David Roche, Debora Gil, & Jesus Giraldo. (2012). Assessing agonist efficacy in an uncertain Em world. In A. Christopoulus and M. Bouvier (Ed.), 40th Keystone Symposia on mollecular and celular biology (79). Keystone Symposia.
Abstract: The operational model of agonism has been widely used for the analysis of agonist action since its formulation in 1983. The model includes the Em parameter, which is defined as the maximum response of the system. The methods for Em estimation provide Em values not significantly higher than the maximum responses achieved by full agonists. However, it has been found that that some classes of compounds as, for instance, superagonists and positive allosteric modulators can increase the full agonist maximum response, implying upper limits for Em and thereby posing doubts on the validity of Em estimates. Because of the correlation between Em and operational efficacy, τ, wrong Em estimates will yield wrong τ estimates.
In this presentation, the operational model of agonism and various methods for the simulation of allosteric modulation will be analyzed. Alternatives for curve fitting will be presented and discussed.
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Debora Gil, Agnes Borras, Manuel Ballester, Francesc Carreras, Ruth Aris, Manuel Vazquez, et al. (2011). MIOCARDIA: Integrating cardiac function and muscular architecture for a better diagnosis. In Association for Computing Machinery (Ed.), 14th International Symposium on Applied Sciences in Biomedical and Communication Technologies. Barcelona, Spain.
Abstract: Deep understanding of myocardial structure of the heart would unravel crucial knowledge for clinical and medical procedures. The MIOCARDIA project is a multidisciplinary project in cooperation with l'Hospital de la Santa Creu i de Sant Pau, Clinica la Creu Blanca and Barcelona Supercomputing Center. The ultimate goal of this project is defining a computational model of the myocardium. The model takes into account the deep interrelation between the anatomy and the mechanics of the heart. The paper explains the workflow of the MIOCARDIA project. It also introduces a multiresolution reconstruction technique based on DT-MRI streamlining for simplified global myocardial model generation. Our reconstructions can restore the most complex myocardial structures and provides evidences of a global helical organization.
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Aura Hernandez-Sabate, & Debora Gil. (2012). The Benefits of IVUS Dynamics for Retrieving Stable Models of Arteries. In Yasuhiro Honda (Ed.), Intravascular Ultrasound (pp. 185–206). Intech.
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Patricia Marquez, Debora Gil, & Aura Hernandez-Sabate. (2011). A Confidence Measure for Assessing Optical Flow Accuracy in the Absence of Ground Truth. In IEEE International Conference on Computer Vision – Workshops (pp. 2042–2049). Barcelona (Spain): IEEE.
Abstract: Optical flow is a valuable tool for motion analysis in autonomous navigation systems. A reliable application requires determining the accuracy of the computed optical flow. This is a main challenge given the absence of ground truth in real world sequences. This paper introduces a measure of optical flow accuracy for Lucas-Kanade based flows in terms of the numerical stability of the data-term. We call this measure optical flow condition number. A statistical analysis over ground-truth data show a good statistical correlation between the condition number and optical flow error. Experiments on driving sequences illustrate its potential for autonomous navigation systems.
Keywords: IEEE International Conference on Computer Vision – Workshops
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Albert Andaluz. (2012). Harmonic Phase Flow: User's guide. Barcelona: CVC.
Abstract: HPF is a plugin for the computation of clinical scores under Osirix.
This manual provides a basic guide for experienced clinical staff. Chapter 1 provides the theoretical background in which this plugin is based.
Next, in chapter 2 we provide basic instructions for installing and uninstalling this plugin. chapter 3we shows a step-by-step scenario to compute clinical scores from tagged-MRI images with HPF. Finally, in chapter 4 we provide a quick guide for plugin developers
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Sergio Vera, Debora Gil, Antonio Lopez, & Miguel Angel Gonzalez Ballester. (2012). Multilocal Creaseness Measure. IJ - The Insight Journal.
Abstract: This document describes the implementation using the Insight Toolkit of an algorithm for detecting creases (ridges and valleys) in N-dimensional images, based on the Local Structure Tensor of the image. In addition to the filter used to calculate the creaseness image, a filter for the computation of the structure tensor is also included in this submission.
Keywords: Ridges, Valley, Creaseness, Structure Tensor, Skeleton,
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Ferran Poveda, Debora Gil, Albert Andaluz, & Enric Marti. (2011). Multiscale Tractography for Representing Heart Muscular Architecture. In In MICCAI 2011 Workshop on Computational Diffusion MRI.
Abstract: Deep understanding of myocardial structure of the heart would unravel crucial knowledge for clinical and medical procedures. Although the muscular architecture of the heart has been debated by countless researchers, the controversy is still alive. Diffusion Tensor MRI, DT-MRI, is a unique imaging technique for computational validation of the muscular structure of the heart. By the complex arrangement of myocites, existing techniques can not provide comprehensive descriptions of the global muscular architecture. In this paper we introduce a multiresolution reconstruction technique based on DT-MRI streamlining for simplified global myocardial model generation. Our reconstructions can restore the most complex myocardial structures and indicate a global helical organization
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David Vazquez, Antonio Lopez, Daniel Ponsa, & Javier Marin. (2011). Virtual Worlds and Active Learning for Human Detection. In 13th International Conference on Multimodal Interaction (pp. 393–400). New York, NY, USA, USA: ACM DL.
Abstract: Image based human detection is of paramount interest due to its potential applications in fields such as advanced driving assistance, surveillance and media analysis. However, even detecting non-occluded standing humans remains a challenge of intensive research. The most promising human detectors rely on classifiers developed in the discriminative paradigm, i.e., trained with labelled samples. However, labeling is a manual intensive step, especially in cases like human detection where it is necessary to provide at least bounding boxes framing the humans for training. To overcome such problem, some authors have proposed the use of a virtual world where the labels of the different objects are obtained automatically. This means that the human models (classifiers) are learnt using the appearance of rendered images, i.e., using realistic computer graphics. Later, these models are used for human detection in images of the real world. The results of this technique are surprisingly good. However, these are not always as good as the classical approach of training and testing with data coming from the same camera, or similar ones. Accordingly, in this paper we address the challenge of using a virtual world for gathering (while playing a videogame) a large amount of automatically labelled samples (virtual humans and background) and then training a classifier that performs equal, in real-world images, than the one obtained by equally training from manually labelled real-world samples. For doing that, we cast the problem as one of domain adaptation. In doing so, we assume that a small amount of manually labelled samples from real-world images is required. To collect these labelled samples we propose a non-standard active learning technique. Therefore, ultimately our human model is learnt by the combination of virtual and real world labelled samples (Fig. 1), which has not been done before. We present quantitative results showing that this approach is valid.
Keywords: Pedestrian Detection; Human detection; Virtual; Domain Adaptation; Active Learning
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David Vazquez, Jiaolong Xu, Sebastian Ramos, Antonio Lopez, & Daniel Ponsa. (2013). Weakly Supervised Automatic Annotation of Pedestrian Bounding Boxes. In CVPR Workshop on Ground Truth – What is a good dataset? (pp. 706–711). IEEE.
Abstract: Among the components of a pedestrian detector, its trained pedestrian classifier is crucial for achieving the desired performance. The initial task of the training process consists in collecting samples of pedestrians and background, which involves tiresome manual annotation of pedestrian bounding boxes (BBs). Thus, recent works have assessed the use of automatically collected samples from photo-realistic virtual worlds. However, learning from virtual-world samples and testing in real-world images may suffer the dataset shift problem. Accordingly, in this paper we assess an strategy to collect samples from the real world and retrain with them, thus avoiding the dataset shift, but in such a way that no BBs of real-world pedestrians have to be provided. In particular, we train a pedestrian classifier based on virtual-world samples (no human annotation required). Then, using such a classifier we collect pedestrian samples from real-world images by detection. After, a human oracle rejects the false detections efficiently (weak annotation). Finally, a new classifier is trained with the accepted detections. We show that this classifier is competitive with respect to the counterpart trained with samples collected by manually annotating hundreds of pedestrian BBs.
Keywords: Pedestrian Detection; Domain Adaptation
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Jiaolong Xu, David Vazquez, Sebastian Ramos, Antonio Lopez, & Daniel Ponsa. (2013). Adapting a Pedestrian Detector by Boosting LDA Exemplar Classifiers. In CVPR Workshop on Ground Truth – What is a good dataset? (pp. 688–693).
Abstract: Training vision-based pedestrian detectors using synthetic datasets (virtual world) is a useful technique to collect automatically the training examples with their pixel-wise ground truth. However, as it is often the case, these detectors must operate in real-world images, experiencing a significant drop of their performance. In fact, this effect also occurs among different real-world datasets, i.e. detectors' accuracy drops when the training data (source domain) and the application scenario (target domain) have inherent differences. Therefore, in order to avoid this problem, it is required to adapt the detector trained with synthetic data to operate in the real-world scenario. In this paper, we propose a domain adaptation approach based on boosting LDA exemplar classifiers from both virtual and real worlds. We evaluate our proposal on multiple real-world pedestrian detection datasets. The results show that our method can efficiently adapt the exemplar classifiers from virtual to real world, avoiding drops in average precision over the 15%.
Keywords: Pedestrian Detection; Domain Adaptation
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Javier Marin, David Vazquez, David Geronimo, & Antonio Lopez. (2010). Learning Appearance in Virtual Scenarios for Pedestrian Detection. In 23rd IEEE Conference on Computer Vision and Pattern Recognition (137–144).
Abstract: Detecting pedestrians in images is a key functionality to avoid vehicle-to-pedestrian collisions. The most promising detectors rely on appearance-based pedestrian classifiers trained with labelled samples. This paper addresses the following question: can a pedestrian appearance model learnt in virtual scenarios work successfully for pedestrian detection in real images? (Fig. 1). Our experiments suggest a positive answer, which is a new and relevant conclusion for research in pedestrian detection. More specifically, we record training sequences in virtual scenarios and then appearance-based pedestrian classifiers are learnt using HOG and linear SVM. We test such classifiers in a publicly available dataset provided by Daimler AG for pedestrian detection benchmarking. This dataset contains real world images acquired from a moving car. The obtained result is compared with the one given by a classifier learnt using samples coming from real images. The comparison reveals that, although virtual samples were not specially selected, both virtual and real based training give rise to classifiers of similar performance.
Keywords: Pedestrian Detection; Domain Adaptation
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David Vazquez, Antonio Lopez, Daniel Ponsa, & David Geronimo. (2013). Interactive Training of Human Detectors. In Multiodal Interaction in Image and Video Applications (Vol. 48, pp. 169–182). Springer Berlin Heidelberg.
Abstract: Image based human detection remains as a challenging problem. Most promising detectors rely on classifiers trained with labelled samples. However, labelling is a manual labor intensive step. To overcome this problem we propose to collect images of pedestrians from a virtual city, i.e., with automatic labels, and train a pedestrian detector with them, which works fine when such virtual-world data are similar to testing one, i.e., real-world pedestrians in urban areas. When testing data is acquired in different conditions than training one, e.g., human detection in personal photo albums, dataset shift appears. In previous work, we cast this problem as one of domain adaptation and solve it with an active learning procedure. In this work, we focus on the same problem but evaluating a different set of faster to compute features, i.e., Haar, EOH and their combination. In particular, we train a classifier with virtual-world data, using such features and Real AdaBoost as learning machine. This classifier is applied to real-world training images. Then, a human oracle interactively corrects the wrong detections, i.e., few miss detections are manually annotated and some false ones are pointed out too. A low amount of manual annotation is fixed as restriction. Real- and virtual-world difficult samples are combined within what we call cool world and we retrain the classifier with this data. Our experiments show that this adapted classifier is equivalent to the one trained with only real-world data but requiring 90% less manual annotations.
Keywords: Pedestrian Detection; Virtual World; AdaBoost; Domain Adaptation
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Yainuvis Socarras, David Vazquez, Antonio Lopez, David Geronimo, & Theo Gevers. (2012). Improving HOG with Image Segmentation: Application to Human Detection. In J. Blanc-Talon et al. (Ed.), 11th International Conference on Advanced Concepts for Intelligent Vision Systems (Vol. 7517, pp. 178–189). LNCS. Springer Berlin Heidelberg.
Abstract: In this paper we improve the histogram of oriented gradients (HOG), a core descriptor of state-of-the-art object detection, by the use of higher-level information coming from image segmentation. The idea is to re-weight the descriptor while computing it without increasing its size. The benefits of the proposal are two-fold: (i) to improve the performance of the detector by enriching the descriptor information and (ii) take advantage of the information of image segmentation, which in fact is likely to be used in other stages of the detection system such as candidate generation or refinement.
We test our technique in the INRIA person dataset, which was originally developed to test HOG, embedding it in a human detection system. The well-known segmentation method, mean-shift (from smaller to larger super-pixels), and different methods to re-weight the original descriptor (constant, region-luminance, color or texture-dependent) has been evaluated. We achieve performance improvements of 4:47% in detection rate through the use of differences of color between contour pixel neighborhoods as re-weighting function.
Keywords: Segmentation; Pedestrian Detection
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Patricia Marquez, Debora Gil, & Aura Hernandez-Sabate. (2012). Error Analysis for Lucas-Kanade Based Schemes. In 9th International Conference on Image Analysis and Recognition (Vol. 7324, pp. 184–191). LNCS. Springer-Verlag Berlin Heidelberg.
Abstract: Optical flow is a valuable tool for motion analysis in medical imaging sequences. A reliable application requires determining the accuracy of the computed optical flow. This is a main challenge given the absence of ground truth in medical sequences. This paper presents an error analysis of Lucas-Kanade schemes in terms of intrinsic design errors and numerical stability of the algorithm. Our analysis provides a confidence measure that is naturally correlated to the accuracy of the flow field. Our experiments show the higher predictive value of our confidence measure compared to existing measures.
Keywords: Optical flow, Confidence measure, Lucas-Kanade, Cardiac Magnetic Resonance
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Sergio Vera, Debora Gil, Agnes Borras, F. Javier Sanchez, Frederic Perez, Marius G. Linguraru, et al. (2012). Computation and Evaluation of Medial Surfaces for Shape Representation of Abdominal Organs. In H. Yoshida et al (Ed.), Workshop on Computational and Clinical Applications in Abdominal Imaging (Vol. 7029, 223–230). LNCS. Berlin: Springer Link.
Abstract: Medial representations are powerful tools for describing and parameterizing the volumetric shape of anatomical structures. Existing methods show excellent results when applied to 2D
objects, but their quality drops across dimensions. This paper contributes to the computation of medial manifolds in two aspects. First, we provide a standard scheme for the computation of medial
manifolds that avoid degenerated medial axis segments; second, we introduce an energy based method which performs independently of the dimension. We evaluate quantitatively the performance of our
method with respect to existing approaches, by applying them to synthetic shapes of known medial geometry. Finally, we show results on shape representation of multiple abdominal organs,
exploring the use of medial manifolds for the representation of multi-organ relations.
Keywords: medial manifolds, abdomen.
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