Automated Discrimination of Pathological Regions in Tissue Images: Unsupervised Clustering vs Supervised SVM Classification

Recognizing and isolating cancerous cells from non pathological tissue areas (e.g. connective stroma) is crucial for fast and objective immunohistochemical analysis of tissue images. This operation allows the further application of fully-automated techniques for quantitative evaluation of protein activity, since it avoids the necessity of a preventive manual selection of the representative pathological areas in the image, as well as of taking pictures only in the pure-cancerous portions of the tissue. In this paper we present a fully-automated method based on unsupervised clustering that performs tissue segmentations highly comparable with those provided by a skilled operator, achieving on average an accuracy of 90%. Experimental results on a heterogeneous dataset of immunohistochemical lung cancer tissue images demonstrate that our proposed unsupervised approach overcomes the accuracy of a theoretically superior supervised method such as Support Vector Machine (SVM) by 8%

Automated segmentation of tissue images for computerized IHC analysis

This paper presents two automated methods for the segmentation ofimmunohistochemical tissue images that overcome the limitations of themanual approach aswell as of the existing computerized techniques. The first independent method, based on unsupervised color clustering, recognizes automatically the target cancerous areas in the specimen and disregards the stroma; the second method, based on colors separation and morphological processing, exploits automated segmentation of the nuclear membranes of the cancerous cells. Extensive experimental results on real tissue images demonstrate the accuracy of our techniques compared to manual segmentations; additional experiments show that our techniques are more effective in immunohistochemical images than popular approaches based on supervised learning or active contours. The proposed procedure can be exploited for any applications that require tissues and cells exploration and to perform reliable and standardized measures of the activity of specific proteins involved in multi-factorial genetic pathologie

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

K-Space at TRECVid 2007

In this paper we describe K-Space participation in TRECVid 2007. K-Space participated in two tasks, high-level feature extraction and interactive search. We present our approaches for each of these activities and provide a brief analysis of our results. Our high-level feature submission utilized multi-modal low-level features which included visual, audio and temporal elements. Specific concept detectors (such as Face detectors) developed by K-Space partners were also used. We experimented with different machine learning approaches including logistic regression and support vector machines (SVM). Finally we also experimented with both early and late fusion for feature combination. This year we also participated in interactive search, submitting 6 runs. We developed two interfaces which both utilized the same retrieval functionality. Our objective was to measure the effect of context, which was supported to different degrees in each interface, on user performance. The first of the two systems was a ‘shot’ based interface, where the results from a query were presented as a ranked list of shots. The second interface was ‘broadcast’ based, where results were presented as a ranked list of broadcasts. Both systems made use of the outputs of our high-level feature submission as well as low-level visual features

Osteoporotic and Neoplastic Compression Fracture Classification on Longitudinal CT

Classification of vertebral compression fractures (VCF) having osteoporotic or neoplastic origin is fundamental to the planning of treatment. We developed a fracture classification system by acquiring quantitative morphologic and bone density determinants of fracture progression through the use of automated measurements from longitudinal studies. A total of 250 CT studies were acquired for the task, each having previously identified VCFs with osteoporosis or neoplasm. Thirty-six features or each identified VCF were computed and classified using a committee of support vector machines. Ten-fold cross validation on 695 identified fractured vertebrae showed classification accuracies of 0.812, 0.665, and 0.820 for the measured, longitudinal, and combined feature sets respectively.Comment: Contributed 4-Page Paper to be presented at the 2016 IEEE International Symposium on Biomedical Imaging (ISBI), April 13-16, 2016, Prague, Czech Republi

Image analysis and statistical modelling for measurement and quality assessment of ornamental horticulture crops in glasshouses

Image analysis for ornamental crops is discussed with examples from the bedding plant industry. Feed-forward artificial neural networks are used to segment top and side view images of three contrasting species of bedding plants. The segmented images provide objective measurements of leaf and flower cover, colour, uniformity and leaf canopy height. On each imaging occasion, each pack was scored for quality by an assessor panel and it is shown that image analysis can explain 88.5%, 81.7% and 70.4% of the panel quality scores for the three species, respectively. Stereoscopy for crop height and uniformity is outlined briefly. The methods discussed here could be used for crop grading at marketing or for monitoring and assessment of growing crops within a glasshouse during all stages of production