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

Classification of Humans into Ayurvedic Prakruti Types using Computer Vision

Ayurveda, a 5000 years old Indian medical science, believes that the universe and hence humans are made up of five elements namely ether, fire, water, earth, and air. The three Doshas (Tridosha) Vata, Pitta, and Kapha originated from the combinations of these elements. Every person has a unique combination of Tridosha elements contributing to a person’s ‘Prakruti’. Prakruti governs the physiological and psychological tendencies in all living beings as well as the way they interact with the environment. This balance influences their physiological features like the texture and colour of skin, hair, eyes, length of fingers, the shape of the palm, body frame, strength of digestion and many more as well as the psychological features like their nature (introverted, extroverted, calm, excitable, intense, laidback), and their reaction to stress and diseases. All these features are coded in the constituents at the time of a person’s creation and do not change throughout their lifetime. Ayurvedic doctors analyze the Prakruti of a person either by assessing the physical features manually and/or by examining the nature of their heartbeat (pulse). Based on this analysis, they diagnose, prevent and cure the disease in patients by prescribing precision medicine. This project focuses on identifying Prakruti of a person by analysing his facial features like hair, eyes, nose, lips and skin colour using facial recognition techniques in computer vision. This is the first of its kind research in this problem area that attempts to bring image processing into the domain of Ayurveda

Functional and structural MRI image analysis for brain glial tumors treatment

Cotutela con il Dipartimento di Biotecnologie e Scienze della Vita, Universiità degli Studi dell'Insubria.openThis Ph.D Thesis is the outcome of a close collaboration between the Center for Research in Image Analysis and Medical Informatics (CRAIIM) of the Insubria University and the Operative Unit of Neurosurgery, Neuroradiology and Health Physics of the University Hospital ”Circolo Fondazione Macchi”, Varese. The project aim is to investigate new methodologies by means of whose, develop an integrated framework able to enhance the use of Magnetic Resonance Images, in order to support clinical experts in the treatment of patients with brain Glial tumor. Both the most common uses of MRI technology for non-invasive brain inspection were analyzed. From the Functional point of view, the goal has been to provide tools for an objective reliable and non-presumptive assessment of the brain’s areas locations, to preserve them as much as possible at surgery. From the Structural point of view, methodologies for fully automatic brain segmentation and recognition of the tumoral areas, for evaluating the tumor volume, the spatial distribution and to be able to infer correlation with other clinical data or trace growth trend, have been studied. Each of the proposed methods has been thoroughly assessed both qualitatively and quantitatively. All the Medical Imaging and Pattern Recognition algorithmic solutions studied for this Ph.D. Thesis have been integrated in GliCInE: Glioma Computerized Inspection Environment, which is a MATLAB prototype of an integrated analysis environment that offers, in addition to all the functionality specifically described in this Thesis, a set of tools needed to manage Functional and Structural Magnetic Resonance Volumes and ancillary data related to the acquisition and the patient.openInformaticaPedoia, ValentinaPedoia, Valentin

The VOISE Algorithm: a Versatile Tool for Automatic Segmentation of Astronomical Images

The auroras on Jupiter and Saturn can be studied with a high sensitivity and resolution by the Hubble Space Telescope (HST) ultraviolet (UV) and far-ultraviolet (FUV) Space Telescope spectrograph (STIS) and Advanced Camera for Surveys (ACS) instruments. We present results of automatic detection and segmentation of Jupiter's auroral emissions as observed by HST ACS instrument with VOronoi Image SEgmentation (VOISE). VOISE is a dynamic algorithm for partitioning the underlying pixel grid of an image into regions according to a prescribed homogeneity criterion. The algorithm consists of an iterative procedure that dynamically constructs a tessellation of the image plane based on a Voronoi Diagram, until the intensity of the underlying image within each region is classified as homogeneous. The computed tessellations allow the extraction of quantitative information about the auroral features such as mean intensity, latitudinal and longitudinal extents and length scales. These outputs thus represent a more automated and objective method of characterising auroral emissions than manual inspection.Comment: 9 pages, 7 figures; accepted for publication in MNRA

Functional and structural MRI image analysis for brain glial tumors treatment

This Ph.D Thesis is the outcome of a close collaboration between the Center for Research in Image Analysis and Medical Informatics (CRAIIM) of the Insubria University and the Operative Unit of Neurosurgery, Neuroradiology and Health Physics of the University Hospital ”Circolo Fondazione Macchi”, Varese. The project aim is to investigate new methodologies by means of whose, develop an integrated framework able to enhance the use of Magnetic Resonance Images, in order to support clinical experts in the treatment of patients with brain Glial tumor. Both the most common uses of MRI technology for non-invasive brain inspection were analyzed. From the Functional point of view, the goal has been to provide tools for an objective reliable and non-presumptive assessment of the brain’s areas locations, to preserve them as much as possible at surgery. From the Structural point of view, methodologies for fully automatic brain segmentation and recognition of the tumoral areas, for evaluating the tumor volume, the spatial distribution and to be able to infer correlation with other clinical data or trace growth trend, have been studied. Each of the proposed methods has been thoroughly assessed both qualitatively and quantitatively. All the Medical Imaging and Pattern Recognition algorithmic solutions studied for this Ph.D. Thesis have been integrated in GliCInE: Glioma Computerized Inspection Environment, which is a MATLAB prototype of an integrated analysis environment that offers, in addition to all the functionality specifically described in this Thesis, a set of tools needed to manage Functional and Structural Magnetic Resonance Volumes and ancillary data related to the acquisition and the patient

Segmentation of Endothelial Cell Boundaries of Rabbit Aortic Images Using a Machine Learning Approach

This paper presents an automatic detection method for thin boundaries of silver-stained endothelial cells (ECs) imaged using light microscopy of endothelium mono-layers from rabbit aortas. To achieve this, a segmentation technique was developed, which relies on a rich feature space to describe the spatial neighbourhood of each pixel and employs a Support Vector Machine (SVM) as a classifier. This segmentation approach is compared, using hand-labelled data, to a number of standard segmentation/thresholding methods commonly applied in microscopy. The importance of different features is also assessed using the method of minimum Redundancy, Maximum Relevance (mRMR), and the effect of different SVM kernels is also considered. The results show that the approach suggested in this paper attains much greater accuracy than standard techniques; in our comparisons with manually labelled data, our proposed technique is able to identify boundary pixels to an accuracy of 93%. More significantly, out of a set of 56 regions of image data, 43 regions were binarised to a useful level of accuracy. The results obtained from the image segmentation technique developed here may be used for the study of shape and alignment of ECs, and hence patterns of blood flow, around arterial branches

A novel edge detection method based on efficient gaussian binomial filter

Most basic and recent image edge detection methods are based on exploiting spatial high-frequency to localize efficiency the boundaries and image discontinuities. These approaches are strictly sensitive to noise, and their performance decrease with the increasing noise level. This research suggests a novel and robust approach based on a binomial Gaussian filter for edge detection. We propose a scheme-based Gaussian filter that employs low-pass filters to reduce noise and gradient image differentiation to perform edge recovering. The results presented illustrate that the proposed approach outperforms the basic method for edge detection. The global scheme may be implemented efficiently with high speed using the proposed novel binomial Gaussian filter

Doctor of Philosophy

dissertationImage segmentation entails the partitioning of an image domain, usually two or three dimensions, so that each partition or segment has some meaning that is relevant to the application at hand. Accurate image segmentation is a crucial challenge in many disciplines, including medicine, computer vision, and geology. In some applications, heterogeneous pixel intensities; noisy, ill-defined, or diffusive boundaries; and irregular shapes with high variability can make it challenging to meet accuracy requirements. Various segmentation approaches tackle such challenges by casting the segmentation problem as an energy-minimization problem, and solving it using efficient optimization algorithms. These approaches are broadly classified as either region-based or edge (surface)-based depending on the features on which they operate. The focus of this dissertation is on the development of a surface-based energy model, the design of efficient formulations of optimization frameworks to incorporate such energy, and the solution of the energy-minimization problem using graph cuts. This dissertation utilizes a set of four papers whose motivation is the efficient extraction of the left atrium wall from the late gadolinium enhancement magnetic resonance imaging (LGE-MRI) image volume. This dissertation utilizes these energy formulations for other applications, including contact lens segmentation in the optical coherence tomography (OCT) data and the extraction of geologic features in seismic data. Chapters 2 through 5 (papers 1 through 4) explore building a surface-based image segmentation model by progressively adding components to improve its accuracy and robustness. The first paper defines a parametric search space and its discrete formulation in the form of a multilayer three-dimensional mesh model within which the segmentation takes place. It includes a generative intensity model, and we optimize using a graph formulation of the surface net problem. The second paper proposes a Bayesian framework with a Markov random field (MRF) prior that gives rise to another class of surface nets, which provides better segmentation with smooth boundaries. The third paper presents a maximum a posteriori (MAP)-based surface estimation framework that relies on a generative image model by incorporating global shape priors, in addition to the MRF, within the Bayesian formulation. Thus, the resulting surface not only depends on the learned model of shapes,but also accommodates the test data irregularities through smooth deviations from these priors. Further, the paper proposes a new shape parameter estimation scheme, in closed form, for segmentation as a part of the optimization process. Finally, the fourth paper (under review at the time of this document) presents an extensive analysis of the MAP framework and presents improved mesh generation and generative intensity models. It also performs a thorough analysis of the segmentation results that demonstrates the effectiveness of the proposed method qualitatively, quantitatively, and clinically. Chapter 6, consisting of unpublished work, demonstrates the application of an MRF-based Bayesian framework to segment coupled surfaces of contact lenses in optical coherence tomography images. This chapter also shows an application related to the extraction of geological structures in seismic volumes. Due to the large sizes of seismic volume datasets, we also present fast, approximate surface-based energy minimization strategies that achieve better speed-ups and memory consumption