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Author Sergio Vera; Debora Gil; Antonio Lopez; Miguel Angel Gonzalez Ballester edit   pdf
url  openurl
  Title Multilocal Creaseness Measure Type Journal
  Year 2012 Publication The Insight Journal Abbreviated Journal IJ  
  Volume Issue Pages  
  Keywords Ridges, Valley, Creaseness, Structure Tensor, Skeleton,  
  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.  
  Address  
  Corporate Author Alma IT Systems Thesis  
  Publisher Place of Publication Editor  
  Language english Summary Language english Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN ISBN Medium  
  Area Expedition Conference (down)  
  Notes IAM;ADAS; Approved no  
  Call Number IAM @ iam @ VGL2012 Serial 1840  
Permanent link to this record
 

 
Author Carles Sanchez edit   pdf
openurl 
  Title Tracheal ring detection in bronchoscopy Type Report
  Year 2011 Publication CVC Technical Report Abbreviated Journal  
  Volume 168 Issue Pages  
  Keywords Bronchoscopy, tracheal ring, segmentation  
  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.
 
  Address  
  Corporate Author Thesis Master's thesis  
  Publisher Place of Publication Editor Debora Gil, F.Javier Sanchez  
  Language english Summary Language english Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN ISBN Medium  
  Area Expedition Conference (down)  
  Notes IAM;MV Approved no  
  Call Number IAM @ iam @ San2011 Serial 1841  
Permanent link to this record
 

 
Author Alberto Hidalgo; Ferran Poveda; Enric Marti;Debora Gil;Albert Andaluz; Francesc Carreras; Manuel Ballester edit   pdf
url  doi
openurl 
  Title Evidence of continuous helical structure of the cardiac ventricular anatomy assessed by diffusion tensor imaging magnetic resonance multiresolution tractography Type Journal Article
  Year 2012 Publication European Radiology Abbreviated Journal ECR  
  Volume 3 Issue 1 Pages 361-362  
  Keywords  
  Abstract Deep understanding of myocardial structure linking morphology and func- tion of the heart would unravel crucial knowledge for medical and surgical clinical procedures and studies. Diffusion tensor MRI provides a discrete measurement of the 3D arrangement of myocardial fibres by the observation of local anisotropic
diffusion of water molecules in biological tissues. In this work, we present a multi- scale visualisation technique based on DT-MRI streamlining capable of uncovering additional properties of the architectural organisation of the heart. Methods and Materials: We selected the John Hopkins University (JHU) Canine Heart Dataset, where the long axis cardiac plane is aligned with the scanner’s Z- axis. Their equipment included a 4-element passed array coil emitting a 1.5 T. For DTI acquisition, a 3D-FSE sequence is apply. We used 200 seeds for full-scale tractography, while we applied a MIP mapping technique for simplified tractographic reconstruction. In this case, we reduced each DTI 3D volume dimensions by order- two magnitude before streamlining.
Our simplified tractographic reconstruction method keeps the main geometric features of fibres, allowing for an easier identification of their global morphological disposition, including the ventricular basal ring. Moreover, we noticed a clearly visible helical disposition of the myocardial fibres, in line with the helical myocardial band ventricular structure described by Torrent-Guasp. Finally, our simplified visualisation with single tracts identifies the main segments of the helical ventricular architecture.
DT-MRI makes possible the identification of a continuous helical architecture of the myocardial fibres, which validates Torrent-Guasp’s helical myocardial band ventricular anatomical model.
 
  Address Viena, Austria  
  Corporate Author Thesis  
  Publisher Springer Link Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1869-4101 ISBN Medium  
  Area Expedition Conference (down)  
  Notes IAM Approved no  
  Call Number IAM @ iam @ HPM2012 Serial 1858  
Permanent link to this record
 

 
Author Albert Andaluz edit   pdf
url  openurl
  Title Harmonic Phase Flow: User's guide Type Manual
  Year 2012 Publication CVC Abbreviated Journal  
  Volume Issue Pages  
  Keywords  
  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
 
  Address Bellaterra, Barcelona (Spain)  
  Corporate Author Computer Vision Center Thesis  
  Publisher CVC Place of Publication Barcelona Editor  
  Language english Summary Language english Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN ISBN Medium  
  Area Expedition Conference (down)  
  Notes IAM Approved no  
  Call Number IAM @ iam @ And2012 Serial 1863  
Permanent link to this record
 

 
Author Ferran Poveda; Enric Marti; Debora Gil; Francesc Carreras; Manel Ballester edit   pdf
url  doi
openurl 
  Title Helical Structure of Ventricular Anatomy by Diffusion Tensor Cardiac MR Tractography Type Journal Article
  Year 2012 Publication Journal of American College of Cardiology Abbreviated Journal JACC  
  Volume 5 Issue 7 Pages 754-755  
  Keywords  
  Abstract It is widely accepted that myocardial fiber architecture plays a critical role in myocardial contractility and relaxation (1). However, there is a lack of consensus about the distribution of the myocardial fibers and their spatial arrangement in the left and right ventricles. An understanding of the cardiac architecture should benefit the ventricular functional assessment, left ventricular reconstructive surgery planning, or resynchronization therapy in heart failure. Researchers have proposed several conceptual models to describe the architecture of the heart, ranging from gross dissection to histological presentation. The cardiac mesh model (2) proposes that the myocytes are arranged longitudinally and radially change their angulation along the myocardial depth. By contrast, the helical ventricular myocardial model states that the ventricular myocardium is a continuous anatomical helical layout of myocardial fibers (1  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1936-878X ISBN Medium  
  Area Expedition Conference (down)  
  Notes IAM Approved no  
  Call Number IAM @ iam @ PMG2012 Serial 1985  
Permanent link to this record
 

 
Author David Roche; Debora Gil; Jesus Giraldo edit  url
doi  openurl
  Title Multiple active receptor conformation, agonist efficacy and maximum effect of the system: the conformation-based operational model of agonism, Type Journal Article
  Year 2013 Publication Drug Discovery Today Abbreviated Journal DDT  
  Volume 18 Issue 7-8 Pages 365-371  
  Keywords  
  Abstract The operational model of agonism assumes that the maximum effect a particular receptor system can achieve (the Em parameter) is fixed. Em estimates are above but close to the asymptotic maximum effects of endogenous agonists. The concept of Em is contradicted by superagonists and those positive allosteric modulators that significantly increase the maximum effect of endogenous agonists. An extension of the operational model is proposed that assumes that the Em parameter does not necessarily have a single value for a receptor system but has multiple values associated to multiple active receptor conformations. The model provides a mechanistic link between active receptor conformation and agonist efficacy, which can be useful for the analysis of agonist response under different receptor scenarios.  
  Address  
  Corporate Author Thesis  
  Publisher Elsevier Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN ISBN Medium  
  Area Expedition Conference (down)  
  Notes IAM; 600.057; 600.054 Approved no  
  Call Number IAM @ iam @ RGG2013a Serial 2190  
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Author Sergio Vera; Debora Gil; Agnes Borras; Marius George Linguraru; Miguel Angel Gonzalez Ballester edit   pdf
url  doi
openurl 
  Title Geometric Steerable Medial Maps Type Journal Article
  Year 2013 Publication Machine Vision and Applications Abbreviated Journal MVA  
  Volume 24 Issue 6 Pages 1255-1266  
  Keywords Medial Representations ,Medial Manifolds Comparation , Surface , Reconstruction  
  Abstract In order to provide more intuitive and easily interpretable representations of complex shapes/organs, medial manifolds should reach a compromise between simplicity in geometry and capability for restoring the anatomy/shape of the organ/volume. Existing morphological 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 avoids degenerated medial axis segments. Second, we introduce a continuous operator for accurate and efficient computation of medial structures of arbitrary dimension. We evaluate quantitatively the performance of our method with respect to existing approaches, by applying them to syn- thetic shapes of known medial geometry. We also show its higher performance for medical imaging applications in terms of simplicity of medial structures and capability for reconstructing the anatomical volume.
 
  Address  
  Corporate Author Thesis  
  Publisher Springer Berlin Heidelberg Place of Publication Editor Mubarak Shah  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0932-8092 ISBN Medium  
  Area Expedition Conference (down)  
  Notes IAM; 605.203; 600.060; 600.044 Approved no  
  Call Number IAM @ iam @ VGB2013 Serial 2192  
Permanent link to this record
 

 
Author Ferran Poveda; Debora Gil; Enric Marti; Albert Andaluz; Manel Ballester;Francesc Carreras Costa edit   pdf
url  doi
openurl 
  Title Helical structure of the cardiac ventricular anatomy assessed by Diffusion Tensor Magnetic Resonance Imaging multi-resolution tractography Type Journal Article
  Year 2013 Publication Revista Española de Cardiología Abbreviated Journal REC  
  Volume 66 Issue 10 Pages 782-790  
  Keywords Heart;Diffusion magnetic resonance imaging;Diffusion tractography;Helical heart;Myocardial ventricular band.  
  Abstract Deep understanding of myocardial structure linking morphology and function of the heart would unravel crucial knowledge for medical and surgical clinical procedures and studies. Several conceptual models of myocardial fiber organization have been proposed but the lack of an automatic and objective methodology prevented an agreement. We sought to deepen in this knowledge through advanced computer graphic representations of the myocardial fiber architecture by diffusion tensor magnetic resonance imaging (DT-MRI).
We performed automatic tractography reconstruction of unsegmented DT-MRI canine heart datasets coming from the public database of the Johns Hopkins University. Full scale tractographies have been build with 200 seeds and are composed by streamlines computed on the vectorial field of primary eigenvectors given at the diffusion tensor volumes. Also, we introduced a novel multi-scale visualization technique in order to obtain a simplified tractography. This methodology allowed to keep the main geometric features of the fiber tracts, making easier to decipher the main properties of the architectural organization of the heart.
On the analysis of the output from our tractographic representations we found exact correlation with low-level details of myocardial architecture, but also with the more abstract conceptualization of a continuous helical ventricular myocardial fiber array.
Objective analysis of myocardial architecture by an automated method, including the entire myocardium and using several 3D levels of complexity, reveals a continuous helical myocardial fiber arrangement of both right and left ventricles, supporting the anatomical model of the helical ventricular myocardial band described by Torrent-Guasp.
 
  Address  
  Corporate Author Thesis  
  Publisher Elsevier Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN ISBN Medium  
  Area Expedition Conference (down)  
  Notes IAM; 600.044; 600.060 Approved no  
  Call Number IAM @ iam @ PGM2013 Serial 2194  
Permanent link to this record
 

 
Author David Roche; Debora Gil; Jesus Giraldo edit  doi
openurl 
  Title Mechanistic analysis of the function of agonists and allosteric modulators: Reconciling two-state and operational models Type Journal Article
  Year 2013 Publication British Journal of Pharmacology Abbreviated Journal BJP  
  Volume 169 Issue 6 Pages 1189-202  
  Keywords  
  Abstract Two-state and operational models of both agonism and allosterism are compared to identify and characterize common pharmacological parameters. To account for the receptor-dependent basal response, constitutive receptor activity is considered in the operational models. By arranging two-state models as the fraction of active receptors and operational models as the fractional response relative to the maximum effect of the system, a one-by-one correspondence between parameters is found. The comparative analysis allows a better understanding of complex allosteric interactions. In particular, the inclusion of constitutive receptor activity in the operational model of allosterism allows the characterization of modulators able to lower the basal response of the system; that is, allosteric modulators with negative intrinsic efficacy. Theoretical simulations and overall goodness of fit of the models to simulated data suggest that it is feasible to apply the models to experimental data and constitute one step forward in receptor theory formalism.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN ISBN Medium  
  Area Expedition Conference (down)  
  Notes IAM; 600.044; 605.203 Approved no  
  Call Number IAM @ iam @ RGG2013b Serial 2195  
Permanent link to this record
 

 
Author David Roche; Debora Gil; Jesus Giraldo edit  doi
isbn  openurl
  Title Mathematical modeling of G protein-coupled receptor function: What can we learn from empirical and mechanistic models? Type Book Chapter
  Year 2014 Publication G Protein-Coupled Receptors – Modeling and Simulation Advances in Experimental Medicine and Biology Abbreviated Journal  
  Volume 796 Issue 3 Pages 159-181  
  Keywords β-arrestin; biased agonism; curve fitting; empirical modeling; evolutionary algorithm; functional selectivity; G protein; GPCR; Hill coefficient; intrinsic efficacy; inverse agonism; mathematical modeling; mechanistic modeling; operational model; parameter optimization; receptor dimer; receptor oligomerization; receptor constitutive activity; signal transduction; two-state model  
  Abstract Empirical and mechanistic models differ in their approaches to the analysis of pharmacological effect. Whereas the parameters of the former are not physical constants those of the latter embody the nature, often complex, of biology. Empirical models are exclusively used for curve fitting, merely to characterize the shape of the E/[A] curves. Mechanistic models, on the contrary, enable the examination of mechanistic hypotheses by parameter simulation. Regretfully, the many parameters that mechanistic models may include can represent a great difficulty for curve fitting, representing, thus, a challenge for computational method development. In the present study some empirical and mechanistic models are shown and the connections, which may appear in a number of cases between them, are analyzed from the curves they yield. It may be concluded that systematic and careful curve shape analysis can be extremely useful for the understanding of receptor function, ligand classification and drug discovery, thus providing a common language for the communication between pharmacologists and medicinal chemists.  
  Address  
  Corporate Author Thesis  
  Publisher Springer Netherlands Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0065-2598 ISBN 978-94-007-7422-3 Medium  
  Area Expedition Conference (down)  
  Notes IAM; 600.075 Approved no  
  Call Number IAM @ iam @ RGG2014 Serial 2197  
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