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| Author | Debora Gil; Sergio Vera; Agnes Borras; Albert Andaluz; Miguel Angel Gonzalez Ballester | ||||
| Title | Anatomical Medial Surfaces with Efficient Resolution of Branches Singularities | Type | Journal Article | ||
| Year | 2017 | Publication | Medical Image Analysis | Abbreviated Journal | MIA |
| Volume | 35 | Issue | Pages | 390-402 | |
| Keywords | Medial Representations; Shape Recognition; Medial Branching Stability ; Singular Points | ||||
| Abstract | Medial surfaces are powerful tools for shape description, but their use has been limited due to the sensibility existing methods to branching artifacts. Medial branching artifacts are associated to perturbations of the object boundary rather than to geometric features. Such instability is a main obstacle for a con dent application in shape recognition and description. Medial branches correspond to singularities of the medial surface and, thus, they are problematic for existing morphological and energy-based algorithms. In this paper, we use algebraic geometry concepts in an energy-based approach to compute a medial surface presenting a stable branching topology. We also present an ecient GPU-CPU implementation using standard image processing tools. We show the method computational eciency and quality on a custom made synthetic database. Finally, we present some results on a medical imaging application for localization of abdominal pathologies. | ||||
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| Publisher | Elsevier B.V. | Place of Publication | Editor | ||
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| Notes | IAM; 600.060; 600.096; 600.075; 600.145 | Approved | no | ||
| Call Number | Admin @ si @ GVB2017 | Serial | 2775 | ||
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| Author | Daniel Hernandez; Alejandro Chacon; Antonio Espinosa; David Vazquez; Juan Carlos Moure; Antonio Lopez | ||||
| Title | Stereo Matching using SGM on the GPU | Type | Report | ||
| Year | 2016 | Publication | Programming and Tuning Massively Parallel Systems | Abbreviated Journal | PUMPS |
| Volume | Issue | Pages | |||
| Keywords | CUDA; Stereo; Autonomous Vehicle | ||||
| Abstract | Dense, robust and real-time computation of depth information from stereo-camera systems is a computationally demanding requirement for robotics, advanced driver assistance systems (ADAS) and autonomous vehicles. Semi-Global Matching (SGM) is a widely used algorithm that propagates consistency constraints along several paths across the image. This work presents a real-time system producing reliable disparity estimation results on the new embedded energy efficient GPU devices. Our design runs on a Tegra X1 at 42 frames per second (fps) for an image size of 640x480, 128 disparity levels, and using 4 path directions for the SGM method. | ||||
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| Area | Expedition | Conference | PUMPS | ||
| Notes | ADAS; 600.085; 600.087; 600.076 | Approved | no | ||
| Call Number | ADAS @ adas @ HCE2016b | Serial | 2776 | ||
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| Author | Joan M. Nuñez; Jorge Bernal; F. Javier Sanchez; Fernando Vilariño | ||||
| Title | Growing Algorithm for Intersection Detection (GRAID) in branching patterns | Type | Journal Article | ||
| Year | 2015 | Publication | Machine Vision and Applications | Abbreviated Journal | MVAP |
| Volume | 26 | Issue | 2 | Pages | 387-400 |
| Keywords | Bifurcation ; Crossroad; Intersection ;Retina ; Vessel | ||||
| Abstract | Analysis of branching structures represents a very important task in fields such as medical diagnosis, road detection or biometrics. Detecting intersection landmarks Becomes crucial when capturing the structure of a branching pattern. We present a very simple geometrical model to describe intersections in branching structures based on two conditions: Bounded Tangency condition (BT) and Shortest Branch (SB) condition. The proposed model precisely sets a geometrical characterization of intersections and allows us to introduce a new unsupervised operator for intersection extraction. We propose an implementation that handles the consequences of digital domain operation that,unlike existing approaches, is not restricted to a particular scale and does not require the computation of the thinned pattern. The new proposal, as well as other existing approaches in the bibliography, are evaluated in a common framework for the first time. The performance analysis is based on two manually segmented image data sets: DRIVE retinal image database and COLON-VESSEL data set, a newly created data set of vascular content in colonoscopy frames. We have created an intersection landmark ground truth for each data set besides comparing our method in the only existing ground truth. Quantitative results confirm that we are able to outperform state-of-the-art performancelevels with the advantage that neither training nor parameter tuning is needed. | ||||
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| Notes | ;SIAI | Approved | no | ||
| Call Number | Admin @ si @MBS2015 | Serial | 2777 | ||
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| Author | Gloria Fernandez Esparrach; Jorge Bernal; Maria Lopez Ceron; Henry Cordova; Cristina Sanchez Montes; Cristina Rodriguez de Miguel; F. Javier Sanchez | ||||
| Title | Exploring the clinical potential of an automatic colonic polyp detection method based on the creation of energy maps | Type | Journal Article | ||
| Year | 2016 | Publication | Endoscopy | Abbreviated Journal | END |
| Volume | 48 | Issue | 9 | Pages | 837-842 |
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| Abstract | Background and aims: Polyp miss-rate is a drawback of colonoscopy that increases significantly in small polyps. We explored the efficacy of an automatic computer vision method for polyp detection.
Methods: Our method relies on a model that defines polyp boundaries as valleys of image intensity. Valley information is integrated into energy maps which represent the likelihood of polyp presence. Results: In 24 videos containing polyps from routine colonoscopies, all polyps were detected in at least one frame. Mean values of the maximum of energy map were higher in frames with polyps than without (p<0.001). Performance improved in high quality frames (AUC= 0.79, 95%CI: 0.70-0.87 vs 0.75, 95%CI: 0.66-0.83). Using 3.75 as maximum threshold value, sensitivity and specificity for detection of polyps were 70.4% (95%CI: 60.3-80.8) and 72.4% (95%CI: 61.6-84.6), respectively. Conclusion: Energy maps showed a good performance for colonic polyp detection. This indicates a potential applicability in clinical practice. |
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| Notes | MV; | Approved | no | ||
| Call Number | Admin @ si @FBL2016 | Serial | 2778 | ||
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| Author | Gloria Fernandez Esparrach; Jorge Bernal; Cristina Rodriguez de Miguel; Debora Gil; Fernando Vilariño; Henry Cordova; Cristina Sanchez Montes; Isis Ara | ||||
| Title | Utilidad de la visión por computador para la localización de pólipos pequeños y planos | Type | Conference Article | ||
| Year | 2016 | Publication | XIX Reunión Nacional de la Asociación Española de Gastroenterología, Gastroenterology Hepatology | Abbreviated Journal | |
| Volume | 39 | Issue | 2 | Pages | 94 |
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| Address | Madrid (Spain) | ||||
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| Area | Expedition | Conference | AEGASTRO | ||
| Notes | MV; IAM; 600.097;SIAI | Approved | no | ||
| Call Number | Admin @ si @FBR2016 | Serial | 2779 | ||
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| Author | E. Tavalera; Mariella Dimiccoli; Marc Bolaños; Maedeh Aghaei; Petia Radeva | ||||
| Title | Regularized Clustering for Egocentric Video Segmentation | Type | Book Chapter | ||
| Year | 2015 | Publication | Pattern Recognition and Image Analysis | Abbreviated Journal | |
| Volume | Issue | Pages | 327-336 | ||
| Keywords | Temporal video segmentation ; Egocentric videos ; Clustering | ||||
| Abstract | In this paper, we present a new method for egocentric video temporal segmentation based on integrating a statistical mean change detector and agglomerative clustering(AC) within an energyminimization framework. Given the tendency of most AC methods to oversegment video sequences when clustering their frames, we combine the clustering with a concept drift detection technique (ADWIN) that has rigorous guarantee of performances. ADWIN serves as a statistical upper bound for the clustering-based video segmentation. We integrate techniques in an energy-minimization framework that serves disambiguate the decision of both techniques and to complete the segmentation taking into account the temporal continuity of video frames We present experiments over egocentric sets of more than 13.000 images acquired with different wearable cameras, showing that our method outperforms state-of-the-art clustering methods. | ||||
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| Publisher | Springer International Publishing | Place of Publication | Editor | ||
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Abbreviated Series Title | LNCS | ||
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| ISSN | ISBN | 978-3-319-19390-8 | Medium | ||
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| Notes | MILAB | Approved | no | ||
| Call Number | Admin @ si @TDB2015a | Serial | 2781 | ||
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| Author | Francesco Ciompi; Simone Balocco; Juan Rigla; Xavier Carrillo; Josefina Mauri; Petia Radeva | ||||
| Title | Computer-Aided Detection of Intra-Coronary Stent in Intravascular Ultrasound Sequences | Type | Journal Article | ||
| Year | 2016 | Publication | Medical Physics | Abbreviated Journal | MP |
| Volume | 43 | Issue | 10 | Pages | |
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| Abstract | Purpose: An intraluminal coronary stent is a metal mesh tube deployed in a stenotic artery during Percutaneous Coronary Intervention (PCI), in order to prevent acute vessel occlusion. The identi cation of struts location and the de nition of the stent shape are relevant for PCI planning 15 and for patient follow-up. We present a fully-automatic framework for Computer-Aided Detection
(CAD) of intra-coronary stents in Intravascular Ultrasound (IVUS) image sequences. The CAD system is able to detect stent struts and estimate the stent shape. Methods: The proposed CAD uses machine learning to provide a comprehensive interpretation of the local structure of the vessel by means of semantic classi cation. The output of the classi cation 20 stage is then used to detect struts and to estimate the stent shape. The proposed approach is validated using a multi-centric data-set of 1,015 images from 107 IVUS sequences containing both metallic and bio-absorbable stents. Results: The method was able to detect structs in both metallic stents with an overall F-measure of 77.7% and a mean distance of 0.15 mm from manually annotated struts, and in bio-absorbable 25 stents with an overall F-measure of 77.4% and a mean distance of 0.09 mm from manually annotated struts. Conclusions: The results are close to the inter-observer variability and suggest that the system has the potential of being used as method for aiding percutaneous interventions. |
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| Notes | MILAB | Approved | no | ||
| Call Number | Admin @ si @ CBR2016 | Serial | 2819 | ||
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| Author | Mariella Dimiccoli | ||||
| Title | Fundamentals of cone regression | Type | Journal | ||
| Year | 2016 | Publication | Journal of Statistics Surveys | Abbreviated Journal | |
| Volume | 10 | Issue | Pages | 53-99 | |
| Keywords | cone regression; linear complementarity problems; proximal operators. | ||||
| Abstract | Cone regression is a particular case of quadratic programming that minimizes a weighted sum of squared residuals under a set of linear inequality constraints. Several important statistical problems such as isotonic, concave regression or ANOVA under partial orderings, just to name a few, can be considered as particular instances of the cone regression problem. Given its relevance in Statistics, this paper aims to address the fundamentals of cone regression from a theoretical and practical point of view. Several formulations of the cone regression problem are considered and, focusing on the particular case of concave regression as an example, several algorithms are analyzed and compared both qualitatively and quantitatively through numerical simulations. Several improvements to enhance numerical stability and bound the computational cost are proposed. For each analyzed algorithm, the pseudo-code and its corresponding code in Matlab are provided. The results from this study demonstrate that the choice of the optimization approach strongly impacts the numerical performances. It is also shown that methods are not currently available to solve efficiently cone regression problems with large dimension (more than many thousands of points). We suggest further research to fill this gap by exploiting and adapting classical multi-scale strategy to compute an approximate solution. | ||||
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| ISSN | 1935-7516 | ISBN | Medium | ||
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| Notes | MILAB; | Approved | no | ||
| Call Number | Admin @ si @Dim2016a | Serial | 2783 | ||
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| Author | Jean-Pascal Jacob; Mariella Dimiccoli; L. Moisan | ||||
| Title | Active skeleton for bacteria modelling | Type | Journal Article | ||
| Year | 2017 | Publication | Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization | Abbreviated Journal | CMBBE |
| Volume | 5 | Issue | 4 | Pages | 274-286 |
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| 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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| 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 | A.S. Coquel; Jean-Pascal Jacob; M. Primet; A. Demarez; Mariella Dimiccoli; T. Julou; L. Moisan; A. Lindner; H. Berry | ||||
| Title | Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect | Type | Journal Article | ||
| Year | 2013 | Publication | Plos Computational Biology | Abbreviated Journal | PCB |
| Volume | 9 | Issue | 4 | Pages | |
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| Abstract | Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of “soft” intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli. | ||||
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| Publisher | Place of Publication | Editor | : Stanislav Shvartsman, Princeton University, United States of America | ||
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| Notes | Approved | no | |||
| Call Number | Admin @ si @CJP2013 | Serial | 2786 | ||
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| Author | Mariella Dimiccoli; Benoît Girard; Alain Berthoz; Daniel Bennequin | ||||
| Title | Striola Magica: a functional explanation of otolith organs | Type | Journal Article | ||
| Year | 2013 | Publication | Journal of Computational Neuroscience | Abbreviated Journal | JCN |
| Volume | 35 | Issue | 2 | Pages | 125-154 |
| Keywords | Otolith organs ;Striola; Vestibular pathway | ||||
| Abstract | Otolith end organs of vertebrates sense linear accelerations of the head and gravitation. The hair cells on their epithelia are responsible for transduction. In mammals, the striola, parallel to the line where hair cells reverse their polarization, is a narrow region centered on a curve with curvature and torsion. It has been shown that the striolar region is functionally different from the rest, being involved in a phasic vestibular pathway. We propose a mathematical and computational model that explains the necessity of this amazing geometry for the striola to be able to carry out its function. Our hypothesis, related to the biophysics of the hair cells and to the physiology of their afferent neurons, is that striolar afferents collect information from several type I hair cells to detect the jerk in a large domain of acceleration directions. This predicts a mean number of two calyces for afferent neurons, as measured in rodents. The domain of acceleration directions sensed by our striolar model is compatible with the experimental results obtained on monkeys considering all afferents. Therefore, the main result of our study is that phasic and tonic vestibular afferents cover the same geometrical fields, but at different dynamical and frequency domains. | ||||
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| Publisher | Springer US | Place of Publication | Editor | ||
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| ISSN | 1573-6873. 2013 | ISBN | Medium | ||
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| Notes | MILAB | Approved | no | ||
| Call Number | Admin @ si @DBG2013 | Serial | 2787 | ||
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| Author | Maria Oliver; Gloria Haro; Mariella Dimiccoli; Baptiste Mazin; Coloma Ballester | ||||
| Title | A computational model of amodal completion | Type | Conference Article | ||
| Year | 2016 | Publication | SIAM Conference on Imaging Science | Abbreviated Journal | |
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| Abstract | This paper presents a computational model to recover the most likely interpretation of the 3D scene structure from a planar image, where some objects may occlude others. The estimated scene interpretation is obtained by integrating some global and local cues and provides both the complete disoccluded objects that form the scene and their ordering according to depth. Our method first computes several distal scenes which are compatible with the proximal planar image. To compute these different hypothesized scenes, we propose a perceptually inspired object disocclusion method, which works by minimizing the Euler's elastica as well as by incorporating the relatability of partially occluded contours and the convexity of the disoccluded objects. Then, to estimate the preferred scene we rely on a Bayesian model and define probabilities taking into account the global complexity of the objects in the hypothesized scenes as well as the effort of bringing these objects in their relative position in the planar image, which is also measured by an Euler's elastica-based quantity. The model is illustrated with numerical experiments on, both, synthetic and real images showing the ability of our model to reconstruct the occluded objects and the preferred perceptual order among them. We also present results on images of the Berkeley dataset with provided figure-ground ground-truth labeling. | ||||
| Address | Albuquerque; New Mexico; USA; May 2016 | ||||
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| Notes | MILAB; 601.235 | Approved | no | ||
| Call Number | Admin @ si @OHD2016a | Serial | 2788 | ||
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| Author | G. de Oliveira; A. Cartas; Marc Bolaños; Mariella Dimiccoli; Xavier Giro; Petia Radeva | ||||
| Title | LEMoRe: A Lifelog Engine for Moments Retrieval at the NTCIR-Lifelog LSAT Task | Type | Conference Article | ||
| Year | 2016 | Publication | 12th NTCIR Conference on Evaluation of Information Access Technologies | Abbreviated Journal | |
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| Abstract | Semantic image retrieval from large amounts of egocentric visual data requires to leverage powerful techniques for filling in the semantic gap. This paper introduces LEMoRe, a Lifelog Engine for Moments Retrieval, developed in the context of the Lifelog Semantic Access Task (LSAT) of the the NTCIR-12 challenge and discusses its performance variation on different trials. LEMoRe integrates classical image descriptors with high-level semantic concepts extracted by Convolutional Neural Networks (CNN), powered by a graphic user interface that uses natural language processing. Although this is just a first attempt towards interactive image retrieval from large egocentric datasets and there is a large room for improvement of the system components and the user interface, the structure of the system itself and the way the single components cooperate are very promising. | ||||
| Address | Tokyo; Japan; June 2016 | ||||
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| Area | Expedition | Conference | NTCIR | ||
| Notes | MILAB; | Approved | no | ||
| Call Number | Admin @ si @OCB2016 | Serial | 2789 | ||
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| Author | G. de Oliveira; Mariella Dimiccoli; Petia Radeva | ||||
| Title | Egocentric Image Retrieval With Deep Convolutional Neural Networks | Type | Conference Article | ||
| Year | 2016 | Publication | 19th International Conference of the Catalan Association for Artificial Intelligence | Abbreviated Journal | |
| Volume | Issue | Pages | 71-76 | ||
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| Address | Barcelona; Spain; October 2016 | ||||
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| Area | Expedition | Conference | CCIA | ||
| Notes | MILAB | Approved | no | ||
| Call Number | Admin @ si @ODR2016 | Serial | 2790 | ||
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| Author | Maedeh Aghaei; Mariella Dimiccoli; Petia Radeva | ||||
| Title | With whom do I interact with? Social interaction detection in egocentric photo-streams | Type | Conference Article | ||
| Year | 2016 | Publication | 23rd International Conference on Pattern Recognition | Abbreviated Journal | |
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| Abstract | Given a user wearing a low frame rate wearable camera during a day, this work aims to automatically detect the moments when the user gets engaged into a social interaction solely by reviewing the automatically captured photos by the worn camera. The proposed method, inspired by the sociological concept of F-formation, exploits distance and orientation of the appearing individuals -with respect to the user- in the scene from a bird-view perspective. As a result, the interaction pattern over the sequence can be understood as a two-dimensional time series that corresponds to the temporal evolution of the distance and orientation features over time. A Long-Short Term Memory-based Recurrent Neural Network is then trained to classify each time series. Experimental evaluation over a dataset of 30.000 images has shown promising results on the proposed method for social interaction detection in egocentric photo-streams. | ||||
| Address | Cancun; Mexico; December 2016 | ||||
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| Area | Expedition | Conference | ICPR | ||
| Notes | MILAB | Approved | no | ||
| Call Number | Admin @ si @ADR2016a | Serial | 2791 | ||
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