Microarray image processing: A novel neural network framework

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Due to the vast success of bioengineering techniques, a series of large-scale analysis tools has been developed to discover the functional organization of cells. Among them, cDNA microarray has emerged as a powerful technology that enables biologists to cDNA microarray technology has enabled biologists to study thousands of genes simultaneously within an entire organism, and thus obtain a better understanding of the gene interaction and regulation mechanisms involved. Although microarray technology has been developed so as to offer high tolerances, there exists high signal irregularity through the surface of the microarray image. The imperfection in the microarray image generation process causes noises of many types, which contaminate the resulting image. These errors and noises will propagate down through, and can significantly affect, all subsequent processing and analysis. Therefore, to realize the potential of such technology it is crucial to obtain high quality image data that would indeed reflect the underlying biology in the samples. One of the key steps in extracting information from a microarray image is segmentation: identifying which pixels within an image represent which gene. This area of spotted microarray image analysis has received relatively little attention relative to the advances in proceeding analysis stages. But, the lack of advanced image analysis, including the segmentation, results in sub-optimal data being used in all downstream analysis methods. Although there is recently much research on microarray image analysis with many methods have been proposed, some methods produce better results than others. In general, the most effective approaches require considerable run time (processing) power to process an entire image. Furthermore, there has been little progress on developing sufficiently fast yet efficient and effective algorithms the segmentation of the microarray image by using a highly sophisticated framework such as Cellular Neural Networks (CNNs). It is, therefore, the aim of this thesis to investigate and develop novel methods processing microarray images. The goal is to produce results that outperform the currently available approaches in terms of PSNR, k-means and ICC measurements.Aleppo University, Syri

Building Mental Experiences: From Scenes to Events

Mental events are central to everyday cognition, be it our continuous perception of the world, recalling autobiographical memories, or imagining the future. Little is known about the fine-grained temporal dynamics of these processes. Given the apparent predominance of scene imagery across cognition, in this thesis I used magnetoencephalography to investigate whether and how activity in the hippocampus and ventromedial prefrontal cortex (vmPFC) supports the mental construction of scenes and the events to which they give rise. In the first experiment, participants gradually imagined scenes and also closely matched non-scene arrays; this allowed me to assess whether any brain regions showed preferential responses to scene imagery. The anterior hippocampus and vmPFC were particularly engaged by the construction of scene imagery, with the vmPFC driving hippocampal activity. In the second experiment, I found that certain objects – those that were space-defining – preferentially engaged the vmPFC and superior temporal gyrus during scene construction, providing insight into how objects affect the creation of scene representations. The third experiment involved boundary extension during scene perception, permitting me to examine how single scenes might be prepared for inclusion into events. I observed changes in evoked responses just 12.5-58 ms after scene onset over fronto-temporal sensors, with again the vmPFC exerting a driving influence on other brain regions, including the hippocampus. In the final experiment, participants watched brief movies of events built from a series of scenes or non-scene patterns. A difference in evoked responses between the two event types emerged during the first frame of the movies, the primary source of which was shown to be the hippocampus. The enduring theme of the results across experiments was scene-specific engagement of the hippocampus and vmPFC, with the latter being the driving influence. Overall, this thesis provides insights into the neural dynamics of how scenes are built, made ready for inclusion into unfolding mental episodes, and then linked to produce our seamless experience of the world

Microarray image processing : a novel neural network framework

Due to the vast success of bioengineering techniques, a series of large-scale analysis tools has been developed to discover the functional organization of cells. Among them, cDNA microarray has emerged as a powerful technology that enables biologists to cDNA microarray technology has enabled biologists to study thousands of genes simultaneously within an entire organism, and thus obtain a better understanding of the gene interaction and regulation mechanisms involved. Although microarray technology has been developed so as to offer high tolerances, there exists high signal irregularity through the surface of the microarray image. The imperfection in the microarray image generation process causes noises of many types, which contaminate the resulting image. These errors and noises will propagate down through, and can significantly affect, all subsequent processing and analysis. Therefore, to realize the potential of such technology it is crucial to obtain high quality image data that would indeed reflect the underlying biology in the samples. One of the key steps in extracting information from a microarray image is segmentation: identifying which pixels within an image represent which gene. This area of spotted microarray image analysis has received relatively little attention relative to the advances in proceeding analysis stages. But, the lack of advanced image analysis, including the segmentation, results in sub-optimal data being used in all downstream analysis methods. Although there is recently much research on microarray image analysis with many methods have been proposed, some methods produce better results than others. In general, the most effective approaches require considerable run time (processing) power to process an entire image. Furthermore, there has been little progress on developing sufficiently fast yet efficient and effective algorithms the segmentation of the microarray image by using a highly sophisticated framework such as Cellular Neural Networks (CNNs). It is, therefore, the aim of this thesis to investigate and develop novel methods processing microarray images. The goal is to produce results that outperform the currently available approaches in terms of PSNR, k-means and ICC measurements.EThOS - Electronic Theses Online ServiceAleppo University, SyriaGBUnited Kingdo

Human-Centric Machine Vision

Recently, the algorithms for the processing of the visual information have greatly evolved, providing efficient and effective solutions to cope with the variability and the complexity of real-world environments. These achievements yield to the development of Machine Vision systems that overcome the typical industrial applications, where the environments are controlled and the tasks are very specific, towards the use of innovative solutions to face with everyday needs of people. The Human-Centric Machine Vision can help to solve the problems raised by the needs of our society, e.g. security and safety, health care, medical imaging, and human machine interface. In such applications it is necessary to handle changing, unpredictable and complex situations, and to take care of the presence of humans

Adaptivity of 3D web content in web-based virtual museums : a quality of service and quality of experience perspective

The 3D Web emerged as an agglomeration of technologies that brought the third dimension to the World Wide Web. Its forms spanned from being systems with limited 3D capabilities to complete and complex Web-Based Virtual Worlds. The advent of the 3D Web provided great opportunities to museums by giving them an innovative medium to disseminate collections' information and associated interpretations in the form of digital artefacts, and virtual reconstructions thus leading to a new revolutionary way in cultural heritage curation, preservation and dissemination thereby reaching a wider audience. This audience consumes 3D Web material on a myriad of devices (mobile devices, tablets and personal computers) and network regimes (WiFi, 4G, 3G, etc.). Choreographing and presenting 3D Web components across all these heterogeneous platforms and network regimes present a significant challenge yet to overcome. The challenge is to achieve a good user Quality of Experience (QoE) across all these platforms. This means that different levels of fidelity of media may be appropriate. Therefore, servers hosting those media types need to adapt to the capabilities of a wide range of networks and devices. To achieve this, the research contributes the design and implementation of Hannibal, an adaptive QoS & QoE-aware engine that allows Web-Based Virtual Museums to deliver the best possible user experience across those platforms. In order to ensure effective adaptivity of 3D content, this research furthers the understanding of the 3D web in terms of Quality of Service (QoS) through empirical investigations studying how 3D Web components perform and what are their bottlenecks and in terms of QoE studying the subjective perception of fidelity of 3D Digital Heritage artefacts. Results of these experiments lead to the design and implementation of Hannibal

Fingerprint-based biometric recognition allied to fuzzy-neural feature classification.

The research investigates fingerprint recognition as one of the most reliable biometrics identification methods. An automatic identification process of humans-based on fingerprints requires the input fingerprint to be matched with a large number of fingerprints in a database. To reduce the search time and computational complexity, it is desirable to classify the database of fingerprints into an accurate and consistent manner so that the input fingerprint is matched only with a subset of the fingerprints in the database. In this regard, the research addressed fingerprint classification. The goal is to improve the accuracy and speed up of existing automatic fingerprint identification algorithms. The investigation is based on analysis of fingerprint characteristics and feature classification using neural network and fuzzy-neural classifiers.The methodology developed, is comprised of image processing, computation of a directional field image, singular-point detection, and feature vector encoding. The statistical distribution of feature vectors was analysed using SPSS. Three types of classifiers, namely, multi-layered perceptrons, radial basis function and fuzzy-neural methods were implemented. The developed classification systems were tested and evaluated on 4,000 fingerprint images on the NIST-4 database. For the five-class problem, classification accuracy of 96.2% for FNN, 96.07% for MLP and 84.54% for RBF was achieved, without any rejection. FNN and MLP classification results are significant in comparison with existing studies, which have been reviewed