Mathematical Morphology for Quantification in Biological & Medical Image Analysis

Mathematical morphology is an established field of image processing first introduced as an application of set and lattice theories. Originally used to characterise particle distributions, mathematical morphology has gone on to be a core tool required for such important analysis methods as skeletonisation and the watershed transform. In this thesis, I introduce a selection of new image analysis techniques based on mathematical morphology. Utilising assumptions of shape, I propose a new approach for the enhancement of vessel-like objects in images: the bowler-hat transform. Built upon morphological operations, this approach is successful at challenges such as junctions and robust against noise. The bowler-hat transform is shown to give better results than competitor methods on challenging data such as retinal/fundus imagery. Building further on morphological operations, I introduce two novel methods for particle and blob detection. The first of which is developed in the context of colocalisation, a standard biological assay, and the second, which is based on Hilbert-Edge Detection And Ranging (HEDAR), with regard to nuclei detection and counting in fluorescent microscopy. These methods are shown to produce accurate and informative results for sub-pixel and supra-pixel object counting in complex and noisy biological scenarios. I propose a new approach for the automated extraction and measurement of object thickness for intricate and complicated vessels, such as brain vascular in medical images. This pipeline depends on two key technologies: semi-automated segmentation by advanced level-set methods and automatic thickness calculation based on morphological operations. This approach is validated and results demonstrating the broad range of challenges posed by these images and the possible limitations of this pipeline are shown. This thesis represents a significant contribution to the field of image processing using mathematical morphology and the methods within are transferable to a range of complex challenges present across biomedical image analysis

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

Earth resources: A continuing bibliography with indexes, issue 18

This bibliography lists 434 reports, articles, and other documents introduced into the NASA scientific and technical information system between April 1 and June 30, 1978. Emphasis is placed on the use of remote sensing and geophysical instrumentation in spacecraft and aircraft to survey and inventory natural resources and urban areas. Subject matter is grouped according to agriculture and forestry, environmental changes and cultural resources, geodesy and cartography, geology and mineral resources, hydrology and water management, data processing and distribution systems, instrumentation and sensors, and economic analysis

Automatic Segmentation and Classification of Red and White Blood cells in Thin Blood Smear Slides

In this work we develop a system for automatic detection and classification of cytological images which plays an increasing important role in medical diagnosis. A primary aim of this work is the accurate segmentation of cytological images of blood smears and subsequent feature extraction, along with studying related classification problems such as the identification and counting of peripheral blood smear particles, and classification of white blood cell into types five. Our proposed approach benefits from powerful image processing techniques to perform complete blood count (CBC) without human intervention. The general framework in this blood smear analysis research is as follows. Firstly, a digital blood smear image is de-noised using optimized Bayesian non-local means filter to design a dependable cell counting system that may be used under different image capture conditions. Then an edge preservation technique with Kuwahara filter is used to recover degraded and blurred white blood cell boundaries in blood smear images while reducing the residual negative effect of noise in images. After denoising and edge enhancement, the next step is binarization using combination of Otsu and Niblack to separate the cells and stained background. Cells separation and counting is achieved by granulometry, advanced active contours without edges, and morphological operators with watershed algorithm. Following this is the recognition of different types of white blood cells (WBCs), and also red blood cells (RBCs) segmentation. Using three main types of features: shape, intensity, and texture invariant features in combination with a variety of classifiers is next step. The following features are used in this work: intensity histogram features, invariant moments, the relative area, co-occurrence and run-length matrices, dual tree complex wavelet transform features, Haralick and Tamura features. Next, different statistical approaches involving correlation, distribution and redundancy are used to measure of the dependency between a set of features and to select feature variables on the white blood cell classification. A global sensitivity analysis with random sampling-high dimensional model representation (RS-HDMR) which can deal with independent and dependent input feature variables is used to assess dominate discriminatory power and the reliability of feature which leads to an efficient feature selection. These feature selection results are compared in experiments with branch and bound method and with sequential forward selection (SFS), respectively. This work examines support vector machine (SVM) and Convolutional Neural Networks (LeNet5) in connection with white blood cell classification. Finally, white blood cell classification system is validated in experiments conducted on cytological images of normal poor quality blood smears. These experimental results are also assessed with ground truth manually obtained from medical experts

Content Recognition and Context Modeling for Document Analysis and Retrieval

The nature and scope of available documents are changing significantly in many areas of document analysis and retrieval as complex, heterogeneous collections become accessible to virtually everyone via the web. The increasing level of diversity presents a great challenge for document image content categorization, indexing, and retrieval. Meanwhile, the processing of documents with unconstrained layouts and complex formatting often requires effective leveraging of broad contextual knowledge. In this dissertation, we first present a novel approach for document image content categorization, using a lexicon of shape features. Each lexical word corresponds to a scale and rotation invariant local shape feature that is generic enough to be detected repeatably and is segmentation free. A concise, structurally indexed shape lexicon is learned by clustering and partitioning feature types through graph cuts. Our idea finds successful application in several challenging tasks, including content recognition of diverse web images and language identification on documents composed of mixed machine printed text and handwriting. Second, we address two fundamental problems in signature-based document image retrieval. Facing continually increasing volumes of documents, detecting and recognizing unique, evidentiary visual entities (\eg, signatures and logos) provides a practical and reliable supplement to the OCR recognition of printed text. We propose a novel multi-scale framework to detect and segment signatures jointly from document images, based on the structural saliency under a signature production model. We formulate the problem of signature retrieval in the unconstrained setting of geometry-invariant deformable shape matching and demonstrate state-of-the-art performance in signature matching and verification. Third, we present a model-based approach for extracting relevant named entities from unstructured documents. In a wide range of applications that require structured information from diverse, unstructured document images, processing OCR text does not give satisfactory results due to the absence of linguistic context. Our approach enables learning of inference rules collectively based on contextual information from both page layout and text features. Finally, we demonstrate the importance of mining general web user behavior data for improving document ranking and other web search experience. The context of web user activities reveals their preferences and intents, and we emphasize the analysis of individual user sessions for creating aggregate models. We introduce a novel algorithm for estimating web page and web site importance, and discuss its theoretical foundation based on an intentional surfer model. We demonstrate that our approach significantly improves large-scale document retrieval performance

Modelling the Eddy Pattern in the harbour of Zeebrugge

Hydrodynamic

On the Enrichment of Magnetic Heavy Minerals in a Coastal Environment : Exploration, Examination, Explanation

In this thesis, an approach for the detailed assessment of magnetic heavy mineral enrichments in a coastal environment using integrated geophysical and sedimentological data is developed, the observed enrichment patterns are interpreted, and their formation mechanisms discussed. Used methods are electromagnetic profiling of the subsurface, close-up seafloor photography, various laboratory techniques to analyze bulk and magnetic grain sizes and mineralogy, and numerical modelling of bi-fractional sediment transport. The studies take place in an exemplary study area in the western Bay of Plenty (New Zealand) with dimensions of 60 km x 7 km in water depths from 2-35 m. Primary instrument is the benthic profiler MARUM NERIDIS III. Overall, the findings of this thesis demonstrate an innovative, effective way to approach an unmapped area and reach detailed results with conclusive interpretations in a relatively short time. It shows the conditions under which natural sorting patterns due to size and density develop along the coast. The basic formation mechanisms are applicable to other areas in similar coastal settings and for a diverse range of heavy minerals