Software Development

A scheme presenting the different dependencies can be found below.

MedINRIA, a free collection of softwares developed within the Asclepios research project

MedINRIA aims at providing to clinicians state-of-the-art algorithms dedicated to medical image processing and visualization. Efforts have been made to simplify the user interface, while keeping high-level algorithms. Each application is called a module, and can be loaded dynamically from a single main window. MedINRIA is available for Microsoft windows XP/Vista, Linux Fedora Core, MacOSX, and is fully multithreaded.

Note: MedINRIA is a free software for non-commercial use only! For other usage, please contact the developers. More details on MedINRIA Web Page.

vtkINRIA3D, a C++ library extending VTK

vtkINRIA3D is a C++ library extending VTK to match specific needs in medical data management and visualization, e.g. synchronized 2D views of volumetric data, 4D handling and interactive manipulation of 3D objects.

vtkINRIA3D is Open Source :)

CardioViz3D, Interactive Visualization of Cardiac activity.

CardioViz3D targets research in cardiac imaging. It is founded by CardioSense3D project and aims at providing the researcher with a set of tools for pre-processing data and to visualize results of cardiac simulations. It has a robust visualization mechanism of any type of data, as well as a complete handling of time sequences of data.

SepINRIA, A Software to Analyse Multiple Sclerosis Brain MRI

SepINRIA is a free software dedicated to Multiple Sclerosis brain MRI analysis. SepINRIA allows to segment MS lesions (manually or automatically) and to evaluate atrophy (manually or automatically). Images can also be registered together and compared. This software is available for Microsoft windows XP, Linux Fedora Core and MacOSX. SepINRIA is based on ITK, VTK, wxWidgets, vtkINRIA3D libraries and the MedINRIA framework.

Some publications can be found here.

MIPS, General-purpose C++ Medical Image Processing and Simulation Library.

This C++ library offers a suite of functionnalities for the processing and visualization of medicales images and geometric meshes. Yav++ is MIPS Graphical User Interface, based on OpenGL and Tcl/Tk. It allows to apply most available algorithms interactively but also to build dedicated applications through the use of Tcl scripting.

Isis, Visual volume reconstruction software from seried slices.

Isis is a tool to help the biologists and researchers to rebuild anatomical volumes from seried slices. It offers accumulatable automatic and interactive manual registration methods.
Coming Soon!

Collaborative developments

the SOFA project

SOFA is an Open Source framework primarily targeted at real-time simulation, with an emphasis on medical simulation. It is mostly intended for the research community to help develop newer algorithms, but can also be used as an efficient prototyping tool.
SOFA is currently developed by 3 INRIA teams: Alcove, Evasion and Asclepios but the project also benefited from the help of the CIMIT Sim Group, ETH Zurich and CSIRO.

Diffeomorphic Demons: diffeomorphic transformation on 2D/3D images

Diffeomorphic Demons is an efficient algorithm for the diffeomorphic registration of N dimensional images. It is based on Thirion's demons algorithm but works on a Lie group structure on diffeomorphic transformations. Typical 3D medical images can be registered in less than three minutes on a 2 x 2.8 GHz quad-core Intel Xeon Apple Mac pro computer. Diffeomorphic demons is now included in MedINRIA's image fusion module. The source code has been integrated into ITK since version 3.8. A command-line software can be found on the Insight Journal. Additionally, some standalone binaries and tutorials may be found on the Stark Lab website.

Spherical Demons: registering closed surfaces

Spherical Demons is an algorithm that registers spherical images. It extends the Demons algorithm in Euclidean space to the sphere. We use it to perform fast diffeomorphic landmark-free surface registration of 2D closed surfaces. We have shown that registration between a subject mesh and an atlas takes less than 5 mins on a Xeon 3.2GHz single processor machine, which is more than 10 times faster than the popular, freely-available FreeSurfer. Our experiments also show that Spherical Demons is at least as accurate as FreeSurfer.

Organisation of software dependencies within Asclepios:

Other developments

CreateROIMask: an Osirix plugin

CreateROIMask The medical imaging software Osirix provides tools to create Region Of Interest and save them into a specific format rois_series. The aim of this plugin is to convert an Osirix ROI into a binary image in Analyze format.

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