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Author |
Jean-Pascal Jacob; Mariella Dimiccoli; L. Moisan |
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Title |
Active skeleton for bacteria modelling |
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Journal Article |
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Year |
2017 |
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Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization |
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CMBBE |
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5 |
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4 |
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274-286 |
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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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Taylor & Francis Group |
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MILAB; |
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Admin @ si @JDM2017 |
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2784 |
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Sumit K. Banchhor; Tadashi Araki; Narendra D. Londhe; Nobutaka Ikeda; Petia Radeva; Ayman El-Baz; Luca Saba; Andrew Nicolaides; Shoaib Shafique; John R. Laird; Jasjit S. Suri |
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Five multiresolution-based calcium volume measurement techniques from coronary IVUS videos: A comparative approach |
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Journal Article |
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Year |
2016 |
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Computer Methods and Programs in Biomedicine |
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CMPB |
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134 |
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237-258 |
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BACKGROUND AND OBJECTIVE:
Fast intravascular ultrasound (IVUS) video processing is required for calcium volume computation during the planning phase of percutaneous coronary interventional (PCI) procedures. Nonlinear multiresolution techniques are generally applied to improve the processing time by down-sampling the video frames.
METHODS:
This paper presents four different segmentation methods for calcium volume measurement, namely Threshold-based, Fuzzy c-Means (FCM), K-means, and Hidden Markov Random Field (HMRF) embedded with five different kinds of multiresolution techniques (bilinear, bicubic, wavelet, Lanczos, and Gaussian pyramid). This leads to 20 different kinds of combinations. IVUS image data sets consisting of 38,760 IVUS frames taken from 19 patients were collected using 40 MHz IVUS catheter (Atlantis® SR Pro, Boston Scientific®, pullback speed of 0.5 mm/sec.). The performance of these 20 systems is compared with and without multiresolution using the following metrics: (a) computational time; (b) calcium volume; (c) image quality degradation ratio; and (d) quality assessment ratio.
RESULTS:
Among the four segmentation methods embedded with five kinds of multiresolution techniques, FCM segmentation combined with wavelet-based multiresolution gave the best performance. FCM and wavelet experienced the highest percentage mean improvement in computational time of 77.15% and 74.07%, respectively. Wavelet interpolation experiences the highest mean precision-of-merit (PoM) of 94.06 ± 3.64% and 81.34 ± 16.29% as compared to other multiresolution techniques for volume level and frame level respectively. Wavelet multiresolution technique also experiences the highest Jaccard Index and Dice Similarity of 0.7 and 0.8, respectively. Multiresolution is a nonlinear operation which introduces bias and thus degrades the image. The proposed system also provides a bias correction approach to enrich the system, giving a better mean calcium volume similarity for all the multiresolution-based segmentation methods. After including the bias correction, bicubic interpolation gives the largest increase in mean calcium volume similarity of 4.13% compared to the rest of the multiresolution techniques. The system is automated and can be adapted in clinical settings.
CONCLUSIONS:
We demonstrated the time improvement in calcium volume computation without compromising the quality of IVUS image. Among the 20 different combinations of multiresolution with calcium volume segmentation methods, the FCM embedded with wavelet-based multiresolution gave the best performance. |
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MILAB; |
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Admin @ si @ BAL2016 |
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2830 |
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Author |
Xavier Perez Sala; Fernando De la Torre; Laura Igual; Sergio Escalera; Cecilio Angulo |
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Title |
Subspace Procrustes Analysis |
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Journal Article |
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Year |
2017 |
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International Journal of Computer Vision |
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IJCV |
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121 |
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3 |
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327–343 |
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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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MILAB; HuPBA; no proj |
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Admin @ si @ PTI2017 |
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2841 |
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Frederic Sampedro; Anna Domenech; Sergio Escalera; Ignasi Carrio |
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Computing quantitative indicators of structural renal damage in pediatric DMSA scans |
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Journal Article |
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Year |
2017 |
Publication |
Revista Española de Medicina Nuclear e Imagen Molecular |
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REMNIM |
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36 |
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2 |
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72-77 |
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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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HuPBA;MILAB; no menciona |
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no |
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Admin @ si @ SDE2017 |
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2842 |
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Author |
Mikkel Thogersen; Sergio Escalera; Jordi Gonzalez; Thomas B. Moeslund |
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Title |
Segmentation of RGB-D Indoor scenes by Stacking Random Forests and Conditional Random Fields |
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Journal Article |
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Year |
2016 |
Publication |
Pattern Recognition Letters |
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PRL |
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80 |
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208–215 |
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This paper proposes a technique for RGB-D scene segmentation using Multi-class
Multi-scale Stacked Sequential Learning (MMSSL) paradigm. Following recent trends in state-of-the-art, a base classifier uses an initial SLIC segmentation to obtain superpixels which provide a diminution of data while retaining object boundaries. A series of color and depth features are extracted from the superpixels, and are used in a Conditional Random Field (CRF) to predict superpixel labels. Furthermore, a Random Forest (RF) classifier using random offset features is also used as an input to the CRF, acting as an initial prediction. As a stacked classifier, another Random Forest is used acting on a spatial multi-scale decomposition of the CRF confidence map to correct the erroneous labels assigned by the previous classifier. The model is tested on the popular NYU-v2 dataset.
The approach shows that simple multi-modal features with the power of the MMSSL
paradigm can achieve better performance than state of the art results on the same dataset. |
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HuPBA; ISE;MILAB; 600.098; 600.119 |
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Admin @ si @ TEG2016 |
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2843 |
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