Digital Morphometry : A Taxonomy Of Morphological Filters And Feature Parameters With Application To Alzheimer\u27s Disease Research

In this thesis the expression digital morphometry collectively describes all those procedures used to obtain quantitative measurements of objects within a two-dimensional digital image. Quantitative measurement is a two-step process: the application of geometrical transformations to extract the features of interest, and then the actual measurement of these features. With regard to the first step the morphological filters of mathematical morphology provide a wealth of suitable geometric transfomations. Traditional radiometric and spatial enhancement techniques provide an additional source of transformations. The second step is more classical (e.g. Underwood, 1970; Bookstein, 1978; and Weibull, 1980); yet here again mathematical morphology is applicable - morphologically derived feature parameters. This thesis focuses on mathematical morphology for digital morphometry. In particular it proffers a taxonomy of morphological filters and investigates the morphologically derived feature parameters (Minkowski functionals) for digital images sampled on a square grid. As originally conceived by Georges Matheron, mathematical morphology concerns the analysis of binary images by means of probing with structuring elements [typically convex geometric shapes] (Dougherty, 1993, preface). Since its inception the theory has been extended to grey-level images and most recently to complete lattices. It is within the very general framework of the complete lattice that the taxonomy of morphological filters is presented. Examples are provided to help illustrate the behaviour of each type of filter. This thesis also introduces DIMPAL (Mehnert, 1994) - a PC-based image processing and analysis language suitable for researching and developing algorithms for a wide range of image processing applications. Though DIMPAL was used to produce the majority of the images in this thesis it was principally written to provide an environment in which to investigate the application of mathematical morphology to Alzheimer\u27s disease research. Alzheimer\u27s disease is a form of progressive dementia associated with the degeneration of the brain. It is the commonest type of dementia and probably accounts for half the dementia of old age (Forsythe, 1990, p. 21 ). Post mortem examination of the brain reveals the presence of characteristic neuropathologic lesions; namely neuritic plaques and neurofibrillary tangles. They occur predominantly in the cerebral cortex and hippocampus. Quantitative studies of the distribution of plaques and tangles in normally aged and Alzheimer brains are hampered by the enormous amount of time and effort required to count and measure these lesions. Here in a morphological algorithm is proposed for the automatic segmentation and measurement of neuritic plaques from light micrographs of post mortem brain tissue

The cell migration monitoring in a microfluidic system by the "Scratch Wound Healing Assay" method

Tato diplomová práce se zabývá popisem principů kultivace embryonálních fibroblastových buněk myší (3T3), lidských endoteliálních buněk odebraných z pupečníkové žily (HUVEC) a epiteliálních buněk vaječníku čínského křečka (CHO) v mikrofluidních systémech simulujících kapiláry. Byly provedeny literární rešerše v oblasti realizací experimentu “Scratch Wound Healing Assay” v mikrofluidních systémech s použitím fibroblastů a endotheliálních buněk. V práci jsou dále popsány principy konfokální a fluorescenční mikroskopie a metody zpracování obrazů pro sledování buněčné migrace. Experimentální nastavení pro mikrofluidní realizaci “Scratch Wound Healing Assay” s použitím trypsinu – EDTA pro vytvoření rýhy, a konfokálního mikroskopu Leica TCS SP8 X pro následující snímání pořízených dat bylo navrženo a otestováno s dostatečným počtem opakování. Vhodný algoritmus pro analýzu buněčné migrace byl napsán v programovacím prostředí Matlab. Závěrem této práce je diskuze získaných výsledků.This thesis describes the cell culture methods of mouse embryonic fibroblast (3T3), human umbilical vein endothelial (HUVEC), and Chinese hamster ovary (CHO) cell lines in microfluidic systems simulating capillary. Literature research for microfluidic realizations of Scratch Wound Healing Assay with fibroblasts and endothelial cell lines was performed in this thesis. The principles of confocal and fluorescence microscopy, and relevant image processing techniques used for quantifying cell migration were studied. Experimental setup for microfluidic Scratch Wound Healing Assay with using of trypsin – EDTA for creation of cell delusion, and confocal microscope Leica TCS SP8 X for subsequent image acquisition was proposed and tested. An appropriate algorithm for cell migration analysis was written in Matlab computing environment. Experiment’s results are discussed in the conclusion of this thesis.

On the development of slime mould morphological, intracellular and heterotic computing devices

The use of live biological substrates in the fabrication of unconventional computing (UC) devices is steadily transcending the barriers between science fiction and reality, but efforts in this direction are impeded by ethical considerations, the field’s restrictively broad multidisciplinarity and our incomplete knowledge of fundamental biological processes. As such, very few functional prototypes of biological UC devices have been produced to date. This thesis aims to demonstrate the computational polymorphism and polyfunctionality of a chosen biological substrate — slime mould Physarum polycephalum, an arguably ‘simple’ single-celled organism — and how these properties can be harnessed to create laboratory experimental prototypes of functionally-useful biological UC prototypes. Computing devices utilising live slime mould as their key constituent element can be developed into a) heterotic, or hybrid devices, which are based on electrical recognition of slime mould behaviour via machine-organism interfaces, b) whole-organism-scale morphological processors, whose output is the organism’s morphological adaptation to environmental stimuli (input) and c) intracellular processors wherein data are represented by energetic signalling events mediated by the cytoskeleton, a nano-scale protein network. It is demonstrated that each category of device is capable of implementing logic and furthermore, specific applications for each class may be engineered, such as image processing applications for morphological processors and biosensors in the case of heterotic devices. The results presented are supported by a range of computer modelling experiments using cellular automata and multi-agent modelling. We conclude that P. polycephalum is a polymorphic UC substrate insofar as it can process multimodal sensory input and polyfunctional in its demonstrable ability to undertake a variety of computing problems. Furthermore, our results are highly applicable to the study of other living UC substrates and will inform future work in UC, biosensing, and biomedicine

Robust Modular Feature-Based Terrain-Aided Visual Navigation and Mapping

The visual feature-based Terrain-Aided Navigation (TAN) system presented in this thesis addresses the problem of constraining inertial drift introduced into the location estimate of Unmanned Aerial Vehicles (UAVs) in GPS-denied environment. The presented TAN system utilises salient visual features representing semantic or human-interpretable objects (roads, forest and water boundaries) from onboard aerial imagery and associates them to a database of reference features created a-priori, through application of the same feature detection algorithms to satellite imagery. Correlation of the detected features with the reference features via a series of the robust data association steps allows a localisation solution to be achieved with a finite absolute bound precision defined by the certainty of the reference dataset. The feature-based Visual Navigation System (VNS) presented in this thesis was originally developed for a navigation application using simulated multi-year satellite image datasets. The extension of the system application into the mapping domain, in turn, has been based on the real (not simulated) flight data and imagery. In the mapping study the full potential of the system, being a versatile tool for enhancing the accuracy of the information derived from the aerial imagery has been demonstrated. Not only have the visual features, such as road networks, shorelines and water bodies, been used to obtain a position ’fix’, they have also been used in reverse for accurate mapping of vehicles detected on the roads into an inertial space with improved precision. Combined correction of the geo-coding errors and improved aircraft localisation formed a robust solution to the defense mapping application. A system of the proposed design will provide a complete independent navigation solution to an autonomous UAV and additionally give it object tracking capability

Image Processing Using FPGAs

This book presents a selection of papers representing current research on using field programmable gate arrays (FPGAs) for realising image processing algorithms. These papers are reprints of papers selected for a Special Issue of the Journal of Imaging on image processing using FPGAs. A diverse range of topics is covered, including parallel soft processors, memory management, image filters, segmentation, clustering, image analysis, and image compression. Applications include traffic sign recognition for autonomous driving, cell detection for histopathology, and video compression. Collectively, they represent the current state-of-the-art on image processing using FPGAs

Image enhancement techniques applied to solar feature detection

This dissertation presents the development of automatic image enhancement techniques for solar feature detection. The new method allows for detection and tracking of the evolution of filaments in solar images. Series of H-alpha full-disk images are taken in regular time intervals to observe the changes of the solar disk features. In each picture, the solar chromosphere filaments are identified for further evolution examination. The initial preprocessing step involves local thresholding to convert grayscale images into black-and-white pictures with chromosphere granularity enhanced. An alternative preprocessing method, based on image normalization and global thresholding is presented. The next step employs morphological closing operations with multi-directional linear structuring elements to extract elongated shapes in the image. After logical union of directional filtering results, the remaining noise is removed from the final outcome using morphological dilation and erosion with a circular structuring element. Experimental results show that the developed techniques can achieve excellent results in detecting large filaments and good detection rates for small filaments. The final chapter discusses proposed directions of the future research and applications to other areas of solar image processing, in particular to detection of solar flares, plages and sunspots