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


Section: Partnerships and Cooperations

National Initiatives

France-BioImaging project

Participants : Charles Kervrann, Patrick Bouthemy, Thierry Pécot, Emmanuel Moebel, Ancageorgiana Caranfil.

The goal of the project is to build a distributed coordinated French infrastructure for photonic and electronic cellular bioimaging dedicated to innovation, training and technology transfer. High-computing capacities are needed to exhaustively analyse image flows. We address the following problems: i/ exhaustive analysis of bioimaging data sets; ii/ deciphering of key steps of biological mechanisms at organ, tissular, cellular and molecular levels through the systematic use of time-lapse 3D microscopy and image processing methods; iii/ storage and indexing of extracted and associated data and metadata through an intelligent data management system. serpico is co-head of the IPDM (Image Processing and Data Management) node of the FBI network composed of 6 nodes.

Table 1.
Funding: Investissement d'Avenir - Infrastructures Nationales en Biologie et Santé ANR (2011-2016).
Partners: CNRS, Institut Jacques Monod, Institut Pasteur, Institut Curie, ENS Ulm, Ecole Polytechnique, INRA, INSERM.

ANR DALLISH project (2016-2020): Data Assimilation and Lattice LIght SHeet imaging for endocytosis/exocytosis pathway modeling in the whole cell

Participants : Charles Kervrann, Patrick Bouthemy, Vincent Briane, Ancageorgiana Caranfil.

The Lattice Light Sheet Microscopy (LLS-M) represents at present the novel generation of 3D fluorescence microscopes dedicated to single cell analysis, generating extraordinarily high resolved and sharp, but huge 3D images and videos: one single live cell experiment in one single condition, imaging two molecular markers of the endocytosis pathway and using cutting-edge LLS-M can result into up to one Terabyte of data, at the spatial resolution of 100-200 nanometers in 3D. In such a situation, it is found the usual conventional image reconstruction algorithms and image analysis methods developed for 3D fluorescence microscopy are likely to fail to process a deluge of voxels generated by LLS-M instruments. The goal of the project is then to develop new paradigms and computational strategies for image reconstruction and 3D molecule tracking/motion estimation. Furthermore, establishing correspondences between the image-based measurements and features (e.g., motion vectors, trajectories), stochastic motion models and the underlying biological and biophysical information remains a challenging task.

The impact of the project will be three-fold. First, our new image processing paradigms and improved algorithms (allowing faster, more resolved and more accurate results) will have direct benefits in modern bioimaging. Second, the methods and algorithms will apply to decipher molecular mechanisms of protein transports, here focused on endocytosis/exocytosis. Finally, in a larger perspective, the quantitative description of protein transport will be a prerequisite for understanding the functioning of a cell in normal and pathological situations, as default in protein transport appeared over the years, as a major contributory factor to a number of diseases, including cancer, viral infection and neurodegenerative diseases.

Table 2.
Funding: ANR - Agence Nationale de la Recherche
Partners: Inria (SERPICO, BEAGLE, Fluminance), INRA MaIAGE Unit Jouy-en-Josas, Institut Curie (UMR CNRS 144 & U1143 Inserm UMR 3666) Paris