Fuzzy C-Means Clustering with Histogram based Cluster Selection for Skin Lesion Segmentation using Non-Dermoscopic Images

Purpose – Pre-screening of skin lesion for malignancy is highly demanded as melanoma being a life-threatening skin cancer due to unpaired DNA damage. In this paper, lesion segmentation based on Fuzzy C-Means clustering using non-dermoscopic images has been proposed. Design/methodology/approach – The proposed methodology consists of automatic cluster selection for FCM using the histogram property. The system used the local maxima along with Euclidean distance to detect the binomial distribution property of the image histogram, to segment the melanoma from normal skin. As the Value channel of HSV color image provides better and distinct histogram distribution based on the entropy, it has been used for segmentation purpose. Findings – The proposed system can effectively segment the lesion region from the normal skin. The system provides a segmentation accuracy of 95.69 % and the comparative analysis has been performed with various segmentation methods. From the analysis, it has been observed that the proposed system can effectively segment the lesion region from normal skin automatically. Originality/Value – This paper suggests a new approach for skin lesion segmentation based on FCM with automatic cluster selection. Here, different color channel has also been analyzed using entropy to select the better channel for segmentation. In future, the classification of melanoma from benign naevi can be performed

Emerging properties of signaling networks in cancer: a data-derived modeling approach

Mammalian signal transduction pathways are highly integrated within extended networks, with crosstalk emerging in space and time. This dynamic circuitry is dependent on changing activity states for proteins and organelles. Network structures govern specificity of cellular responses to external stimuli, including proliferation and cell death. Loss of regulation virtually underlies all disease. However, while the contributions of individual components to phenotype are mostly well understood, systematic elucidation for the emergence or loss of crosstalk and impact on phenotype remains a fundamental challenge in classical biology that can be investigated by systems biology. To that end, we established a mathematical modeling platform, at the interface between experimental and theoretical approaches, to integrate prior literature knowledge with high-content, heterogeneous datasets for the non-intuitive prediction of adaptive signaling events. In the first part of this work, we investigated high-content microscopy datasets of morphological, bio-energetic and functional features of mitochondria in response to pro- apoptotic treatment in MCF-7 breast cancer cells. Data pretreatment techniques were used to unify the heterogeneous datasets. Using fuzzy logic, we established a generalized data-driven modeling formalism to model signaling events solely based on measurements, capable of high simulation accuracy via non-discrete rule sets. Employing neural networks, a generalized fuzzy logic system, i.e. its rules and membership functions, could be parameterized for each potential signaling interaction. An exhaustive search approach identified models with least error, i.e. the most related signaling events, and predicted a hierarchy of apoptotic events, in which upon activation of pro-apoptotic Bax, mitochondrial fragmentation propagates apoptosis, which is consistent with reported literature. Hence, we established a predictive approach for investigation of protein and organelle interactions utilizing cell-to-cell heterogeneity, a critical source of biologically relevant information. In the second part of this work, we sought to identify network evolution in the topology of MAPK signaling in the A-375 melanoma cell line. To that end, the modeling method was extended to incorporate temporal and topological structure from phosphorylation profiles of key MAPK intermediates treated with different pharmacological inhibitors and acquired over 96 hours. To increase prediction power, a parameter reduction strategy was developed to identify and fix parameters with lowest contribution to model performance. Therefore, training datasets were bootstrapped and signatures of deviation in flexibility and accuracy were calculated. This novel strategy achieved an optimal set of free parameters. Finally, a reduced multi-treatment model encoding the behavior of the full MAPK dataset was systematically trained to a sequentially increasing subset of time points, enabling time-defined identification of discrepancies in reported vs. acquired network topology. To that end, an objective function for fuzzy logic model optimization was implemented, which accounted for time-defined model training. Analysis led to the identification of emerging discrepancies between model and data at specific time points, thus characterizing a potential network rearrangement upstream of MAPK kinase MEK1, consistent with studies reporting increased resistance to apoptosis exhibited by A-375 melanoma cell line. The approach presented here was successfully benchmarked against a recently published fuzzy-logic-based analysis of signal transduction

Image analysis for diagnostic support in biomedicine: neuromuscular diseases and pigmented lesions

Tesis descargada desde TESEOEsta tesis presenta dos sistemas implementados mediante técnicas de procesamiento de imagen, para ayuda al diagnóstico de enfermedades neuromusculares a partir de imágenes de microscopía de fluorescencia y análisis de lesiones pigmentadas a partir de imágenes dermoscópicas. El diagnóstico de enfermedades neuromusculares se basa en la evaluación visual de las biopsias musculares por parte del patólogo especialista, lo que conlleva una carga subjetiva. El primer sistema propuesto en esta tesis analiza objetivamente las biopsias musculares y las clasifica en distrofias, atrofias neurógenas o control (sin enfermedad) a través de imágenes de microscopía de fluorescencia. Su implementación reúne los elementos propios de un sistema de ayuda al diagnóstico asistido por ordenador: segmentación, extracción de características, selección de características y clasificación. El procedimiento comienza con una segmentación precisa de las fibras musculares usando morfología matemática y una transformada Watershed. A continuación, se lleva a cabo un paso de extracción de características, en el cual reside la principal contribución del sistema, ya que no solo se extraen aquellas que los patólogos tienen en cuenta para diagnosticar sino características que se escapan de la visión humana. Estas nuevas características se extraen suponiendo que la estructura de la biopsia se comporta como un grafo, en el que los nodos se corresponden con las fibras musculares, y dos nodos están conectados si dos fibras son adyacentes. Para estudiar la efectividad que estos dos conjuntos presentan en la categorización de las biopsias, se realiza una selección de características y una clasi- ficación empleando una red neuronal Fuzzy ARTMAP. El procedimiento concluye con una estimación de la severidad de las biopsias con patrón distrófico. Esta caracterización se realiza mediante un análisis de componentes principales. Para la validación del sistema se ha empleado una base de datos compuesta por 91 imágenes de biopsias musculares, de las cuales 71 se consideran imágenes de entrenamiento y 20 imágenes de prueba. Se consigue una elevada tasa de aciertos de clasificacion y se llega a la importante conclusión de que las nuevas características estructurales que no pueden ser detectadas por inspección visual mejoran la identificación de biopsias afectadas por atrofia neurógena. La segunda parte de la tesis presenta un sistema de clasificación de lesiones pigmentadas. Primero se propone un algoritmo de segmentación de imágenes en color para ais lar la lesión de la piel circundante. Su desarrollo se centra en conseguir un algoritmo relacionado con las diferencias color percibidas por el ojo humano. Consiguiendo así, no solo un método de segmentación de lesiones pigmentadas sino un algoritmo de segmentación de propósito general. El método de segmentación propuesto se basa en un gradiente para imágenes en color integrado en una técnica de level set para detección de bordes. La elección del gradiente se derivada a partir de un análisis de tres gradientes de color implementados en el espacio de color uniforme CIE L∗a∗b∗ y basados en las ecuaciones de diferencia de color desarrolladas por la comisión internacional de iluminación (CIELAB, CIE94 y CIEDE2000). El principal objetivo de este análisis es estudiar cómo estas ecuaciones afectan en la estimación de los gradientes en términos de correlación con la percepción visual del color. Una técnica de level-set se aplica sobre estos gradientes consiguiendo así un detector de borde que permite evaluar el rendimiento de dichos gradientes. La validación se lleva a cabo sobre una base de datos compuesta por imágenes sintéticas diseñada para tal fin. Se realizaron tanto medidas cuantitativas como cualitativas. Finalmente, se concluye que el detector de bordes basado en la ecuación de diferencias de color CIE94 presenta la mayor correlación con la percepción visual del color. A partir de entonces, la tesis intenta emular el método de análisis de patrones, la técnica de diagnóstico de lesiones pigmentadas de la piel más empleada por los dermatólogos. Este método trata de identificar patrones específicos, pudiendo ser tanto globales como locales. En esta tesis se presenta una amplia revisión de los métodos algorítmicos, publicados en la literatura, que detectan automáticamente dichos patrones a partir de imágenes dermoscópicas de lesiones pigmentadas. Tras esta revisón se advierte que numerosos trabajos se centran en la detección de patrones locales, pero solo unos pocos abordan la detección de patrones globales. El siguiente paso de esta tesis, por tanto, es la propuesta de diferentes métodos de clasi- ficación de patrones globales. El objetivo es identificar tres patrones: reticular, globular y empedrado (considerado un solo patrón) y homogéneo. Los métodos propuestos se basan en un análisis de textura mediante técnicas de modelado. En primer lugar una imagen demoscópica se modela mediante campos aleatorios de Markov, los parámetros estimados de este modelo se consideran características. A su vez, se supone que la distribución de estas características a lo largo de la lesión sigue diferentes modelos: un modelo gaussiano, un modelo de mezcla de gaussianas o un modelo de bolsa de características. La clasificación se lleva a cabo mediante una recuperación de imágenes basada en diferentes métricas de distancia. Para validar los métodos se emplea un conjunto significativo de imágenes dermatológicas, concluyendo que el modelo basado en mezcla de gaussianas proporciona la mejor tasa de clasificación. Además, se incluye una evaluación adicional en la que se clasifican melanomas con patrón multicomponente obteniendo resultados prometedores. Finalmente, se presenta una discusión sobre los hallazgos y conclusiones más relevantes extraídas de esta tesis, así como las líneas futuras que se derivan de este trabajo.Premio Extraordinario de Doctorado U

Advances in quantitative microscopy

Microscopy allows us to peer into the complex deeply shrouded world that the cells of our body grow and thrive in. With the emergence of automated digital microscopes and software for anlysing and processing the large numbers of image that they produce; quantitative microscopy approaches are now allowing us to answer ever larger and more complex biological questions. In this thesis I explore two trends. Firstly, that of using quantitative microscopy for performing unbiased screens, the advances made here include developing strategies to handle imaging data captured from physiological models, and unsupervised analysis screening data to derive unbiased biological insights. Secondly, I develop software for analysing live cell imaging data, that can now be captured at greater rates than ever before and use this to help answer key questions covering the biology of how cells make the decision to arrest or proliferate in response to DNA damage. Together this thesis represents a view of the current state of the art in high-throughput quantitative microscopy and details where the field is heading as machine learning approaches become ever more sophisticated.Open Acces

Advanced Computational Methods for Oncological Image Analysis

[Cancer is the second most common cause of death worldwide and encompasses highly variable clinical and biological scenarios. Some of the current clinical challenges are (i) early diagnosis of the disease and (ii) precision medicine, which allows for treatments targeted to specific clinical cases. The ultimate goal is to optimize the clinical workflow by combining accurate diagnosis with the most suitable therapies. Toward this, large-scale machine learning research can define associations among clinical, imaging, and multi-omics studies, making it possible to provide reliable diagnostic and prognostic biomarkers for precision oncology. Such reliable computer-assisted methods (i.e., artificial intelligence) together with clinicians’ unique knowledge can be used to properly handle typical issues in evaluation/quantification procedures (i.e., operator dependence and time-consuming tasks). These technical advances can significantly improve result repeatability in disease diagnosis and guide toward appropriate cancer care. Indeed, the need to apply machine learning and computational intelligence techniques has steadily increased to effectively perform image processing operations—such as segmentation, co-registration, classification, and dimensionality reduction—and multi-omics data integration.

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

Unraveling the intricacies of spatial organization of the ErbB receptors and downstream signaling pathways

Faced with the complexity of diseases such as cancer which has 1012 mutations, altering gene expression, and disrupting regulatory networks, there has been a paradigm shift in the biological sciences and what has emerged is a much more quantitative field of biology. Mathematical modeling can aid in biological discovery with the development of predictive models that provide future direction for experimentalist. In this work, I have contributed to the development of novel computational approaches which explore mechanisms of receptor aggregation and predict the effects of downstream signaling. The coupled spatial non-spatial simulation algorithm, CSNSA is a tool that I took part in developing, which implements a spatial kinetic Monte Carlo for capturing receptor interactions on the cell membrane with Gillespies stochastic simulation algorithm, SSA, for temporal cytosolic interactions. Using this framework we determine that receptor clustering significantly enhances downstream signaling. In the next study the goal was to understand mechanisms of clustering. Cytoskeletal interactions with mobile proteins are known to hinder diffusion. Using a Monte Carlo approach we simulate these interactions, determining at what cytoskeletal distribution and receptor concentration optimal clustering occurs and when it is inhibited. We investigate oligomerization induced trapping to determine mechanisms of clustering, and our results show that the cytoskeletal interactions lead to receptor clustering. After exploring the mechanisms of clustering we determine how receptor aggregation effects downstream signaling. We further proceed by implementing the adaptively coarse grained Monte Carlo, ACGMC to determine if \u27receptor-sharing\u27 occurs when receptors are clustered. In our proposed \u27receptor-sharing\u27 mechanism a cytosolic species binds with a receptor then disassociates and rebinds a neighboring receptor. We tested our hypothesis using a novel computational approach, the ACGMC, an algorithm which enables the spatial temporal evolution of the system in three dimensions by using a coarse graining approach. In this framework we are modeling EGFR reaction-diffusion events on the plasma membrane while capturing the spatial-temporal dynamics of proteins in the cytosol. From this framework we observe \u27receptor-sharing\u27 which may be an important mechanism in the regulation and overall efficiency of signal transduction. In summary, I have helped to develop predictive computational tools that take systems biology in a new direction.\u2

Supervised saliency map driven segmentation of lesions in dermoscopic images

Lesion segmentation is the first step in most automatic melanoma recognition systems. Deficiencies and difficulties in dermoscopic images such as color inconstancy, hair occlusion, dark corners, and color charts make lesion segmentation an intricate task. In order to detect the lesion in the presence of these problems, we propose a supervised saliency detection method tailored for dermoscopic images based on the discriminative regional feature integration (DRFI). A DRFI method incorporates multilevel segmentation, regional contrast, property, background descriptors, and a random forest regressor to create saliency scores for each region in the image. In our improved saliency detection method, mDRFI, we have added some new features to regional property descriptors. Also, in order to achieve more robust regional background descriptors, a thresholding algorithm is proposed to obtain a new pseudo-background region. Findings reveal that mDRFI is superior to DRFI in detecting the lesion as the salient object in dermoscopic images. The proposed overall lesion segmentation framework uses detected saliency map to construct an initial mask of the lesion through thresholding and postprocessing operations. The initial mask is then evolving in a level set framework to fit better on the lesion's boundaries. The results of evaluation tests on three public datasets show that our proposed segmentation method outperforms the other conventional state-of-the-art segmentation algorithms and its performance is comparable with most recent approaches that are based on deep convolutional neural networks

Imparting 3D representations to artificial intelligence for a full assessment of pressure injuries.

During recent decades, researches have shown great interest to machine learning techniques in order to extract meaningful information from the large amount of data being collected each day. Especially in the medical field, images play a significant role in the detection of several health issues. Hence, medical image analysis remarkably participates in the diagnosis process and it is considered a suitable environment to interact with the technology of intelligent systems. Deep Learning (DL) has recently captured the interest of researchers as it has proven to be efficient in detecting underlying features in the data and outperformed the classical machine learning methods. The main objective of this dissertation is to prove the efficiency of Deep Learning techniques in tackling one of the important health issues we are facing in our society, through medical imaging. Pressure injuries are a dermatology related health issue associated with increased morbidity and health care costs. Managing pressure injuries appropriately is increasingly important for all the professionals in wound care. Using 2D photographs and 3D meshes of these wounds, collected from collaborating hospitals, our mission is to create intelligent systems for a full non-intrusive assessment of these wounds. Five main tasks have been achieved in this study: a literature review of wound imaging methods using machine learning techniques, the classification and segmentation of the tissue types inside the pressure injury, the segmentation of these wounds and the design of an end-to-end system which measures all the necessary quantitative information from 3D meshes for an efficient assessment of PIs, and the integration of the assessment imaging techniques in a web-based application