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


Section: New Software and Platforms

Cryo-Seg

Keywords: Bioinformatics - Biomedical imaging

Functional Description:  The Cryo-Seg software has been developed to detect microtubule structures and helical structures in 2D cryo-electron microscope images. Cryo-electron tomography allows 3D observation of biological specimens in their hydrated state. Segmentation is formulated as Maximum A Posteriori estimation problem and exploits image patches to take into account spatial contexts (Markov Random Fields). Because of the contrast anisotropy in the specimen thickness direction, the whole tomogram is segmented section by section, with an automatic update of reference patches. This algorithm has been evaluated on synthetic data and on cryo-electron tomograms of in vitro microtubules. On real data, this segmentation method extracts the most contrasted regions of microtubules, and 3D visualization is improved.

  • Participants: Denis Chrétien, Charles Kervrann, Sophie Blestel.

  • Contact: Denis Chrétien.

  • Partners: University of Rennes 1, CNRS.

  • Languages:  C/C++ and Java (plug-in ImageJ : http://rsbweb.nih.gov/ij/ )