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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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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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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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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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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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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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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Carles Sanchez. (2011). Tracheal ring detection in bronchoscopy (F. J. S. Debora Gil, Ed.) (Vol. 168). Master's thesis, , .
Abstract: Endoscopy is the process in which a camera is introduced inside a human.
Given that endoscopy provides realistic images (in contrast to other modalities) and allows non-invase minimal intervention procedures (which can aid in diagnosis and surgical interventions), its use has spreaded during last decades.
In this project we will focus on bronchoscopic procedures, during which the camera is introduced through the trachea in order to have a diagnostic of the patient. The diagnostic interventions are focused on: degree of stenosis (reduction in tracheal area), prosthesis or early diagnosis of tumors. In the first case, assessment of the luminal area and the calculation of the diameters of the tracheal rings are required. A main limitation is that all the process is done by hand,
which means that the doctor takes all the measurements and decisions just by looking at the screen. As far as we know there is no computational framework for helping the doctors in the diagnosis.
This project will consist of analysing bronchoscopic videos in order to extract useful information for the diagnostic of the degree of stenosis. In particular we will focus on segmentation of the tracheal rings. As a result of this project several strategies (for detecting tracheal rings) had been implemented in order to compare their performance.
Keywords: Bronchoscopy, tracheal ring, segmentation
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