Section: New Software and Platforms

Image Processing software distribution and Mobyle plateform

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

Figure 2. Mobyle@SERPICO web portal.

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. 2 ) is to demonstrate the performance of the programs developed by the team: C-CRAFT [13] , atlas [23] , HotSpotDetection [51] , Hullkground [35] , KLTracker [50] , Motion2D [49] , MS-detect [37] , 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 [35] , Motion2D [49] , HotSpotDetection [51] . The C-CRAFT algorithm [13] has been developped for the image processing ICY platform (http://icy.bioimageanalysis.org/ ).

  • Institut Curie CID iManage database: The microscopy facility of Institut Curie has co-developped a commercial database system (CID iManage/Strand Avadis company). The database can be searched via meta-data and includes menu selections that enable to run remote processing from a cluster. We have integrated nD-Safir and Hullkground in the interface environment to allow the database users to process their images easily, and store associated results and parameters used.

Collaborators: Charles Deltel (Inria Rennes SED) and Perrine Paul-Gilloteaux (UMR 144 CNRS-Institut Curie, STED team and PICT-IBiSA).