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Open positions in Computational Cardiac Image Processing and Modelling
(2 PhD positions)
PhD project 1: Quantification of regional contraction in cardiomyocytes
From cellular electrophysiological studies, a lot is known about how cardiac muscle cells (cardiomyocytes)
contract. Knowledge on different ion-channels and the resulting electrical activation and calcium handling
in the different cell compartments, resulting in force development, is detailed. However, deformation of the
cell is mostly only studied at the whole cell level while recent reports show that the deformation is actually
non-homogeneous throughout a single cell.
Therefore, this research project focuses on image processing methods to extract the quantitative
information on regional deformation (strain and strain rate) heterogeneity from experimentally obtained
real-time microscopy images.
In order to quantify the regional deformation, the contraction of single myocytes (isolated from the left
ventricle of animal hearts), that are electrically stimulated, are imaged in real-time using line-scans with
both transmission as well as confocal microscopy, providing details on myocyte striation and its changes
during contraction. Additional, local calcium transient can be acquired [1].
From these images, local displacement or velocities can be quantified. From this, (rate of) deformation can
be quantified and visualized. This information can then be correlated with the local calcium transient to
study excitation-contraction coupling.
The project consists of studying different methods for the extraction of regional velocities and deformation,
the quantitation of these in relation with calcium transients and creating the proper tools to perform studies
in cells from different species with different cardiac problems. Besides developing the algorithms for the
image processing, input in the optimization of the imaging approach as well as in supporting the biological
studies is required.
[1] Hohendanner F, Ljubojević S, MacQuaide N, Sacherer M, Sedej S, Biesmans L, Wakula P, Platzer D, Sokolow S, Herchuelz A, Antoons G,
Sipido K, Pieske B, Heinzel FR. Intracellular dyssynchrony of diastolic cytosolic [Ca²⁺] decay in ventricular cardiomyocytes in cardiac
remodeling and human heart failure. Circ Res. 2013 Aug 16;113(5):527-38.
PhD project 2: Electrophysiological modelling in ventricular tachycardia
Ventricular tachycardia (VT) is a life-threatening arrhythmia arising from functional and structural
disorders of the heart such as ectopic foci or ventricular scar post myocardial infarction. Radio-Frequency
Ablation (RFA) of VTs has demonstrated to be a good therapy in most cases. However, in many of these
patients this expensive, long and invasive procedure has to be repeated a number of times as a number of
them do not benefit from the initial procedure due to some uncertainties on different aspects such as the
optimal ablation sites. In order to optimize the planning of this ablation procedure, the identification of the
VT origin has proven to be crucial using patient-specific electrical and scar information [1,2].
Therefore, the main goal of this PhD is to develop personalized computational models for the in silico
study of new ablation strategies integrating richer multimodal data in the simulations. The developed
computational models will be tuned to reproduce radiofrequency ablation sites defined by abnormal
ectopic foci, the cardiac conduction system and 3D morphological scar information obtained from electro-
anatomical maps and from delay-enhancement magnetic resonance images. Different in silico ablation
strategies (e.g. [3]) will be tested to assess the ablation strategy in different groups of patients. Results
from the simulations will be compared against the actual choices taken by the electrophysiologist.
This work will be part of a long-standing close collaboration with the Hospital Clínic i Provincial de
Barcelona (HCPB), having Dr. Antonio Berruezo as co-supervisor of the PhD to assure clinically relevant
research (the PhD student will be physically located at HCPB some days during the week). Furthermore,
this work will be in connection with other scientific and clinical partners with strong expertise on
computational models of the heart such as the Barcelona Supercomputing Centre (BSC) and the
Universitat de València. Therefore, the candidate must be prone to collaborate with international fellow
PhD students and to spend short stays in partners’ research centres.
[1] Herczku C, Berruezo A, Andreu D, Fernández-Armenta J, Mont L, Borràs R, Arbelo E, Tolosana JM, Trucco E, Ríos J, Brugada J. Mapping
data predictors of a left ventricular outflow tract origin of idiopathic ventricular tachycardia with V3 transition and septal earliest
activation. Circ Arrhythm Electrophysiol. 2012 Jun 1;5(3):484-91.
[2] Andreu D, Berruezo A, Ortiz-Pérez JT, Silva E, Mont L, Borràs R, de Caralt TM, Perea RJ, Fernández-Armenta J, Zeljko H, Brugada J.
Integration of 3D Electroanatomic Maps and Magnetic Resonance Scar Characterization Into the Navigation System to Guide Ventricular
Tachycardia Ablation. Circ Arrhythm Electrophysiol. 2011 Oct 1;4(5):674-83.
[3] Fernández-Armenta J, Camara O, Silva E, Mont L, Andreu D, Diaz E, Sitges M, Herzcku C., Frangi AF, Brugada J, Berruezo A. Three-
dimensional Architecture Of Scar And Conducting Channels Based On High Resolution ce-CMR. Insights For Ventricular Tachycardia
Ablation. In Heart Rhythm (HR’11), San Francisco, CA, USA, May 2011
Workplace
These positions are for doing research towards obtaining a PhD degree at the Department of Information
& Communication Technologies (DTIC) of the Universitat Pompeu Fabra (UPF), Barcelona, Spain
(http://www.upf.edu/dtic_doctorate/). UPF is ranked as the most productive university in Spain in terms of
research outcome and attraction of funding (>140 European FP7 projects, 19 ERC Grants), and the DTIC
ranked among the top 100 computer science departments in the world, according to the ARWU/Shangai
ranking.
The projects will be conducted in the PhySense research group (http://physense.upf.edu), supervised by
ICREA Research Prof. B. Bijnens and Dr. Oscar Camara. PhySense was recently established (2011) and
focuses on integrating engineering/physics knowledge with physiology in order to provide an
interdisciplinary research environment, working closely together with internationally known academic and
clinical centres. This is approached by integrating and improving information acquisition, handling and
processing techniques, combined with basic knowledge on pathophysiology, in order to advance clinical
sciences.
Requirements
The candidates should have a BEng or preferentially MSc, mainly in engineering, physics or computer
science, strong background on applied mathematics, good computer programming skills (C++, Matlab),
and preferentially experience in image processing and/or computational modelling. Fluency in English is
highly recommended.
Contact
Applicants should send a curriculum vitae and a letter describing their research interests to Oscar Camara
(oscar.camara@upf.edu) or Bart Bijnens (bart.bijnens@upf.edu).
Application deadline: 1st
September 2014

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PhD positions in Computational Cardiac Image Processing and Modelling

  • 1. Open positions in Computational Cardiac Image Processing and Modelling (2 PhD positions) PhD project 1: Quantification of regional contraction in cardiomyocytes From cellular electrophysiological studies, a lot is known about how cardiac muscle cells (cardiomyocytes) contract. Knowledge on different ion-channels and the resulting electrical activation and calcium handling in the different cell compartments, resulting in force development, is detailed. However, deformation of the cell is mostly only studied at the whole cell level while recent reports show that the deformation is actually non-homogeneous throughout a single cell. Therefore, this research project focuses on image processing methods to extract the quantitative information on regional deformation (strain and strain rate) heterogeneity from experimentally obtained real-time microscopy images. In order to quantify the regional deformation, the contraction of single myocytes (isolated from the left ventricle of animal hearts), that are electrically stimulated, are imaged in real-time using line-scans with both transmission as well as confocal microscopy, providing details on myocyte striation and its changes during contraction. Additional, local calcium transient can be acquired [1]. From these images, local displacement or velocities can be quantified. From this, (rate of) deformation can be quantified and visualized. This information can then be correlated with the local calcium transient to study excitation-contraction coupling. The project consists of studying different methods for the extraction of regional velocities and deformation, the quantitation of these in relation with calcium transients and creating the proper tools to perform studies in cells from different species with different cardiac problems. Besides developing the algorithms for the image processing, input in the optimization of the imaging approach as well as in supporting the biological studies is required. [1] Hohendanner F, Ljubojević S, MacQuaide N, Sacherer M, Sedej S, Biesmans L, Wakula P, Platzer D, Sokolow S, Herchuelz A, Antoons G, Sipido K, Pieske B, Heinzel FR. Intracellular dyssynchrony of diastolic cytosolic [Ca²⁺] decay in ventricular cardiomyocytes in cardiac remodeling and human heart failure. Circ Res. 2013 Aug 16;113(5):527-38.
  • 2. PhD project 2: Electrophysiological modelling in ventricular tachycardia Ventricular tachycardia (VT) is a life-threatening arrhythmia arising from functional and structural disorders of the heart such as ectopic foci or ventricular scar post myocardial infarction. Radio-Frequency Ablation (RFA) of VTs has demonstrated to be a good therapy in most cases. However, in many of these patients this expensive, long and invasive procedure has to be repeated a number of times as a number of them do not benefit from the initial procedure due to some uncertainties on different aspects such as the optimal ablation sites. In order to optimize the planning of this ablation procedure, the identification of the VT origin has proven to be crucial using patient-specific electrical and scar information [1,2]. Therefore, the main goal of this PhD is to develop personalized computational models for the in silico study of new ablation strategies integrating richer multimodal data in the simulations. The developed computational models will be tuned to reproduce radiofrequency ablation sites defined by abnormal ectopic foci, the cardiac conduction system and 3D morphological scar information obtained from electro- anatomical maps and from delay-enhancement magnetic resonance images. Different in silico ablation strategies (e.g. [3]) will be tested to assess the ablation strategy in different groups of patients. Results from the simulations will be compared against the actual choices taken by the electrophysiologist. This work will be part of a long-standing close collaboration with the Hospital Clínic i Provincial de Barcelona (HCPB), having Dr. Antonio Berruezo as co-supervisor of the PhD to assure clinically relevant research (the PhD student will be physically located at HCPB some days during the week). Furthermore, this work will be in connection with other scientific and clinical partners with strong expertise on computational models of the heart such as the Barcelona Supercomputing Centre (BSC) and the Universitat de València. Therefore, the candidate must be prone to collaborate with international fellow PhD students and to spend short stays in partners’ research centres. [1] Herczku C, Berruezo A, Andreu D, Fernández-Armenta J, Mont L, Borràs R, Arbelo E, Tolosana JM, Trucco E, Ríos J, Brugada J. Mapping data predictors of a left ventricular outflow tract origin of idiopathic ventricular tachycardia with V3 transition and septal earliest activation. Circ Arrhythm Electrophysiol. 2012 Jun 1;5(3):484-91. [2] Andreu D, Berruezo A, Ortiz-Pérez JT, Silva E, Mont L, Borràs R, de Caralt TM, Perea RJ, Fernández-Armenta J, Zeljko H, Brugada J. Integration of 3D Electroanatomic Maps and Magnetic Resonance Scar Characterization Into the Navigation System to Guide Ventricular Tachycardia Ablation. Circ Arrhythm Electrophysiol. 2011 Oct 1;4(5):674-83. [3] Fernández-Armenta J, Camara O, Silva E, Mont L, Andreu D, Diaz E, Sitges M, Herzcku C., Frangi AF, Brugada J, Berruezo A. Three- dimensional Architecture Of Scar And Conducting Channels Based On High Resolution ce-CMR. Insights For Ventricular Tachycardia Ablation. In Heart Rhythm (HR’11), San Francisco, CA, USA, May 2011
  • 3. Workplace These positions are for doing research towards obtaining a PhD degree at the Department of Information & Communication Technologies (DTIC) of the Universitat Pompeu Fabra (UPF), Barcelona, Spain (http://www.upf.edu/dtic_doctorate/). UPF is ranked as the most productive university in Spain in terms of research outcome and attraction of funding (>140 European FP7 projects, 19 ERC Grants), and the DTIC ranked among the top 100 computer science departments in the world, according to the ARWU/Shangai ranking. The projects will be conducted in the PhySense research group (http://physense.upf.edu), supervised by ICREA Research Prof. B. Bijnens and Dr. Oscar Camara. PhySense was recently established (2011) and focuses on integrating engineering/physics knowledge with physiology in order to provide an interdisciplinary research environment, working closely together with internationally known academic and clinical centres. This is approached by integrating and improving information acquisition, handling and processing techniques, combined with basic knowledge on pathophysiology, in order to advance clinical sciences. Requirements The candidates should have a BEng or preferentially MSc, mainly in engineering, physics or computer science, strong background on applied mathematics, good computer programming skills (C++, Matlab), and preferentially experience in image processing and/or computational modelling. Fluency in English is highly recommended. Contact Applicants should send a curriculum vitae and a letter describing their research interests to Oscar Camara (oscar.camara@upf.edu) or Bart Bijnens (bart.bijnens@upf.edu). Application deadline: 1st September 2014