SOFA project

Internship on NeuroLOG/SepINRIA

School projects

I'm currently working as developing engineer for the project SOFA. My first year annual report can be found here in pdf format (in French):




Context: Read more

Recent works:

• Implementation of Manifold triangulation and tetrahedrization as specification of general triangle and tetrahedron classes in SOFA. Thus, the handling of topological modifications has been expanded to manifold triangulation. This avoids removing or adding triangles when the manifold configuration won't be respected.
• Implementation of topological modifications only possible in manifold configuration. Like, for example, edge swapping between two adjacent triangles.
• Creation of a user interface to use topological operations.

Demo movie: Resection and addition of triangles in a triangular mesh. Here

Using elementary topological changes like removing and adding triangles, an algorithm of incision in triangular meshes has been designed with care of handling data based on this mesh.

An improvement of this method has been done on different aspects:

• Possibility to perform successive incisions.
• Two types of incision: from click to click and continually (following the mouse).
• A user interaction interface (GUI).
• Globalization of the declaration of incision path.
• The handling of snapping point on the incision path and on the border.

Some results:



Demo movie: Example of incision using snaping and surface resection Here

Implementation of a new mesh loaders factory that provide specific loaders, as components of SOFA, corresponding to specific mesh file format. The interest is to be able to load specific information from files and link them directly to other components.
In more details, all the data loaded from mesh files are stored into C++ containers, call "Data" in SOFA. These containers are C++ components members reachable in the XML scene files. Thus, mechanisms have been done to first, link some Data array with topological elements and then to allow the handling of topological changes. For example heart fiber directions can be loaded, then used in the anisotropic diffusion module and finally handle tissue resections.

Some results:



Demo movie: Example of data loaded (mesh zones, fibers directions, ...). Here

SOFA has been meanly designed for the simulation of mechanical object interaction but not, for example, for the simulation of electrophysiology propagation and it's coupling with mechanical objects. Thus, we have extended the SOFA framework in order to simulate the evolution of a physical field (scalar, vectorial or tensorial quantity) an the coupling with mechanical model evolution.

A first step has been to simulate reaction and diffusion models in triangular or tetrahedral meshes. Some work has also been done on specific first order solver and visualization tools.


Some results:


Demo movies:

• Example of isotropic and anisotropic diffusion in a tetrahedral mesh. Here
• Example of reaction-diffusion model using anisotropic diffusion and a mouse interaction to inject potentials. Here
• Example of coupling between mechanical and physical field behaviours using mouse interactions. Here

A second step was to be able to have real-time modeling of electrophysiology which is suitable for representing simple cases of arrhythmia (ectopic focus, ventricular tachycardia) for heart simulation. To this end, we use an anisotropic multi-front fast marching method to simulate transmembrane potential propagation in cardiac tissues. The electric propagation is coupled with a pre-recorded beating heart model.

Finally, a prototype has been developped for rehearsing radio-frequency ablation of the myocardium in the context of cardiac arrhythmia has been developped. Indeed, thanks to a 3D user interface, the user can interactively measure the local extracellular potential, pace locally the myocardium or simulate the burning of cardiac tissue as done in radio-frequency ablation interventions.

Those steps take into account the developement of drivers interface for haptic tools: Xitact ITP and IHP from Mentice .

Complete description of this work can be found in the article: Interactive real time simulation of cardiac radio-frequency. In VCBM 2010. (soon available)


Some results:



Demo movie: Movie given as multimedia support for the VCBM's article. Here

In the context of the disease of the tetralogy of Fallot, work has been done to simulate the resection of cardiac tissues from a dilated ventricule and then perform a suture. This pipeline allow to minimise the volume of the ventricule and thus optimise the cardiac performances.

In addition to that, we focus on the fact that these operations should update the heart fiber directions data.

Some results:



Demo movie: Whole pipeline done in SOFA using mouse interactions. Here

In the continuity of precedent work done in the context of the tetralogy of Fallot, recent developements on haptic tool have been modified to recreate a new simulation of heart suture using haptic device.

This work has been shown at the conference of Health-e-Child (ref a venir).


Some results:





Demo movie: Some movies done during the conference. Here