, this demand is still highly promoted to utilise these technologies effectively. Health-care systems are one of the domains yielding explosive data growth. Especially when considering their modern scanners abilities, which annually produce higher-resolution and more densely sampled medical images, with increasing requirements for massive storage capacity. The bottleneck in data transmission and storage would essentially be handled with an effective compression method. Since medical information is critical and imposes an influential role in diagnosis accuracy, it is strongly encouraged to guarantee exact reconstruction with no loss in quality, which is the main objective of any lossless compression algorithm. Given the revolutionary impact of Deep Learning (DL) methods in solving many tasks while achieving the state of the art results, includ-ing data compression, this opens tremendous opportunities for contributions. While considerable efforts have been made to address lossy performance using learning-based approaches, less attention was paid to address lossless compression. This PhD thesis investigates and proposes novel learning-based approaches for compressing 3D medical images losslessly.Firstly, we formulate the lossless compression task as a supervised sequential prediction problem, whereby a model learns a projection function to predict a target voxel given sequence of samples from its spatially surrounding voxels. Using such 3D local sampling information efficiently exploits spatial similarities and redundancies in a volumetric medical context by utilising such a prediction paradigm. The proposed NN-based data predictor is trained to minimise the differences with the original data values while the residual errors are encoded using arithmetic coding to allow lossless reconstruction.Following this, we explore the effectiveness of Recurrent Neural Networks (RNNs) as a 3D predictor for learning the mapping function from the spatial medical domain (16 bit-depths). We analyse Long Short-Term Memory (LSTM) models’ generalisabil-ity and robustness in capturing the 3D spatial dependencies of a voxel’s neighbourhood while utilising samples taken from various scanning settings. We evaluate our proposed MedZip models in compressing unseen Computerized Tomography (CT) and Magnetic Resonance Imaging (MRI) modalities losslessly, compared to other state-of-the-art lossless compression standards.This work investigates input configurations and sampling schemes for a many-to-one sequence prediction model, specifically for compressing 3D medical images (16 bit-depths) losslessly. The main objective is to determine the optimal practice for enabling the proposed LSTM model to achieve a high compression ratio and fast encoding-decoding performance. A solution for a non-deterministic environments problem was also proposed, allowing models to run in parallel form without much compression performance drop. Compared to well-known lossless codecs, experimental evaluations were carried out on datasets acquired by different hospitals, representing different body segments, and have distinct scanning modalities (i.e. CT and MRI).To conclude, we present a novel data-driven sampling scheme utilising weighted gradient scores for training LSTM prediction-based models. The objective is to determine whether some training samples are significantly more informative than others, specifically in medical domains where samples are available on a scale of billions. The effectiveness of models trained on the presented importance sampling scheme was evaluated compared to alternative strategies such as uniform, Gaussian, and sliced-based sampling

Fractal image compression and the self-affinity assumption : a stochastic signal modelling perspective

Bibliography: p. 208-225.Fractal image compression is a comparatively new technique which has gained considerable attention in the popular technical press, and more recently in the research literature. The most significant advantages claimed are high reconstruction quality at low coding rates, rapid decoding, and "resolution independence" in the sense that an encoded image may be decoded at a higher resolution than the original. While many of the claims published in the popular technical press are clearly extravagant, it appears from the rapidly growing body of published research that fractal image compression is capable of performance comparable with that of other techniques enjoying the benefit of a considerably more robust theoretical foundation. . So called because of the similarities between the form of image representation and a mechanism widely used in generating deterministic fractal images, fractal compression represents an image by the parameters of a set of affine transforms on image blocks under which the image is approximately invariant. Although the conditions imposed on these transforms may be shown to be sufficient to guarantee that an approximation of the original image can be reconstructed, there is no obvious theoretical reason to expect this to represent an efficient representation for image coding purposes. The usual analogy with vector quantisation, in which each image is considered to be represented in terms of code vectors extracted from the image itself is instructive, but transforms the fundamental problem into one of understanding why this construction results in an efficient codebook. The signal property required for such a codebook to be effective, termed "self-affinity", is poorly understood. A stochastic signal model based examination of this property is the primary contribution of this dissertation. The most significant findings (subject to some important restrictions} are that "self-affinity" is not a natural consequence of common statistical assumptions but requires particular conditions which are inadequately characterised by second order statistics, and that "natural" images are only marginally "self-affine", to the extent that fractal image compression is effective, but not more so than comparable standard vector quantisation techniques

Classification of Human Epithelial Type 2 Cell Indirect Immunofluoresence Images via Codebook Based Descriptors

The Anti-Nuclear Antibody (ANA) clinical pathology test is commonly used to identify the existence of various diseases. A hallmark method for identifying the presence of ANAs is the Indirect Immunofluorescence method on Human Epithelial (HEp-2) cells, due to its high sensitivity and the large range of antigens that can be detected. However, the method suffers from numerous shortcomings, such as being subjective as well as time and labour intensive. Computer Aided Diagnostic (CAD) systems have been developed to address these problems, which automatically classify a HEp-2 cell image into one of its known patterns (eg., speckled, homogeneous). Most of the existing CAD systems use handpicked features to represent a HEp-2 cell image, which may only work in limited scenarios. In this paper, we propose a cell classification system comprised of a dual-region codebook-based descriptor, combined with the Nearest Convex Hull Classifier. We evaluate the performance of several variants of the descriptor on two publicly available datasets: ICPR HEp-2 cell classification contest dataset and the new SNPHEp-2 dataset. To our knowledge, this is the first time codebook-based descriptors are applied and studied in this domain. Experiments show that the proposed system has consistent high performance and is more robust than two recent CAD systems