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Frederic Sampedro, Sergio Escalera, Anna Domenech, & Ignasi Carrio. (2015). Automatic Tumor Volume Segmentation in Whole-Body PET/CT Scans: A Supervised Learning Approach Source. JMIHI - Journal of Medical Imaging and Health Informatics, 5(2), 192–201.
Abstract: Whole-body 3D PET/CT tumoral volume segmentation provides relevant diagnostic and prognostic information in clinical oncology and nuclear medicine. Carrying out this procedure manually by a medical expert is time consuming and suffers from inter- and intra-observer variabilities. In this paper, a completely automatic approach to this task is presented. First, the problem is stated and described both in clinical and technological terms. Then, a novel supervised learning segmentation framework is introduced. The segmentation by learning approach is defined within a Cascade of Adaboost classifiers and a 3D contextual proposal of Multiscale Stacked Sequential Learning. Segmentation accuracy results on 200 Breast Cancer whole body PET/CT volumes show mean 49% sensitivity, 99.993% specificity and 39% Jaccard overlap Index, which represent good performance results both at the clinical and technological level.
Keywords: CONTEXTUAL CLASSIFICATION; PET/CT; SUPERVISED LEARNING; TUMOR SEGMENTATION; WHOLE BODY
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Jean-Pascal Jacob, Mariella Dimiccoli, & Lionel Moisan. (2016). Active skeleton for bacteria modeling. CMBBE - Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization, 5(4), 274–286.
Abstract: The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at this http URL
Keywords: Bacteria modelling; medial axis; active contours; active skeleton; shape contraints
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Jean-Pascal Jacob, Mariella Dimiccoli, & L. Moisan. (2017). Active skeleton for bacteria modelling. CMBBE - Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization, 5(4), 274–286.
Abstract: The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modelling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness and orientation), an improved boundary accuracy in noisy images and a natural bacteria-centred coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimising an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modelling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.
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Marc Oliu, Ciprian Corneanu, Kamal Nasrollahi, Olegs Nikisins, Sergio Escalera, Yunlian Sun, et al. (2016). Improved RGB-D-T based Face Recognition. BIO - IET Biometrics, 5(4), 297–303.
Abstract: Reliable facial recognition systems are of crucial importance in various applications from entertainment to security. Thanks to the deep-learning concepts introduced in the field, a significant improvement in the performance of the unimodal facial recognition systems has been observed in the recent years. At the same time a multimodal facial recognition is a promising approach. This study combines the latest successes in both directions by applying deep learning convolutional neural networks (CNN) to the multimodal RGB, depth, and thermal (RGB-D-T) based facial recognition problem outperforming previously published results. Furthermore, a late fusion of the CNN-based recognition block with various hand-crafted features (local binary patterns, histograms of oriented gradients, Haar-like rectangular features, histograms of Gabor ordinal measures) is introduced, demonstrating even better recognition performance on a benchmark RGB-D-T database. The obtained results in this study show that the classical engineered features and CNN-based features can complement each other for recognition purposes.
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Md. Mostafa Kamal Sarker, Hatem A. Rashwan, Farhan Akram, Estefania Talavera, Syeda Furruka Banu, Petia Radeva, et al. (2019). Recognizing Food Places in Egocentric Photo-Streams Using Multi-Scale Atrous Convolutional Networks and Self-Attention Mechanism. ACCESS - IEEE Access, 7, 39069–39082.
Abstract: Wearable sensors (e.g., lifelogging cameras) represent very useful tools to monitor people's daily habits and lifestyle. Wearable cameras are able to continuously capture different moments of the day of their wearers, their environment, and interactions with objects, people, and places reflecting their personal lifestyle. The food places where people eat, drink, and buy food, such as restaurants, bars, and supermarkets, can directly affect their daily dietary intake and behavior. Consequently, developing an automated monitoring system based on analyzing a person's food habits from daily recorded egocentric photo-streams of the food places can provide valuable means for people to improve their eating habits. This can be done by generating a detailed report of the time spent in specific food places by classifying the captured food place images to different groups. In this paper, we propose a self-attention mechanism with multi-scale atrous convolutional networks to generate discriminative features from image streams to recognize a predetermined set of food place categories. We apply our model on an egocentric food place dataset called “EgoFoodPlaces” that comprises of 43 392 images captured by 16 individuals using a lifelogging camera. The proposed model achieved an overall classification accuracy of 80% on the “EgoFoodPlaces” dataset, respectively, outperforming the baseline methods, such as VGG16, ResNet50, and InceptionV3.
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