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Bilateral Contracts and Grants with Industry
Bibliography
Bilateral Contracts and Grants with Industry
Bibliography


Section: New Software and Platforms

Platforms

Mobyle@Serpico plateform and software distribution

Figure 2. Mobyle@Serpico web portal.
IMG/MobyleatSERPICO.png

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 [26] , Atlas [12] , HotSpotDetection [57] , Hullkground [43] , KLTracker [55] , Motion2D [54] , MS-detect [45] , ND-Safir [4] , OpticalFlow and Flux Estimation [26] . 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 (500 MegaBytes for each user / Data is saved for 3 months).

 

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 [43] , Motion2D [54] , HotSpotDetection [57] , Stlas [12] . The C-Craft algorithm [26] 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.

 

  • Participants: Thierry Pécot, Charles Kervrann, Charles Deltel (Inria Rennes SED).

  • Contact: Thierry Pécot, Charles Kervrann.

     

IGRIDA-Serpico cluster

The IGRIDA-Serpico cluster of 200 nodes is opened for end-users for large scale computing and data sets processing (200 TeraBytes).

  • Batch Scheduler: OAR

  • File management: Puppet / Git / Capistrano

  • OS: Linux Debian 7

  • User connexion: public ssh key

  • Contact: Thierry Pécot, Charles Kervrann, Charles Deltel (Inria Rennes SED).