Section: Partnerships and Cooperations

National Initiatives

France-BioImaging project

Participants: Sylvain Prigent, Patrick Bouthemy, Charles Kervrann, Jean Salamero.

Duration: 2011 – 2024.

The goal of the France-BioImaging project (http://france-bioimaging.org/) 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. Serpico is co-head of the IPDM (Image Processing and Data Management) node of the FBI network composed of 6 nodes. In this context, we address the following scientific 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 recruited R&D engineers to disseminate image processing software, to build the Mobyle@serpico web portal and to manage the IGRIDA-Serpico cluster (200 nodes; batch scheduler: OAR; File management: Puppet/Git/Capistrano; OS: Linux Debian 7; User connexion: public ssh key) opened for end-users and dedicated to large scale computing and data sets processing (storage: 200 TeraBytes) (see Section 6.13).

Funding: Investissement d'Avenir, ANR INBS-PIA 2011.

Coordinator: CNRS (J. Salamero, UMS 3714 CEMIBIO & CNRS-UMR 144, Institut Curie, PSL Research University).

Partners: CNRS, University of Paris-Diderot-Paris 7, Aix-Marseille University, University of Bordeaux, University of Montpellier, Institut Pasteur, Institut Curie, Inria, ENS Paris, University of Paris Descartes, UPMC, Ecole Polytechnique, INSERM.

 

ANR NucleoPLASTIC: Plasticity of the Nuclear Pore Complex

Participant: Jean Salamero.

Duration: 48 months (Oct 2015 – Sep 2019).

In this project, we have deciphered molecular/structural changes on the nuclear face of the Nuclear Pore Complex, their dynamics during cell division, and highlighted their role in the dynamics of association with the heart of the pore with consequences on maintaining the integrity of the genome. This was possible through the development of a 3D localization software GenLoc3D (https://team.inria.fr/serpico/software/genloc3d/, FIJI/ImageJ plug-in).

Funding: ANR (Agence Nationale de la Recherche).

Coordinator:  C. Dargemont (INSERM, Hopital St Louis, Paris).

Partners: CNRS-UMR 144, Institut Curie, PSL Research, Paris.

 

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

Participants: Antoine Salomon, Anca-Georgiana Caranfil, Sandeep Manandhar, Cesar Augusto Valades Cruz, Patrick Bouthemy, Ludovic Leconte, Jean Salamero, Charles Kervrann.

Duration: 48 months (Oct 2016 – Sep 2020).

Cutting-edge Light Lattice Sheet microscopy represents 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 biological condition can result into up to one terabyte of data.The goal of the project is to develop new paradigms and computational strategies for image reconstruction and 3D molecule motion estimation and tracking. Furthermore, establishing correspondences between image-based measurements and features, stochastic motion models, and underlying biological and biophysical information remains a challenging task. In a larger perspective, the quantitative description of image data corresponding to protein transport will be a prerequisite for understanding the functioning of a cell in normal and pathological situations including cancer, viral infection and neurodegenerative diseases (see Sections 7.2–7.6 and 7.8).

Funding: ANR (Agence Nationale de la Recherche) PRC (Collaborative Research Project).

Coordinator:  C. Kervrann.

Partners: Inria (serpico, beagle, fluminance teams), INRA MaIAGE Unit Jouy-en-Josas, Institut Curie (CNRS-UMR 144 & U1143 INSERM / UMR 3666) Paris.

 

Inria Project Labs (IPL / DEFI), Exploratory Research Actions and Technological Development Actions

NAVISCOPE: image-guided NAvigation and VISualization of large data sets in live cell imaging and microCOPy

Participants: Gwendal Fouché, Cesar Augusto Valades Cruz, Ludovic Leconte, Anais Badoual, Jean Salamero, Charles Kervrann.

Duration: 60 months (2018 – 2022).

In the frame of the "Naviscope" IPL project (https://project.inria.fr/naviscope/), our objective is to develop original and cutting-edge visualization and navigation methods to assist scientists, enabling semi-automatic analysis, manipulation, and investigation of temporal series of multi-valued volumetric images, with a strong focus on live cell imaging and microscopy application domains. Naviscope, built upon the strength of scientific visualization and machine learning methods, will provide systems capable to assist the scientist to obtain a better understanding of massive amounts of information. Such systems will be able to recognize and highlight the most informative regions of the dataset by reducing the amount of information displayed and guiding the observer attention. We address the three following challenges and issues:

• Novel machine learning methods able to detect the main regions of interest, and automatic quantification of sparse sets of molecular interactions and cell processes during navigation to save memory and computational resources.

• Novel visualization methods able to encode 3D motion and deformation vectors and dynamics features with color and texture-based and non-sub-resolved representations, abstractions, and discretization, as used to display 2D motion and deformation vectors and patterns.

• Effective machine learning-driven navigation and interaction techniques for complex functional 3D+Time data enabling the analysis of sparse sets of localized intra-cellular events and cell processes (migration, division, etc.) (see Section 7.9).

Meanwhile, we address the technological challenge of gathering up the software developed in each team to provide a unique original tool for users in biological imaging, and potentially in medical imaging.

Funding: Inria (IPL / DEFI).

Coordinator:  C. Kervrann.

Partners:  aviz Inria team (Saclay); beagle Inria team (Lyon), hybrid Inria team (Rennes), morpheme Inria team (Sophia-Antipolis); mosaic Inria team (Lyon), parietal Inria team (Saclay), serpico Inria team (Rennes); MaIAGE INRA Unit (Jouy-en-Josas); CNRS-UMR 144, Institut Curie, PSL Research University (Paris).