Section: Software and Platforms

Image Processing software distribution

Participants : Tristan Lecorgne, Tinaherinantenaina Rakotoarivelo, Thierry Pécot [(contact)] , Charles Kervrann.

The objective is to disseminate the distribution of serpico image processing software for biologist users:

• Free binaries: software packages have been compiled for the main operating systems (Linux, MacOS, Windows) using CMake (see http://www.cmake.org/ ). They are freely available on the team website under a proprietary license (e.g. nD-Safir and Hullkground are distributed this way at http://serpico.rennes.inria.fr/doku.php?id=software:index ).

• Mobyle@SERPICO web portal: An on-line version of the image processing algorithms has been developped using the Mobyle framework (Institut Pasteur, see http://mobyle.pasteur.fr/ ). The main role of this web portal (see Fig. 5 ) is to demonstrate the performance of the programs developed by the team: CRFMovingSpotDetection (under review), HotSpotDetection [50] , Hullkground [32] , KLTracker [48] , Motion2D [19] , MS-detect [35] , nD-Safir [4] and OpticalFlow . The web interface makes our image processing methods available for biologist users at Mobyle@SERPICO (http://mobyle-serpico.rennes.inria.fr/cgi-bin/portal.py#welcome ) without any installation or configuration on their own. The size of submitted images is limited to 200 MegaBytes per user and all the results are kept 15 days. The web portal and calculations run on a server with 2 CPU x 8 cores, 64 GigaBytes of RAM.

• ImageJ plug-ins: ImageJ (see http://rsb.info.nih.gov/ij/ ) is a widely used image visualization and analysis software for biologist users. We have developed ImageJ plug-in java versions of the following software: nD-Safir [4] , Hullkground [32] (see Fig. 4 ), Motion2D [19] , HotSpotDetection [50] .

• Institut Curie CID iManage database: Institut Curie is currently acquiring a commercial database system (CID iManage / Strand Avadis company) to store mass of data. The database can be searched via meta-data and includes menu selections that enable to run remote processing. We have integrated nD-Safir in the interface environment to allow the database users to denoise images easily.

Partners: C. Deltel (Inria Rennes SED) and Perrine Paul-Gilloteaux (UMR 144, PICT IBiSA, CNRS-Institut Curie)

Figure 5. Mobyle@SERPICO web portal.