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33. Segmentation with Active Contours

Author

Pierre-Frédéric Villard, Timothé Ruel, Clémence Bigeard, Fabien Pierre, Mathieu Amendola, Recalage visuel avec des modèles physiquement réalistes (TANGRAM), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), and Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
medicine.diagnostic_test, business.industry, Computer science, Active contours, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, medical imaging, Computed tomography, Area of interest, Image segmentation, Initial topology, 3. Good health, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], Signal Processing, Medical imaging, medicine, Computer vision, Segmentation, Polygon mesh, Artificial intelligence, MATLAB, business, computer, image segmentation, Software, computer.programming_language
Abstract

International audience; Active contours (also known as snakes) have shown their ability to introduce regularity on image segmentation. In contrast with level-set approaches, the active contours techniques based on a contour parameterization are able to maintain the initial topology of the area of interest. For this reason, it has been used in recent medical research for diaphragm segmentation. Most of the on-line codes for 2D/3D segmentation, as well as built-in Matlab toolboxes are based on level-set methods. Moreover, in the literature, the implementation details of active contours methods with meshes in three dimensions are tight, making tedious any reproduction of these techniques. In this paper, we give some details of the implementation of active contours in 2D/3D with meshes, especially about the choice of the use of a 2D/3D mesh and its refinement. We also explore the choice of the parameters with a quantitative study of their influence on the segmentation results. The 3D segmentation method has been applied to CT scan images of the lungs.

Published
2021
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34. Automatic extraction of the mitral valve chordae geometry for biomechanical simulation

Author

Marie-Odile Berger, Peter E. Hammer, Daryna Panicheva, Douglas P. Perrin, Pierre-Frédéric Villard, Recalage visuel avec des modèles physiquement réalistes (TANGRAM), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS), Harvard University, Harvard Medical School [Boston] (HMS), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Harvard University [Cambridge]

Subjects
Computer science, Open problem, Pipeline (computing), 0206 medical engineering, Biomedical Engineering, Health Informatics, Topology (electrical circuits), Geometry, 02 engineering and technology, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Mitral valve, medicine, Radiology, Nuclear Medicine and imaging, Segmentation, [INFO]Computer Science [cs], Computational model, Biomechanical simulation, General Medicine, 020601 biomedical engineering, Computer Graphics and Computer-Aided Design, Computer Science Applications, medicine.anatomical_structure, Metric (mathematics), Image-based modeling, Graph (abstract data type), Graph-based validation, Surgery, Computer Vision and Pattern Recognition
Abstract

Mitral valve computational models are widely studied in the literature. They can be used for preoperative planning or anatomical understanding. Manual extraction of the valve geometry on medical images is tedious and requires special training, while automatic segmentation is still an open problem. We propose here a fully automatic pipeline to extract the valve chordae architecture compatible with a computational model. First, an initial segmentation is obtained by sub-mesh topology analysis and RANSAC-like model-fitting procedure. Then, the chordal structure is optimized with respect to objective functions based on mechanical, anatomical, and image-based considerations. The approach has been validated on 5 micro-CT scans with a graph-based metric and has shown an $$87.5\%$$ accuracy rate. The method has also been tested within a structural simulation of the mitral valve closed state. Our results show that the chordae architecture resulting from our algorithm can give results similar to experienced users while providing an equivalent biomechanical simulation.

Published
2021
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36. A first meshless approach to simulation of the elastic behaviour of the diaphragm

Author

Igor Tominec, Elisabeth Larsson, Marco Meggiolaro, Alberto Lauro, Pierre-Frédéric Villard, Nicola Cacciani, Alessio Scatto, Karolinska Institutet [Stockholm], Uppsala University, University - Hospital of Padova [Italy], University-Hospital of Padova, Augmentation visuelle d'environnements complexes (MAGRIT-POST), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Visual Augmentation of Complex Environments (MAGRIT), Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria), Sherwin S., Moxey D., Peiró J., Vincent P., Schwab C., and Azienda Ospedale Università di Padova = Hospital-University of Padua (AOUP)

Subjects
Work (thermodynamics), Computer simulation, Computer science, Beräkningsmatematik, Process (computing), Computational mathematics, 020206 networking & telecommunications, Diaphragm (mechanical device), 02 engineering and technology, Mechanics, Function (mathematics), Controlled mechanical ventilation, musculoskeletal system, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Computational Mathematics, 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, Boundary value problem
Abstract

The diaphragm is the main muscle that regulates the human respiration. When a patient is put under controlled mechanical ventilation, the diaphragm is exposed to forces that damage the muscle function. The long-term aim of this work is to study this process through numerical simulation. Here, we take the first steps in developing a meshless numerical simulation method for the diaphragm. We describe how the diaphragm geometry can be extracted from medical images, and then be used in the meshless method. We show that for a thin volume like the diaphragm, the resolution of the thin dimension is highly relevant for the accuracy of the approximation, and we also show that the method converges for a test case, where realistic displacements are used as boundary conditions.

Published
2020
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37. Fast image-based mitral valve simulation from individualized geometry

Author

Pedro J. del Nido, Robert D. Howe, Pierre-Frédéric Villard, Douglas P. Perrin, and Peter E. Hammer

Subjects
medicine.medical_specialty, Leak, Computer science, 0206 medical engineering, Biophysics, 02 engineering and technology, 030204 cardiovascular system & hematology, 020601 biomedical engineering, Finite element method, Computer Science Applications, Modeling and simulation, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Internal medicine, Mitral valve, medicine, Cardiology, Surgery, Sensitivity (control systems), Systole, Chordae tendineae, Image based, Biomedical engineering
Abstract

Background: Common surgical procedures on the mitral valve of the heart include modifications to the chordae tendineae. Such interventions are used when there is extensive leaflet prolapse caused by chordae rupture or elongation. Understanding the role of individual chordae tendineae before operating could be helpful to predict if the mitral valve will be competent at peak systole. Biomechanical modeling and simulation can achieve this goal. Methods: We present a method to semi-automatically build a mitral valve computational model from micro CT (computed tomography) scans: after manually picking chordae fiducial points, the leaflets are segmented and the boundary conditions as well as the loading conditions are automatically defined. Fast Finite Element Method (FEM) simulation is carried out using Simulation Open Framework Architecture (SOFA) to reproduce leaflet closure at peak systole. We develop three metrics to evaluate simulation results: i) point-to-surface error with the ground truth reference extracted from the CT image, ii) coaptation surface area of the leaflets and iii) an indication if the simulated closed leaflets leak. Results: We validate our method on three explanted porcine hearts and show that our model predicts the closed valve surface with point-to-surface error of appoximately 1mm, a reasonable coaptation surface area, and absence of leak at peak systole (maximum closed pressure). We also evaluate the sensitivity of our model to changes in various parameters (tissue elasticity, mesh accuracy, and the transformation matrix used for CT scan registration). We also measure the influence of the chordae tendineae positions on simulation results and show that marginal chordae have a greater influence on the final shape than intermediate chordae. Conclusions: The mitral valve simulation can help the surgeon understand valve behaviour and anticipate the outcome of a procedure.

Published
2018
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38. Using a biomechanical model for tongue tracking in ultrasound images

Author

Marie-Odile Berger, Pierre-Frédéric Villard, Matthieu Loosvelt, Visual Augmentation of Complex Environments (MAGRIT), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria), and Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Inria Nancy - Grand Est

Subjects
Engineering, Quantitative Biology::Neurons and Cognition, business.industry, Ultrasound, Physics::Medical Physics, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, 02 engineering and technology, Deformation (meteorology), Tracking (particle physics), [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Tongue, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], 0202 electrical engineering, electronic engineering, information engineering, medicine, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, 020201 artificial intelligence & image processing, Computer vision, Biomechanical model, Artificial intelligence, business, ComputingMethodologies_COMPUTERGRAPHICS
Abstract

International audience; We propose in this paper a new method for tongue tracking in ultrasound images which is based on a biomechanical model of the tongue. The deformation is guided both by points tracked at the surface of the tongue and by inner points of the tongue. Possible uncertainties on the tracked points are handled by the algorithm. Experiments prove that the method is efficient even in case of abrupt movements.

Published
2014

39. Preliminary Study of Rib Articulated Model based on Dynamic Fluoroscopy Images

Author

Marie-Odile Berger, Pierre Escamilla, Yves Trousset, Sebastien Gorges, Erwan Kerrien, Pierre-Frédéric Villard, Visual Augmentation of Complex Environments (MAGRIT), INRIA Lorraine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), General Electric Medical Systems [Buc] (GE Healthcare), General Electric Medical Systems, Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), and Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)

Subjects
Rib cage, fluoroscopy processing, articulated model, medicine.diagnostic_test, business.industry, Computer science, Interventional radiology, Respiration model, Image plane, Tracking (particle physics), [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, image driven simulation, 3. Good health, medicine, Fluoroscopy, Computer vision, Tomography, Artificial intelligence, business
Abstract

International audience; We present in this paper a preliminary study of rib motion tracking during Interventional Radiology (IR) fluoroscopy guided procedures. It consists in providing a physician with moving rib three-dimensional (3D) models projected in the fluoroscopy plane during a treatment. The strategy is to help to quickly recognize the target and the no-go areas i.e. the tumor and the organs to avoid. The method consists in i) elaborating a kinematic model of each rib from a preoperative computerized tomography (CT) scan, ii) processing the on-line fluoroscopy image and iii) optimizing the parameters of the kinematic law such as the transformed 3D rib projected on the medical image plane fit well with the previously processed image. The results show a visually good rib tracking that has been quantitatively validated by showing a periodic motion as well as a good synchronism between ribs.

Published
2014
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40. A method to compute respiration parameters for patient-based simulators

Author

Pierre-Frédéric, Villard, Franck P, Vidal, Fernando, Bello, and Nigel W, John

Subjects
Motion, Imaging, Three-Dimensional, Respiration, Abdomen, Biopsy, Fine-Needle, Humans, Computer Simulation, Tomography, X-Ray Computed, Models, Biological, Algorithms
Abstract

We propose a method to automatically tune a patient-based virtual environment training simulator for abdominal needle insertion. The key attributes to be customized in our framework are the elasticity of soft-tissues and the respiratory model parameters. The estimation is based on two 3D Computed Tomography (CT) scans of the same patient at two different time steps. Results are presented on four patients and show that our new method leads to better results than our previous studies with manually tuned parameters.

Published
2012

41. Virtual Reality Simulation of Liver Biopsy with a Respiratory Component

Author

Fernando Bello, Piers R. Boshier, Pierre-Frédéric Villard, and Derek A. Gould

Subjects
Flexibility (engineering), Engineering, business.industry, Cost effectiveness, media_common.quotation_subject, Fidelity, 020207 software engineering, 02 engineering and technology, Virtual reality, Field (computer science), 030218 nuclear medicine & medical imaging, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Test case, Learning curve, Component (UML), 0202 electrical engineering, electronic engineering, information engineering, business, Simulation, media_common
Abstract

The field of computer-based simulators has grown exponentially in the last few decades, especially in Medicine. Advantages of medical simulators include: (1) provision of a platform where trainees can practice procedures without risk of harm to patients; (2) anatomical fidelity; (3) the ability to train in an environment wherein physiological behaviour is observed, something that is not permitted where in-vitro phantoms are used; (4) flexibility regarding anatomical and pathological variation of test cases that is valuable in the acquisition of experience; (5) quantification of metrics relating to task performance that can be used to monitor trainee performance throughout the learning curve; and (6) cost effectiveness. In this chapter, we will focus on the current state of the art of medical simulators, the relevant parameters required to design a medical simulator, the basic framework of the simulator, methods to produce a computer-based model of patient respiration and finally a description of a simulator for ultrasound guided for liver biopsy. The model that is discussed presents a framework that accurately simulates respiratory motion, allowing for the fine tuning of relevant parameters in order to produce a patient-specific breathing pattern that can then be incorporated into a simulation with real-rime haptic interaction. Thus work was conducted as part CRaIVE collaboration [1], whose aim is to develop simulators specific to interventional radiology.

Published
2011
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42. Interactive Simulation of Diaphragm Motion Through Muscle and Rib Kinematics

Author

Wesley Bourne, Pierre-Frédéric Villard, Fernando Bello, Imperial College London, Visual Augmentation of Complex Environments (MAGRIT), INRIA Lorraine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS), Nadia Magnenat-Thalmann, Jian J. Zhang, David D. Feng, CRaIVE, and Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Lorraine (INPL)-Université Nancy 2-Université Henri Poincaré - Nancy 1 (UHP)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Lorraine (INPL)-Université Nancy 2-Université Henri Poincaré - Nancy 1 (UHP)

Subjects
Engineering, business.industry, Spring system, Kinematics, Structural engineering, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Interactive simulation, Tensegrity, Boundary value problem, business, Tissue composition, 030217 neurology & neurosurgery, Simulation, Physiological Phenomenon
Abstract

ISBN-10: 1848825641/ ISBN-13: 978-1848825642 / The original publication is available at www.springerlink.com; Modelling of diaphragm behaviour is of relevance to a number of clini cal procedures such as lung cancer radiotherapy and liver access interventions. The heterogeneity in tissue composition of the diaphragm, as well as the various physiological phenomena influencing its behaviour, requires a complex model in order to accurately capture its motion. In this paper we present a novel methodology based on a heterogeneous model composed of mass-spring and tensegrity elements. The physiological boundary conditions have been carefully taken into account and applied to our model. Thus, it incorporates the influence of the rib kinematics, the muscle natural contraction/relaxation and the motion of the sternum. Initial validation results show that the behaviour of the model closely follows that of a real diaphragm.

Published
2009
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43. Developing an immersive ultrasound guided needle puncture simulator

Author

Franck P, Vidal, Pierre-Frédéric, Villard, Richard, Holbrey, Nigel W, John, Fernando, Bello, Andrew, Bulpitt, and Derek A, Gould

Subjects
User-Computer Interface, Computer Simulation, Punctures, Radiography, Interventional, Ultrasonography, Interventional
Abstract

We present an integrated system for training ultrasound guided needle puncture. Our aim is to provide a cost effective and validated training tool that uses actual patient data to enable interventional radiology trainees to learn how to carry out image-guided needle puncture. The input data required is a computed tomography scan of the patient that is used to create the patient specific models. Force measurements have been made on real tissue and the resulting data is incorporated into the simulator. Respiration and soft tissue deformations are also carried out to further improve the fidelity of the simulator.

Published
2009

44. CT scan merging to enhance navigation in interventional radiology simulation

Author

Pierre-Frédéric, Villard, Vincent, Luboz, Paul, Neumann, Stéphane, Cotin, and Steve, Dawson

Subjects
Imaging, Three-Dimensional, Humans, Computer Simulation, Radiography, Interventional, Tomography, X-Ray Computed
Abstract

We present a method to merge two distinct CT scans acquired from different patients such that the second scan can supplement the first when it is missing necessary supporting anatomy. The aim is to provide vascular intervention simulations with full body anatomy. Often, patient CT scans are confined to a localised region so that the patient is not exposed to more radiation than necessary and to increase scanner throughput. Unfortunately, this localised scanning region may be limiting for some applications where surrounding anatomy may be required and where approximate supporting anatomy is acceptable. The resulting merged scan can enhance body navigation simulations with X-ray rendering by providing a complete anatomical reference which may be useful in training and rehearsal. An example of the use of our CT scan merging technique in the field of interventional radiology is described.

Published
2009

45. A prototype percutaneous transhepatic cholangiography training simulator with real-time breathing motion

Author

Franck Vidal, Nigel W. John, Carrie Hunt, Fernando Bello, Derek A. Gould, Sheena Johnson, Pierre-Frédéric Villard, Imperial College London, Visual Augmentation of Complex Environments (MAGRIT), INRIA Lorraine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Lorraine (INPL)-Université Nancy 2-Université Henri Poincaré - Nancy 1 (UHP)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Lorraine (INPL)-Université Nancy 2-Université Henri Poincaré - Nancy 1 (UHP), Bangor University, Manchester Business School (MBS), University of Manchester [Manchester], Royal Liverpool University Hospital, University of Liverpool-Royal Liverpool and Broadgreen University Hospital NHS Trust, CRaIVE, and Institut National de Recherche en Informatique et en Automatique (Inria)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)

Subjects
020205 medical informatics, Computer science, medicine.medical_treatment, 02 engineering and technology, Kinematics, Haptics, Percutaneous transhepatic cholangiography, Radiography, Interventional, Virtual environments, 030218 nuclear medicine & medical imaging, User-Computer Interface, 0302 clinical medicine, Anesthesiology, 0202 electrical engineering, electronic engineering, information engineering, Fluoroscopy, Computer vision, Haptic technology, medicine.diagnostic_test, Respiration, General Medicine, Computer Graphics and Computer-Aided Design, Computer Science Applications, Task analysis, Breathing, Computer Vision and Pattern Recognition, Algorithms, Cholangiography, Biomedical Engineering, Graphics processing unit, Health Informatics, Feedback, 03 medical and health sciences, Respiration simulation, medicine, Humans, Radiology, Nuclear Medicine and imaging, Computer Simulation, Simulation, ComputingMethodologies_COMPUTERGRAPHICS, X-ray simulation, Interventional radiology, business.industry, Needle puncture, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Reaction, Touch, Surgery, Artificial intelligence, business
Abstract

The original publication is available at www.springerlink.com; International audience; Purpose : We present here a simulator for interventional radiology focusing on percutaneous transhepatic cholangiography (PTC). This procedure consists of inserting a needle into the biliary tree using fluoroscopy for guidance. Methods : The requirements of the simulator have been driven by a task analysis. The three main components have been identified: the respiration, the real-time X-ray display (fluoroscopy) and the haptic rendering (sense of touch). The framework for modelling the respiratory motion is based on kinematics laws and on the Chainmail algorithm. The fluoroscopic simulation is performed on the graphic card and makes use of the Beer-Lambert law to compute the X-ray attenuation. Finally, the haptic rendering is integrated to the virtual environment and takes into account the soft-tissue reaction force feedback and maintenance of the initial direction of the needle during the insertion. Results : Five training scenarios have been created using patient-specific data. Each of these provides the user with variable breathing behaviour, fluoroscopic display tuneable to any device parameters and needle force feedback. Conclusions : A detailed task analysis has been used to design and build the PTC simulator described in this paper. The simulator includes real-time respiratory motion with two independent parameters (rib kinematics and diaphragm action), on-line fluoroscopy implemented on the Graphics Processing Unit and haptic feedback to feel the soft-tissue behaviour of the organs during the needle insertion.

Published
2009
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46. A Comparison Framework for Breathing Motion Estimation Methods From 4-D Imaging

Author

S. Delhay, David Sarrut, Michael Beuve, Vlad Boldea, Pierre-Frédéric Villard, Patrick Clarysse, Centre de Recherche et d'Application en Traitement de l'Image et du Signal (CREATIS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École Supérieure Chimie Physique Électronique de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Simulation, Analyse et Animation pour la Réalité Augmentée (SAARA), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Université Lumière - Lyon 2 (UL2), Extraction de Caractéristiques et Identification (imagine), Institut de Physique Nucléaire de Lyon (IPNL), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Centre de Recherche et d'Application en Traitement de l'Image et du Signal ( CREATIS ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -École Supérieure Chimie Physique Électronique de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Simulation, Analyse et Animation pour la Réalité Augmentée ( SAARA ), Laboratoire d'InfoRmatique en Image et Systèmes d'information ( LIRIS ), Université Lumière - Lyon 2 ( UL2 ) -École Centrale de Lyon ( ECL ), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ) -Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Université Lumière - Lyon 2 ( UL2 ) -École Centrale de Lyon ( ECL ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ), Extraction de Caractéristiques et Identification ( imagine ), Institut de Physique Nucléaire de Lyon ( IPNL ), and Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
[ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, Time Factors, Movement, Motion (geometry), Image registration, Deformable registration, Tracking (particle physics), Models, Biological, Sensitivity and Specificity, 030218 nuclear medicine & medical imaging, Pattern Recognition, Automated, 03 medical and health sciences, 0302 clinical medicine, Imaging, Three-Dimensional, validation, Motion estimation, [ INFO.INFO-TI ] Computer Science [cs]/Image Processing, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Humans, Computer vision, Electrical and Electronic Engineering, Lung, radiotherapy, Physics, thorax, Landmark, Radiological and Ultrasound Technology, [ INFO.INFO-IM ] Computer Science [cs]/Medical Imaging, business.industry, Radiotherapy Planning, Computer-Assisted, Reproducibility of Results, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Computer Science Applications, Exhalation, 030220 oncology & carcinogenesis, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], Metric (mathematics), Trajectory, A priori and a posteriori, Artificial intelligence, business, Artifacts, Tomography, X-Ray Computed, Software, Algorithms
Abstract

International audience; Motion estimation is an important issue in radia- tion therapy of moving organs. In particular, motion estimates from 4-D imaging can be used to compute the distribution of an absorbed dose during the therapeutic irradiation. We propose a strategy and criteria incorporating spatiotemporal information to evaluate the accuracy of model-based methods capturing breathing motion from 4-D CT images. This evaluation relies on the identification and tracking of landmarks on the 4-D CT images by medical experts. Three different experts selected more than 500 landmarks within 4-D CT images of lungs for three patients. Landmark tracking was performed at four instants of the expi- ration phase. Two metrics are proposed to evaluate the tracking performance of motion-estimation models. The first metric cumu- lates over the four instants the errors on landmark location. The second metric integrates the error over a time interval according to an a priori breathing model for the landmark spatiotemporal trajectory. This latter metric better takes into account the dy- namics of the motion. A second aim of this paper is to estimate the impact of considering several phases of the respiratory cycle as compared to using only the extreme phases (end-inspiration and end-expiration). The accuracy of three motion estimation models (two image registration-based methods and a biomechanical method) is compared through the proposed metrics and statistical tools. This paper points out the interest of taking into account more frames for reliably tracking the respiratory motion.

Published
2007
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47. Mechanical role of pleura on lung motion during breathing

Author

Michael Beuve, Anne-Laure Didier, Behzad Shariat, Pierre-Frédéric Villard, Simulation, Analyse et Animation pour la Réalité Augmentée (SAARA), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Université Lumière - Lyon 2 (UL2), Institut de Physique Nucléaire de Lyon (IPNL), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), and SI LIRIS, Équipe gestionnaire des publications

Subjects
medicine.medical_specialty, Biomedical Engineering, Bioengineering, 030204 cardiovascular system & hematology, [INFO] Computer Science [cs], 030218 nuclear medicine & medical imaging, 03 medical and health sciences, Key point, 0302 clinical medicine, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Medicine, [INFO]Computer Science [cs], Lung, Motion simulation, business.industry, General Medicine, Anatomy, respiratory system, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [INFO.INFO-GR]Computer Science [cs]/Graphics [cs.GR], Computer Science Applications, Surgery, respiratory tract diseases, Human-Computer Interaction, medicine.anatomical_structure, Breathing, business
Abstract

International audience; Organs motions, in particular due to patient's breathing are crucial for the accuracy of radiotherapy and hadrontherapy treatments. We developped a pulmonary motion simulation (Villard et al.2006) based on continuous mechanical framework. A key point of our model is the inclusion of the pleura action, letting the lungs slide agains the chest wall during the simulation of the respiration toquantify the actual role of the pleura on the lung motion. We compared the imulation of the lung displacements obtaines by allowing or blocking these slidings.

Published
2007
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48. Breathing Thorax Simulation based on Pleura Physiology and Rib Kinematics

Author

J.-Y. Bayle, Michael Beuve, Behzad Shariat, Anne-Laure Didier, and Pierre-Frédéric Villard

Subjects
Thorax, Rib cage, Computer science, Quantitative Biology::Tissues and Organs, Screw axis, Breathing, Physiology, Anatomy, Kinematics, Simulation based, Finite element method
Abstract

To monitor a lung mechanical model and then predict tumour motion we proposed a approach based on the pleura physiology. By comparing the predictions to landmarks set by medical experts, we observed better results with regards to the one obtained with approaches found in the literature. Beside, we focus on the rib cage kinematics, which play a significant role in the pleura outer-surface motion and therefore in the lung motion. We proposed a kinematic model of the rib cage based on the finite helical axis method and we show out interesting results.

Published
2007
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49. SU-GG-I-120: Joint Simulation of Transmission X-Ray Imaging on GPU and Patient's Respiration on CPU

Author

Manuel Garnier, Franck Vidal, Pierre-Frédéric Villard, Nigel W. John, Nicolas Freud, Fernando Bello, and Jean Michel Létang

Subjects
Rib cage, Unsharpness, Point source, Computer science, medicine.medical_treatment, Acoustics, OpenGL, General Medicine, Kinematics, Percutaneous transhepatic cholangiography, Rendering (computer graphics), Organ Motion, Polygon, medicine, Medical imaging, Polygon mesh
Abstract

Purpose: We previously proposed to compute the X‐ray attenuation from polygons directly on the GPU, using OpenGL, to significantly increase performance without loss of accuracy. The method has been deployed into a training simulator for percutaneous transhepatic cholangiography. The simulations were however restricted to monochromatic X‐rays using a point source. They now take into account both the geometrical blur and polychromatic X‐rays. Method and Materials: To implement the Beer‐Lambert law with a polychromatic beam, additional loops have been included in the simulation pipeline. It is split into rendering passes and uses frame buffer objects to store intermediate results. The source shape is modeled using a variable number of point sources and the incident beam is split into discrete energy channels. The respiration model is composed of ribs, spine, lungs,liver, diaphragm and the external skin. The organ motion simulation is based on anatomical and physiological studies: the model is monitored by two independent active components: the ribs with a kinematics law and the diaphragm tendon with an up and down translation. Other soft‐tissue components are passively deformed using a 3D extension of the ChainMail algorithm. The respiration rate is also tunable to modify the respiratory profile. Results: We have extended the simulation pipeline to take into account focal spots that cause geometric unsharpness and polychromatic X‐rays, and dynamic polygon meshes of a breathing patient can be used as input data. Conclusions: X‐ray transmission images can be fully simulated on the GPU, by using the Beer‐Lambert law with polychromatism and taking into account the shape of the source. The respiration of the patient can be modeled to produce dynamic meshes. This is a useful development to improve the level of realism in simulations, when it is needed to retain both speed and accuracy.

Published
2010
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50. PoLAR: a Portable Library for Augmented Reality

Author

Pierre-Jean Petitprez, Erwan Kerrien, Pierre-Frédéric Villard, Visual Augmentation of Complex Environments (MAGRIT), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Algorithms, Computation, Image and Geometry (LORIA - ALGO), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), IEEE, Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), and Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Image manipulation, Computer science, business.industry, 020207 software engineering, 02 engineering and technology, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Visualization, Human–computer interaction, 020204 information systems, Computer graphics (images), 0202 electrical engineering, electronic engineering, information engineering, Augmented reality, business, Graphical user interface, Coding (social sciences)
Abstract

International audience; We present here a novel cross-platform library to facilitate research and development applications dealing with augmented reality (AR). Features include 2D and 3D objects visualization and interaction, camera flow and image manipulation, and soft-body deformation. Our aim is to provide computer vision specialists' with tools to facilitate AR application development by providing easy and state of the art access to GUI creation, visualization and hardware management. We demonstrate both the simplicity and the efficiency of coding AR applications through three detailed examples. PoLAR can be downloaded at http://polar.inria.fr and is distributed under the GPL licence.

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