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Patrick Clarysse

Centre National de la Recherche Scientifique / French National Centre for Scientific Research, CREATIS CNRS UMR 5220, Inserm U1044, INSA Lyon, Université Claude Bernard Lyon 1, Faculty Member

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Patrick Clarysse received a MSc degree in 1987 and a PhD in 1991 from the Scientific and Technological University of Lille, France. Since 1992, he is with the French National Center for Scientific Research (CNRS) at CREATIS, University of Lyon, CNRS UMR 5220, Inserm U1206, Lyon, France. Currently, he is Research Director and heads the ‘Thoracic and Vascular Imaging and Modeling’ group. His primary research interests are in the bioengineering and medical image analysis fields, and include medical image processing workflows, multidimensional/multimodal image segmentation and registration, motion estimation and deformable models with applications to the 3D analysis and modeling of heart functions and motion of thoracic structures. Patrick Clarysse has coauthored more than 110 papers in international journals and conferences in the field and 3 books. He is a member of IEEE, EMBS and of the French Society of BioEngineering (SFGBM).

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Towards a multi-scale virtual heart model

2020 15th IEEE International Conference on Signal Processing (ICSP), 2020

Deep Group-Wise Angular Translation of Cardiac Diffusion MRI in q-space via Manifold Regularized GAN

2020 15th IEEE International Conference on Signal Processing (ICSP), 2020

Using an elastic deformable template for the segmentation of ultrasound cardiac radio frequency images based on the velocity information

2002 IEEE Ultrasonics Symposium, 2002. Proceedings.

In the context of echocardiographic imaging, we investigate the feasibility of segmentation based... more In the context of echocardiographic imaging, we investigate the feasibility of segmentation based on the velocity information, estimated by tracking radiofrequency patterns in consecutive frames. We subsequently segment the variance of the velocity by means of a deformable template, which is constrained by an elasticity term and evolves attracted by the edges of the velocity variance. Segmentation of a simulated image and of an entire cardiac sequence proves a good performance of our method. Since the velocity information is complementary with respect to the classically used envelope one, it could be used to increase reliability of the detection of cardiac structure.

Time-evolution analysis of differential features on 3D surfaces of the heart walls

Proceedings of 1994 IEEE Nuclear Science Symposium - NSS'94

Variability of the Human Cardiac Laminar Structure

Lecture Notes in Computer Science, 2012

Statistical Atlas of Human Cardiac Fibers: Comparison with Abnormal Hearts

Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges, 2012

Incorporating Low-Level Constraints for the Retrieval of Personalised Heart Models from Dynamic MRI

Lecture Notes in Computer Science, 2010

A New Dynamic Elastic Model for Cardiac Image Analysis

2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2007

We believe that strong prior models are a pre-requisite for reliable spatio-temporal cardiac imag... more We believe that strong prior models are a pre-requisite for reliable spatio-temporal cardiac image analysis. While several cardiac models have been presented in the past, many of them are either too complex for their parameters to be estimated on the sole basis of MR Images, or overly simplified. In this paper, we present a novel bio-inspired dynamic model, based on the equation of dynamics for elastic materials. The explicit use of dynamics allows us to enforce periodicity and temporal smoothness constraints. We study two different methods for solving the resulting equations, and show them to be equivalent. We show how temporal filtering can help to remove noise and ensure the periodicity and smoothness of solutions. Finally, we show some results in 1D and on a synthetic model to illustrate the benefits of our new dynamic model and to show how it can be used to analyze cardiac MR images.

Driving Dynamic Cardiac Model Adaptation with MR-Tagging Displacement Information

Lecture Notes in Computer Science, 2011

Evaluation of the dynamic elastic template model for the segmentation of the heart in mri sequences

International audienc

Extraction et segmentation de structures dans des séquences d’images

ABSTRACT Cet ouvrage fait suite au traité intitulé Imagerie dynamique cardiaque et thoracique qui... more ABSTRACT Cet ouvrage fait suite au traité intitulé Imagerie dynamique cardiaque et thoracique qui proposait un panorama des modalités et systèmes d’imagerie d’exploration du cœur et du thorax. L’objectif du présent ouvrage est de réaliser un état de l’art des méthodes de traitement, d’analyse et de modélisation des images produites par ses systèmes dans le domaine de l’imagerie cardiaque. Une première partie présente des concepts et méthodes génériques du traitement d’images en précisant les approches proposées pour leur adaptation à l’imagerie du cœur. Ainsi, les chapitres 1 à 4 traitent respectivement de l’extraction des contours/surfaces du cœur, de la quantification et l’analyse du mouvement, des approches de modélisation et de quantification de la perfusion et de la décomposition de séquences dynamiques d’images pour l’analyse de prise de contraste et du mouvement. La seconde partie présente plusieurs exemples d’applications. Enfin, la combinaison de méthodes avancées de traitement de données et d’images et de modèles complexes permet de préparer une cardiologie patient spécifique. C’est cette perspective qu’introduit le chapitre 9 dans une troisième et dernière partie.

Integrating Fiber Orientation Constraint into a Spatio-temporal FEM Model for Heart Borders and Motion Tracking in Dynamic MRI

Lecture Notes in Computer Science, 2013

ABSTRACT The dynamic deformable elastic template (DET) model has been previously introduced for t... more ABSTRACT The dynamic deformable elastic template (DET) model has been previously introduced for the retrieval of personalized anatomical and functional models of the heart from dynamic cardiac image sequences. The dynamic DET model is a finite element deformable model, for which the minimum of the energy must satisfy a simplified equation of Dynamics. In this paper, we extend the model by integrating fiber constraints in order to improve the retrieval of cardiac deformations from cinetic magnetic resonance imaging (cineMRI). Evaluation conducted until now on cine MRI sequences shows an improvement of the recovery of the motion in images that present a low level of obvious rotation.

Simultaneous segmentation of the left and right heart ventricles in 3D cine MR images of small animals

Computers in Cardiology, 2005, 2005

Optimal extended optical flow subject to a statistical constraint

Journal of Computational and Applied Mathematics, 2010

Constraint 3D elastic model for the segmentation in cardiac MRI

Computers in Cardiology, 2005, 2005

Modèle numérique d'estimation 2D de la déformation des tissus mous biologiques à partir d'images échographiques radiofréquence : Résultats sur simulations numériques et données expérimentales

The aim of this study is the estimation of the 2D strain occurring in soft biological tissues und... more The aim of this study is the estimation of the 2D strain occurring in soft biological tissues under load, from the processing of radiofrequency ultrasound images. Few works have been performed on that subject. In this article, we propose a new adaptive and iterative 2D numerical model, allowing full-resolved strain parameters estimation. This model is based on an objective function minimization with linear inequalities constraints. Lateral and axial, displacement and strain fields are presented, that corroborate the theory. 1 Contexte et objectifs L’elastographie est une technique d’imagerie emergente, basee sur l’echographie. Son but est de fournir au medecin une information sur l’elasticite locale du tissu. Ce parametre, non disponible avec les modalites d’imagerie actuelles, presente un interet majeur en diagnostic clinique car le developpement d’une pathologie s’accompagne souvent d’une modification de l’elasticite des tissus. A titre d’exemple, certaines tumeurs cancereuses com...

Phase Extraction Of The Analytic Video Signal In Clifford Algebra

The paper presents an algebraic framework for (2D+t) video analytic signals and a numerical imple... more The paper presents an algebraic framework for (2D+t) video analytic signals and a numerical implementation thereof using Clifford biquaternions and Clifford Fourier transforms. Though the basic concepts of Clifford Fourier transforms are well-known, an implementation of analytic video sequences using multiquaternion algebras does not seem to have been realized so far. A biquaternion algebraic framework is developed to express Clifford Fourier transforms and (2D+ t) video analytic signals in standard and polar form constituted by a scalar, a pseudo-scalar and six phases. The phase extraction procedure is provided. Then a numerical implementation using discrete fast Fourier transforms of an analytic multiquaternion video signal is proposed. When considering a progressive plane wave, the proposed numerical estimation retrieves correctly the six phases and the linear relationships with the time, horizontal position and vertical position of video signal. Liang Wang Université de Lyon, CR...

3D Clifford Analytic Signal for 3D Envelope Detection on Ultrasound Volume

2021 IEEE International Ultrasonics Symposium (IUS)

Automated Quantification of Myocardial Infarction Using a Hidden Markov Random Field Model and the EM Algorithm

Lecture Notes in Computer Science, 2015

Infarct size has been recognized as a good indicator of the functional status of the ischemic hea... more Infarct size has been recognized as a good indicator of the functional status of the ischemic heart and to evaluate the impact of myocardial infarction therapies. Its assessment can be performed from late gadolinium enhancement magnetic resonance images. A number of methods have been proposed for the semi-automatic and automatic quantification of necrosis. We developed an automatic method based on a Markov random field framework and a region growing approach within an EM optimization, which enables segmentation of both necrosis and microvascular obstructions. The method has been evaluated on both synthetic data and 10 clinical cases in 3D and lead to the best results as compared to other conventional approaches and expertise.

A New Method for the Registration of Cardiac PET and MR Images Using Deformable Model Based Segmentation of the Main Thorax Structures

… Image Computing and …, 2010

1 Laboratory of Biomedical Engineering, Helsinki University of Technology, POB 2200, FIN-02015 HU... more

Towards a multi-scale virtual heart model

2020 15th IEEE International Conference on Signal Processing (ICSP), 2020

Deep Group-Wise Angular Translation of Cardiac Diffusion MRI in q-space via Manifold Regularized GAN

2020 15th IEEE International Conference on Signal Processing (ICSP), 2020

Using an elastic deformable template for the segmentation of ultrasound cardiac radio frequency images based on the velocity information

2002 IEEE Ultrasonics Symposium, 2002. Proceedings.

In the context of echocardiographic imaging, we investigate the feasibility of segmentation based... more In the context of echocardiographic imaging, we investigate the feasibility of segmentation based on the velocity information, estimated by tracking radiofrequency patterns in consecutive frames. We subsequently segment the variance of the velocity by means of a deformable template, which is constrained by an elasticity term and evolves attracted by the edges of the velocity variance. Segmentation of a simulated image and of an entire cardiac sequence proves a good performance of our method. Since the velocity information is complementary with respect to the classically used envelope one, it could be used to increase reliability of the detection of cardiac structure.

Time-evolution analysis of differential features on 3D surfaces of the heart walls

Proceedings of 1994 IEEE Nuclear Science Symposium - NSS'94

Variability of the Human Cardiac Laminar Structure

Lecture Notes in Computer Science, 2012

Statistical Atlas of Human Cardiac Fibers: Comparison with Abnormal Hearts

Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges, 2012

Incorporating Low-Level Constraints for the Retrieval of Personalised Heart Models from Dynamic MRI

Lecture Notes in Computer Science, 2010

A New Dynamic Elastic Model for Cardiac Image Analysis

2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2007

We believe that strong prior models are a pre-requisite for reliable spatio-temporal cardiac imag... more We believe that strong prior models are a pre-requisite for reliable spatio-temporal cardiac image analysis. While several cardiac models have been presented in the past, many of them are either too complex for their parameters to be estimated on the sole basis of MR Images, or overly simplified. In this paper, we present a novel bio-inspired dynamic model, based on the equation of dynamics for elastic materials. The explicit use of dynamics allows us to enforce periodicity and temporal smoothness constraints. We study two different methods for solving the resulting equations, and show them to be equivalent. We show how temporal filtering can help to remove noise and ensure the periodicity and smoothness of solutions. Finally, we show some results in 1D and on a synthetic model to illustrate the benefits of our new dynamic model and to show how it can be used to analyze cardiac MR images.

Driving Dynamic Cardiac Model Adaptation with MR-Tagging Displacement Information

Lecture Notes in Computer Science, 2011

Evaluation of the dynamic elastic template model for the segmentation of the heart in mri sequences

International audienc

Extraction et segmentation de structures dans des séquences d’images

ABSTRACT Cet ouvrage fait suite au traité intitulé Imagerie dynamique cardiaque et thoracique qui... more ABSTRACT Cet ouvrage fait suite au traité intitulé Imagerie dynamique cardiaque et thoracique qui proposait un panorama des modalités et systèmes d’imagerie d’exploration du cœur et du thorax. L’objectif du présent ouvrage est de réaliser un état de l’art des méthodes de traitement, d’analyse et de modélisation des images produites par ses systèmes dans le domaine de l’imagerie cardiaque. Une première partie présente des concepts et méthodes génériques du traitement d’images en précisant les approches proposées pour leur adaptation à l’imagerie du cœur. Ainsi, les chapitres 1 à 4 traitent respectivement de l’extraction des contours/surfaces du cœur, de la quantification et l’analyse du mouvement, des approches de modélisation et de quantification de la perfusion et de la décomposition de séquences dynamiques d’images pour l’analyse de prise de contraste et du mouvement. La seconde partie présente plusieurs exemples d’applications. Enfin, la combinaison de méthodes avancées de traitement de données et d’images et de modèles complexes permet de préparer une cardiologie patient spécifique. C’est cette perspective qu’introduit le chapitre 9 dans une troisième et dernière partie.

Integrating Fiber Orientation Constraint into a Spatio-temporal FEM Model for Heart Borders and Motion Tracking in Dynamic MRI

Lecture Notes in Computer Science, 2013

ABSTRACT The dynamic deformable elastic template (DET) model has been previously introduced for t... more ABSTRACT The dynamic deformable elastic template (DET) model has been previously introduced for the retrieval of personalized anatomical and functional models of the heart from dynamic cardiac image sequences. The dynamic DET model is a finite element deformable model, for which the minimum of the energy must satisfy a simplified equation of Dynamics. In this paper, we extend the model by integrating fiber constraints in order to improve the retrieval of cardiac deformations from cinetic magnetic resonance imaging (cineMRI). Evaluation conducted until now on cine MRI sequences shows an improvement of the recovery of the motion in images that present a low level of obvious rotation.

Simultaneous segmentation of the left and right heart ventricles in 3D cine MR images of small animals

Computers in Cardiology, 2005, 2005

Optimal extended optical flow subject to a statistical constraint

Journal of Computational and Applied Mathematics, 2010

Constraint 3D elastic model for the segmentation in cardiac MRI

Computers in Cardiology, 2005, 2005

Modèle numérique d'estimation 2D de la déformation des tissus mous biologiques à partir d'images échographiques radiofréquence : Résultats sur simulations numériques et données expérimentales

The aim of this study is the estimation of the 2D strain occurring in soft biological tissues und... more The aim of this study is the estimation of the 2D strain occurring in soft biological tissues under load, from the processing of radiofrequency ultrasound images. Few works have been performed on that subject. In this article, we propose a new adaptive and iterative 2D numerical model, allowing full-resolved strain parameters estimation. This model is based on an objective function minimization with linear inequalities constraints. Lateral and axial, displacement and strain fields are presented, that corroborate the theory. 1 Contexte et objectifs L’elastographie est une technique d’imagerie emergente, basee sur l’echographie. Son but est de fournir au medecin une information sur l’elasticite locale du tissu. Ce parametre, non disponible avec les modalites d’imagerie actuelles, presente un interet majeur en diagnostic clinique car le developpement d’une pathologie s’accompagne souvent d’une modification de l’elasticite des tissus. A titre d’exemple, certaines tumeurs cancereuses com...

Phase Extraction Of The Analytic Video Signal In Clifford Algebra

The paper presents an algebraic framework for (2D+t) video analytic signals and a numerical imple... more The paper presents an algebraic framework for (2D+t) video analytic signals and a numerical implementation thereof using Clifford biquaternions and Clifford Fourier transforms. Though the basic concepts of Clifford Fourier transforms are well-known, an implementation of analytic video sequences using multiquaternion algebras does not seem to have been realized so far. A biquaternion algebraic framework is developed to express Clifford Fourier transforms and (2D+ t) video analytic signals in standard and polar form constituted by a scalar, a pseudo-scalar and six phases. The phase extraction procedure is provided. Then a numerical implementation using discrete fast Fourier transforms of an analytic multiquaternion video signal is proposed. When considering a progressive plane wave, the proposed numerical estimation retrieves correctly the six phases and the linear relationships with the time, horizontal position and vertical position of video signal. Liang Wang Université de Lyon, CR...

3D Clifford Analytic Signal for 3D Envelope Detection on Ultrasound Volume

2021 IEEE International Ultrasonics Symposium (IUS)

Automated Quantification of Myocardial Infarction Using a Hidden Markov Random Field Model and the EM Algorithm

Lecture Notes in Computer Science, 2015

Infarct size has been recognized as a good indicator of the functional status of the ischemic hea... more Infarct size has been recognized as a good indicator of the functional status of the ischemic heart and to evaluate the impact of myocardial infarction therapies. Its assessment can be performed from late gadolinium enhancement magnetic resonance images. A number of methods have been proposed for the semi-automatic and automatic quantification of necrosis. We developed an automatic method based on a Markov random field framework and a region growing approach within an EM optimization, which enables segmentation of both necrosis and microvascular obstructions. The method has been evaluated on both synthetic data and 10 clinical cases in 3D and lead to the best results as compared to other conventional approaches and expertise.

A New Method for the Registration of Cardiac PET and MR Images Using Deformable Model Based Segmentation of the Main Thorax Structures

… Image Computing and …, 2010

1 Laboratory of Biomedical Engineering, Helsinki University of Technology, POB 2200, FIN-02015 HU... more