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Author Jean-Pascal Jacob; Mariella Dimiccoli; L. Moisan edit   pdf
url  openurl
  Title Active skeleton for bacteria modelling Type Journal Article
  Year (up) 2017 Publication Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization Abbreviated Journal CMBBE  
  Volume 5 Issue 4 Pages 274-286  
  Keywords  
  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.  
  Address  
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  Publisher Taylor & Francis Group Place of Publication Editor  
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  Notes MILAB; Approved no  
  Call Number Admin @ si @JDM2017 Serial 2784  
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Author Xavier Perez Sala; Fernando De la Torre; Laura Igual; Sergio Escalera; Cecilio Angulo edit  url
openurl 
  Title Subspace Procrustes Analysis Type Journal Article
  Year (up) 2017 Publication International Journal of Computer Vision Abbreviated Journal IJCV  
  Volume 121 Issue 3 Pages 327–343  
  Keywords  
  Abstract Procrustes Analysis (PA) has been a popular technique to align and build 2-D statistical models of shapes. Given a set of 2-D shapes PA is applied to remove rigid transformations. Then, a non-rigid 2-D model is computed by modeling (e.g., PCA) the residual. Although PA has been widely used, it has several limitations for modeling 2-D shapes: occluded landmarks and missing data can result in local minima solutions, and there is no guarantee that the 2-D shapes provide a uniform sampling of the 3-D space of rotations for the object. To address previous issues, this paper proposes Subspace PA (SPA). Given several
instances of a 3-D object, SPA computes the mean and a 2-D subspace that can simultaneously model all rigid and non-rigid deformations of the 3-D object. We propose a discrete (DSPA) and continuous (CSPA) formulation for SPA, assuming that 3-D samples of an object are provided. DSPA extends the traditional PA, and produces unbiased 2-D models by uniformly sampling different views of the 3-D object. CSPA provides a continuous approach to uniformly sample the space of 3-D rotations, being more efficient in space and time. Experiments using SPA to learn 2-D models of bodies from motion capture data illustrate the benefits of our approach.
 
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  Notes MILAB; HuPBA; no proj Approved no  
  Call Number Admin @ si @ PTI2017 Serial 2841  
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Author Frederic Sampedro; Anna Domenech; Sergio Escalera; Ignasi Carrio edit  doi
openurl 
  Title Computing quantitative indicators of structural renal damage in pediatric DMSA scans Type Journal Article
  Year (up) 2017 Publication Revista Española de Medicina Nuclear e Imagen Molecular Abbreviated Journal REMNIM  
  Volume 36 Issue 2 Pages 72-77  
  Keywords  
  Abstract OBJECTIVES:
The proposal and implementation of a computational framework for the quantification of structural renal damage from 99mTc-dimercaptosuccinic acid (DMSA) scans. The aim of this work is to propose, implement, and validate a computational framework for the quantification of structural renal damage from DMSA scans and in an observer-independent manner.
MATERIALS AND METHODS:
From a set of 16 pediatric DMSA-positive scans and 16 matched controls and using both expert-guided and automatic approaches, a set of image-derived quantitative indicators was computed based on the relative size, intensity and histogram distribution of the lesion. A correlation analysis was conducted in order to investigate the association of these indicators with other clinical data of interest in this scenario, including C-reactive protein (CRP), white cell count, vesicoureteral reflux, fever, relative perfusion, and the presence of renal sequelae in a 6-month follow-up DMSA scan.
RESULTS:
A fully automatic lesion detection and segmentation system was able to successfully classify DMSA-positive from negative scans (AUC=0.92, sensitivity=81% and specificity=94%). The image-computed relative size of the lesion correlated with the presence of fever and CRP levels (p<0.05), and a measurement derived from the distribution histogram of the lesion obtained significant performance results in the detection of permanent renal damage (AUC=0.86, sensitivity=100% and specificity=75%).
CONCLUSIONS:
The proposal and implementation of a computational framework for the quantification of structural renal damage from DMSA scans showed a promising potential to complement visual diagnosis and non-imaging indicators.
 
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  Notes HuPBA;MILAB; no menciona Approved no  
  Call Number Admin @ si @ SDE2017 Serial 2842  
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Author Jose Garcia-Rodriguez; Isabelle Guyon; Sergio Escalera; Alexandra Psarrou; Andrew Lewis; Miguel Cazorla edit  doi
openurl 
  Title Editorial: Special Issue on Computational Intelligence for Vision and Robotics Type Journal Article
  Year (up) 2017 Publication Neural Computing and Applications Abbreviated Journal Neural Computing and Applications  
  Volume 28 Issue 5 Pages 853–854  
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  Notes HuPBA;MILAB; no menciona Approved no  
  Call Number Admin @ si @ GGE2017 Serial 2845  
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Author Karim Lekadir; Alfiia Galimzianova; Angels Betriu; Maria del Mar Vila; Laura Igual; Daniel L. Rubin; Elvira Fernandez-Giraldez; Petia Radeva; Sandy Napel edit  doi
openurl 
  Title A Convolutional Neural Network for Automatic Characterization of Plaque Composition in Carotid Ultrasound Type Journal Article
  Year (up) 2017 Publication IEEE Journal Biomedical and Health Informatics Abbreviated Journal J-BHI  
  Volume 21 Issue 1 Pages 48-55  
  Keywords  
  Abstract Characterization of carotid plaque composition, more specifically the amount of lipid core, fibrous tissue, and calcified tissue, is an important task for the identification of plaques that are prone to rupture, and thus for early risk estimation of cardiovascular and cerebrovascular events. Due to its low costs and wide availability, carotid ultrasound has the potential to become the modality of choice for plaque characterization in clinical practice. However, its significant image noise, coupled with the small size of the plaques and their complex appearance, makes it difficult for automated techniques to discriminate between the different plaque constituents. In this paper, we propose to address this challenging problem by exploiting the unique capabilities of the emerging deep learning framework. More specifically, and unlike existing works which require a priori definition of specific imaging features or thresholding values, we propose to build a convolutional neural network (CNN) that will automatically extract from the images the information that is optimal for the identification of the different plaque constituents. We used approximately 90 000 patches extracted from a database of images and corresponding expert plaque characterizations to train and to validate the proposed CNN. The results of cross-validation experiments show a correlation of about 0.90 with the clinical assessment for the estimation of lipid core, fibrous cap, and calcified tissue areas, indicating the potential of deep learning for the challenging task of automatic characterization of plaque composition in carotid ultrasound.  
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  Notes MILAB; no menciona Approved no  
  Call Number Admin @ si @ LGB2017 Serial 2931  
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