Biology, physics, applied mathematics and complex systems modelling

IdFsud gathers an important task force in biology, physics, applied mathematics and complex systems modelling. These disciplines synergize to develop innovative methodologies and tools in microscopy imaging and image analysis for applications in developmental biology, cell biology, plant biology, physiopathology and neurosciences. IdF Sud gathers three core partners with internationally acknowledged expertise: BioEmergences (CNRS-IBiSA), Imagerie-Gif and Polytechnique LOB (Lab for optics & biosciences, CNRS – INSERM).
The imaging facilities of IdFsud are developed and coordinated by: Nadine Peyrieras (INAF, CNRS, Gif-sur-Yvette), Béatrice Satiat-Jeunemaitre (I2BC, CNRS, Gif sur Yvette), Emmanuel Beaurepaire (Ecole Polytechnique, CNRS, Palaiseau).
The activity of the Ile-de-France Sud node (IdFsud) consists in developing novel optical biological imaging methods, in giving access to a broad range of imaging approaches to a large community, and in providing adequate training in light microscopy and CLEM.

2018 in numbers

  • hosted projects
  • publications
  • training programs
  • patents since 2011

Technological Innovations

  • New non-linear contrast: probing lipid order with polarized THG. LOB. Phys Rev X (2013)
  • Multicolor 2P Imaging of Brainbow tissue LOB/Inst Vision/ENS. Neuron (2014)
  • 3D+time image analysis of the digital lineage trees with the BioEmergences workflow (Nature Comm. 2016)

Some of the Innovative systems operated

  • Multicolor and polarisation multi-photon microscopy
  • Horizontal 2-photon microscope
  • Light-sheet microscopy

Tech transfer

  • Biosensors & Applications
  • Industrial partnershipp for light sheet microscopy
  • 3D+time multiscale data reconstruction workflows
  • Correlative microscopy


↗ Website + Info

Facility: Imagerie-Gif

Head: Béatrice Satiat-Jeunemaitre

I2BC, Gif-sur-Yvette, France

The cell biology pole Imagerie-Gif is localized on the CNRS campus of Gif sur Yvette, in a new building dedicated to platform activity. This IBiSA platform provides efficient access to high quality services and state of the art technologies. It is open to the whole academic scientific community and to industrial partners. The management and development of this pole is under the responsibility of the team “Dynamics of cell compartmentation” (group leader B. Satiat-Jeunemaitre, Institut des Sciences du Végétal, Gif sur Yvette). It uses cell biology approaches and multiscale imaging (cytometry, bio-imaging and electron microscopy) to explore the cell. The development of new protocols and the mastering of update imaging approaches are part of the R & D objectives of the platform. Those are then transferred to platform services and disseminated through numerous training and teaching events, and opened to the whole scientific community. The cell biology pole of Imagerie-Gif activities contributes to the working groups “super resolution”, “Probe development” and “CLEM” within the France-BioImaging consortium.

Services on this Facility


Microscopy Technologies



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Facility: BioEmergences

Head: Nadine Peyréras

Université Paris-Sud, Rue Georges Clemenceau, Orsay, France

 The BioEmergences platform (UPS in 2014) develops, applies to specific case studies, and offers as services, original methodologies and tools for the multi-scale phenomenological and theoretical reconstruction of the development of model organisms, animal or vegetal. The work is organized along the lines of an applied epistemology that we defined in the context of the Institute for Complex Systems which is part of the national and international roadmap established by the Complex Systems community We developed a workflow going from photonic microscopy for in vivo and in toto imaging of developing organisms to the automated reconstruction of 3D+time data, analysis of digital specimens and modeling of morphogenetic processes. In this context provide collaborative services that most of the time, correspond to new challenging applications (WP1b, WP1d, WP2, WP3). FBI funding is used to develop a so-called artificial assistant based on a SPIM or MLMS imaging concept with real time image processing and feedback on the imaging scheme. All our activity involves image processing (WP4), that’s why we are involved in IPDM node too. We expect to provide the community with original webservices to access the BioEmergences reconstruction workflow and grid computing.

Services on this Facility


Image Data Handling


Microscopy Technologies

R&D team


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R&D team: LOB

Head: Emmanuel Beaurepaire

FCS Campus Paris-Saclay, Saint-Aubin, France

Ecole Polytechnique is an internationally attractive institution combining research, teaching and innovation. Laboratory for Optics and Biosciences (LOB) is affiliated with the French Research institutions Inserm and CNRS, and Ecole Polytechnique. The Laboratory employs researchers with expertise in optics, molecular and cellular biology with the aim to explore new concepts and methods. Two LOB research teams are involved in optical imaging developments co-funded by France BioImaging. Access to instruments is currently provided on a collaborative basis and will be extended within the timeframe of the project.
* “Advanced Microscopies and Tissue Physiology” (E. Beaurepaire, M.-C. Schanne-Klein, W. Supatto, G. Gallot, M. Joffre et al). LOB “advanced microscopies” pole is a leading group in nonlinear microscopy of live tissues and small organisms, and develops pioneering approaches based on multimodal multiphoton imaging (multicolor 2PEF, SHG, THG, FWM, CARS), polarimetry, light-sheet illumination (SPIM), photomanipulation, wavefront control, pulse shaping.
* “Nanoemitters and Single Molecule Tracking” (A. Alexandrou, C. Bouzigues, et al). LOB “nanoemitters” team develops innovative assays based on non-blinking lanthanide-ion doped nanoprobes and microfluidics devices to study signaling processes in live cells.

Key publications

  • A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage. Emmanuel Faure et al. Nature Communications volume7, Article number: 8674 (2016)
  • Efficient second-harmonic imaging of collagen in histological slides using Bessel beam excitation. Nelly Vuillemin, Pierre Mahou, Delphine Débarre, Thierry Gacoin, Pierre-Louis Tharaux, Marie-Claire Schanne-Klein, Willy Supatto & Emmanuel Beaurepaire. Scientific Reports volume 6, Article number: 29863 (2016)
  • Self-organization of the human embryo in the absence of maternal tissues
    Marta N. Shahbazi, Agnieszka Jedrusik, Sanna Vuoristo, Gaelle Recher, Anna Hupalowska, Virginia Bolton, Norah M. E. Fogarty, Alison Campbell, Liani G. Devito, Dusko Ilic, Yakoub Khalaf, Kathy K. Niakan, Simon Fishel & Magdalena Zernicka-Goetz. Nature Cell Biology volume 18, pages 700–708 (2016)