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J.P. 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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David Rotger, Misael Rosales, Jaume Garcia, Oriol Pujol, Josefina Mauri, & Petia Radeva. (2003). Active Vessel: A New Multimedia Workstation for Intravascular Ultrasound and Angiography Fusion. Computers in Cardiology, 30, 65–68.
Abstract: AcriveVessel is a new multimedia workstation which enables the visualization, acquisition and handling of both image modalities, on- and ofline. It enables DICOM v3.0 decompression and browsing, video acquisition,repmduction and storage for IntraVascular UltraSound (IVUS) and angiograms with their corresponding ECG,automatic catheter segmentation in angiography images (using fast marching algorithm). BSpline models definition for vessel layers on IVUS images sequence and an extensively validated tool to fuse information. This approach defines the correspondence of every IVUS image with its correspondent point in the angiogram and viceversa. The 3 0 reconstruction of the NUS catheterhessel enables real distance measurements as well as threedimensional visualization showing vessel tortuosity in the space.
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Alejandro Cartas, Petia Radeva, & Mariella Dimiccoli. (2020). Activities of Daily Living Monitoring via a Wearable Camera: Toward Real-World Applications. ACCESS - IEEE Access, 8, 77344–77363.
Abstract: Activity recognition from wearable photo-cameras is crucial for lifestyle characterization and health monitoring. However, to enable its wide-spreading use in real-world applications, a high level of generalization needs to be ensured on unseen users. Currently, state-of-the-art methods have been tested only on relatively small datasets consisting of data collected by a few users that are partially seen during training. In this paper, we built a new egocentric dataset acquired by 15 people through a wearable photo-camera and used it to test the generalization capabilities of several state-of-the-art methods for egocentric activity recognition on unseen users and daily image sequences. In addition, we propose several variants to state-of-the-art deep learning architectures, and we show that it is possible to achieve 79.87% accuracy on users unseen during training. Furthermore, to show that the proposed dataset and approach can be useful in real-world applications, where data can be acquired by different wearable cameras and labeled data are scarcely available, we employed a domain adaptation strategy on two egocentric activity recognition benchmark datasets. These experiments show that the model learned with our dataset, can easily be transferred to other domains with a very small amount of labeled data. Taken together, those results show that activity recognition from wearable photo-cameras is mature enough to be tested in real-world applications.
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Michal Drozdzal, Santiago Segui, Carolina Malagelada, Fernando Azpiroz, & Petia Radeva. (2013). Adaptable image cuts for motility inspection using WCE. CMIG - Computerized Medical Imaging and Graphics, 37(1), 72–80.
Abstract: The Wireless Capsule Endoscopy (WCE) technology allows the visualization of the whole small intestine tract. Since the capsule is freely moving, mainly by the means of peristalsis, the data acquired during the study gives a lot of information about the intestinal motility. However, due to: (1) huge amount of frames, (2) complex intestinal scene appearance and (3) intestinal dynamics that make difficult the visualization of the small intestine physiological phenomena, the analysis of the WCE data requires computer-aided systems to speed up the analysis. In this paper, we propose an efficient algorithm for building a novel representation of the WCE video data, optimal for motility analysis and inspection. The algorithm transforms the 3D video data into 2D longitudinal view by choosing the most informative, from the intestinal motility point of view, part of each frame. This step maximizes the lumen visibility in its longitudinal extension. The task of finding “the best longitudinal view” has been defined as a cost function optimization problem which global minimum is obtained by using Dynamic Programming. Validation on both synthetic data and WCE data shows that the adaptive longitudinal view is a good alternative to the traditional motility analysis done by video analysis. The proposed novel data representation a new, holistic insight into the small intestine motility, allowing to easily define and analyze motility events that are difficult to spot by analyzing WCE video. Moreover, the visual inspection of small intestine motility is 4 times faster then by means of video skimming of the WCE.
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O. Rodriguez-Leor, E Fernandez-Nofrerias, J. Mauri, R. Villuendas, C. Garcia, V. Valle, et al. (2003). An empiric model for three-dimensional reconstruction of coronary vessels from X-ray angiography. European Heart Journal (IF: 5.997), ESC Congress 2003.
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