List of facilities and R&D teams

Facility

UTechS UBI – Pasteur

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Facility: UTechS UBI – Pasteur

Head: Jacomine Krijnse-Locker

jacomina.krijnse-locker@pasteur.fr
Institut Pasteur 25-28 Rue du Docteur Roux 75724, Paris CEDEX 15

Member of C2RT (Center for Resources and Research in Technology) the Unit for service and technology in ultra-structural bio-imaging  (UBI) at Pasteur provides technical and scientific support in electron microscopy, mainly, but not exclusively, to the Pasteur community, analyzing host-pathogen interactions at the ultra-structural level. Our equipment enables us to do state-of-the-art EM for life sciences that includes three dimensional EM by tomography and focused ion beam SEM. The ultrapole is run by ten members (eight engineers and two technicians), each specialized in certain techniques. We put a big emphasis on correlate light- and electron microscopy to study key (rare events) of host-pathogen interactions and we have designed several protocols to combine room temperature LM and cryo-LM with FIB-SEM, cryo-SEM and cryo-tomography.

The UBI also has a small research group focusing on large DNA-viruses. Through this research theme we wish to establish and develop robust, new protocols for various EM-techniques.

Services on this Facility

Service

Microscopy Technologies

Facility

PICT-IBiSA Curie

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Facility: PICT-IBiSA Curie

Head: Olivier Renaud (PICT-LM) & Daniel Levy (PICT-EM)

Info.pict@curie.fr
Institut Curie, Rue d'Ulm, Paris, France

The Cell and Tissue Imaging Platform (PICT-IBiSA) of the Institut Curie brings together advanced microscopy technologies. Its main objective is to provide researchers in cell biology, development, structural, chemistry and biophysics with imaging approaches at different spatial and dynamic scales ranging from the molecule, to the cell, to the organism in healthy or pathological contexts.

The platform is organized around 3 poles: photonic microscopy, high-content screening, electron microscopy and cryo-electron microscopy. Photonic microscopy extends from dynamic imaging to high resolution. High throughput microscopy allows cellular screening of chemical and siRNA banks. Electron microscopy and cryo-microscopy provide the molecular structure and cellular ultrastructure of biological samples. The platform also offers expertise in data processing and analysis.

Services on this Facility

Service

HCS & HTP facilities

Service

Image Data Handling

Service

Microscopy Technologies

Facility

Imagerie-Gif

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Facility: Imagerie-Gif

Head: Sandrine LECART

Plateforme Imagerie-gif, Avenue de la Terrasse, 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 S. Lecart, 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.

Microscopy systems available @Imagerie-Gif

Services on this Facility

Service

Microscopy Technologies

Facility

ImaChem – IBENS

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Facility: ImaChem – IBENS

Head: Laurent Bourdieu

École Normale Supérieure, Rue d'Ulm, Paris, France

The Imachem imaging platform provides advanced light and electronic microscopy techniques to IBENS researchers and external users. Imachem is operated by 5 engineers. The main originality of IMACHEM is its ability to undertake innovative technical developments in optical microscopy and to make them available to all users. The first expertise of the platform is super-resolution microscopy, with the development of 3D-PALM using adaptive optic methods. It can perform ultra-structural imaging and single-particle tracking in 3D with a few tens of nanometers of spatial resolution. The second expertise is ultrafast two-photon microscopy for in vivo functional recordings with a temporal resolution in the msec range. A two-photon microscope using acousto-optic scanners for 2D scanning was first designed and installed in the platform. A new system providing ultrafast 3D scanning is currently under development. Additionally, electron microscopy using high-pressure freezing will be developed for correlative light and EM imaging.

Services on this Facility

Service

Microscopy Technologies

Facility

Montpellier Resource Imaging

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Facility: Montpellier Resource Imaging

Scientific director: Patrick Lemaire

patrick.lemaire@crbm.cnrs.fr
Université Montpellier 1, Montpellier, France

Montpellier Ressources Imagerie (MRI) is a distributed imaging facility present on six sites in Montpellier (www.mri.cnrs.fr). MRI is labeled IBiSA and certified ISO9001-2008 LQRA. It has a staff of 30 engineers and is directed by P. Lemaire (CNRS). MRI manages numerous microscopes (36 photonic and 2 electron microscopes) and 14 analysis workstations, and especially microscopes for long term or short live experiments. MRI offers a complete set of state-of-the-art technologies, from single molecule to small organism imaging. The platform offers and develops 3D-SIM, SPIM, FCS/FCCS, CLEM and 2photons microscopies, and also develops a new service of High Content Screening, with a specific emphasis on gene expression analysis by smFISH techniques. MRI organizes regular training sessions with theoretical presentations and practical sessions about advanced light microscopy and image analysis. Once trained, a user can freely access microscopes on a pay-per-use basis. For the screening facility, the access is evaluated on a project-by-project basis.

Microscopy systems available @MRI

Services on this Facility

Service

HCS & HTP facilities

Service

Microscopy Technologies

Facility

PICsL (Shared Imaging Platform of Luminy Campus)

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Facility: PICsL (Shared Imaging Platform of Luminy Campus)

Head: Pierre-François Lenne

Faculté des Sciences de Luminy, Avenue de Luminy, Marseille, France

The  PICsL is located on the Luminy campus on two sites (IBDM and CIML ) that are within walking distance of each other. The PICSL offers a variety of state-of-the art imaging systems (multiphoton, confocal imaging, light sheet microscopy, super-resolution microscopy, electron microscopy). Mainly dedicated to developmental biology and immunology, the PICSL facility provides approaches for dynamic imaging, such as light sheet microscopy, super-resolution for tissue imaging (STED), multiphoton imaging but also more standard techniques such as time lapse imaging and confocal microscopy. Such methods are key to study quantitatively, the development of various animal species, and to decipher the operating mechanisms of the immune system, from molecules to whole organisms, such as Drosophila, C. elegans, Xenopus, chick, mice but also organotypic cultures and more recently organoids. The IBDM site also hosts an electron microscopy (EM) service. The EM service provides the scientific community with the expertise, material and electron microscopes necessary for molecular, cellular and tissue-level imaging by EM. Our service offer comprises the sample preparation with the following methods: negative staining, plastic embedding, immuno-labelling, high pressure freezing, freeze substitution, (cryo)-ultramicrotomy. We routinely use advanced imaging modes such as electron tomography (ET), Scanning Transmission Electron Microscopy (STEM), Scanning Electron Microscopy in « Serial Block-Face » mode, Correlative Light and Electron Microscopy (CLEM).

Microscopy systems available @PICsL

Services on this Facility

Service

Microscopy Technologies

Facility

IPAM

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Facility: IPAM

Head: Chrystel Lafont and Pierre Fontanaud

Chrystel.lafont@igf.cnrs.fr and Pierre.Fontanaud@igf.cnrs.fr
Hôpital Arnaud-de-Villeneuve, Montpellier, France

IPAM is a platform for the investigation of small animals. IPAM platform is under ISO9001 certification (starting from June 2014) and a labeled IBiSA facility. IPAM is headed by P. Mollard (CNRS, IGF) and with help of C. Lafont (tech leader). IPAM-IGF is dedicated to cellular in vivo imaging techniques in both anesthetized and vigile animal models. Our latest development involves 2-photon cellular in vivo microscopy with long-range objectives (Mitutoyo, wd: 2cm, x20 magnification, NIR transmission) readily applicable to imaging of deep tissues structures (metabolic brain, pancreatic islets from animal models of diabetes) in anesthetized animal models. Access to IPAM-IGF equipment is based on project selection (http://www.ipam.cnrs.fr/), IPAM-IGF is also an international member of the National Biophotonics and Imaging Platform Ireland (NBIPI, http://www.nbipireland.ie/ ).

Microscopy systems available @IPAM

Services on this Facility

Service

Microscopy Technologies

Facility

Bordeaux Imaging Center

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Facility: Bordeaux Imaging Center

Head: Daniel Choquet

bic@u-bordeaux.fr
Bordeaux Imaging Center, BIC, Bordeaux, France

The BIC (Bordeaux Imaging Center) offers resources in photonic and electronic imaging, mainly in life, health and plant sciences. It is a core facility identified at the national level as IBISA that gathers 12 highly skilled engineers. It has the ISO9001 label. The different components of the BIC are: PHOTONIC imaging, ELECTRONIC imaging, PLANT imaging. The Bordeaux Imaging Center offers access to the most advanced bio-imaging techniques for fixed and live cell imaging such as video-microscopy, confocal microscopy, multiphoton microscopy, transmission electron microscopy and scanning electron microscopy. The BIC provides a unique set of high-end equipment for super- resolution microscopy such as STED confocal microscopy, FRAP video-microscopy, lifetime imaging FLIM for the measurement of molecular interactions. We also provide access to equipment for sample preparation such as ultra-microtoms, high pressure freeze (HPF) and we can host live samples.

Microscopy systems available @BIC

Services on this Facility

Service

Microscopy Technologies

Facility

UTechS PBI – Pasteur

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Facility: UTechS PBI – Pasteur

Head: Spencer Shorte

pbi.contact@pasteur.fr
Institut Pasteur, Rue du Docteur Roux, Paris, France

Photonic BioImaging is a Unit of Technology and Service (UTechS) providing optical imaging expertise in life sciences and especially their application in studies on infectious biology.

Our activities include service rendering, training, technology-driven research and technology development. They are highly multi-disciplined, and collaborative, with the mission goal focused on the use of quantitative imaging and analysis to understand the processes of cell/tissue-biology, and their usurpation by infection and disease. The R&D is founded upon the need to develop optical imaging methods that bring new understanding of host-pathogen interactions and in situ high-content imaging techniques and their application to infection, cell biology, cellular microbiology, and microbiology. We work on novel techniques extrapolating quantitative information on spatiotemporal dynamics in situ and we push the limits of existing approaches aiming to enhance their performance thereby broadening their experimental utility.

Services on this Facility

Service

HCS & HTP facilities

Service

Microscopy Technologies

Facility

Imagoseine – Institut Jacques Monod

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Facility: Imagoseine – Institut Jacques Monod

Coordinator: René-Marc Mège

rene-marc.mege@ijm.fr
Institut Jacques Monod, Paris, France

ImagoSeine imaging facility gathers advanced light microscopy, cytometry and electronic microscopy activities, installed on 450 m² at IJM. Rooms for cells and tissues manipulations are provided to external users. ImagoSeine has been assessed and found to meet the requirements of ISO 9001 by AFNOR Certification. ImagoSeine brings together technologies and expertise in these fields, thanks to the 7 permanent and 2 contractual engineers. The originality of ImagoSeine-IJM is the close collaboration between the imaging facility which have a long experience of making available standard approaches but also new developments to the biological community and a research team involved in the development of state of the art functional imaging technologies (FLIM-FRET; FCCS) and more recently superresolution and non-linear microscopy. The ultimate goal is to provide access and training to these emerging techniques and methods for the realization of competitive biological projects.

Services on this Facility

Service

Microscopy Technologies

Facility

Image Analysis Hub – Institut Pasteur

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Facility: Image Analysis Hub – Institut Pasteur

Head: Jean-Yves Tinevez

iah@pasteur.fr
Institut Pasteur, Paris, France

About

The Image Analysis Hub is an open access, equal access core facility committed to offering support in image analysis. Our webpage is: https://research.pasteur.fr/en/team/image-analysis-hub/

What we do.

As part of the C2RT, we strive to ensure the continuity between image acquisition and image analysis. To this end we rely on our expertise in imaging and collaborate with other facilities such as the UTechS-PBI and UTechS-UBI when pertinent. All requests involving images are considered.

 

Our services follow four axes:

1. Offer walk-in support and trainings for questions involving image analysis.

This activity aims at offering to users quick answers to scientific questions involving well-established pipelines, for which a commercial or published tool exists and can be used conveniently. Users can address their question to the facility during open-desk sessions or directly via one-to-one requests. Depending on the effort involved, the solution is derived and proposed onsite, or individual  trainings are scheduled. For general topics, the Hub organises regular courses and workshops, possibly involving external teachers or providers.

For instance, see below for the announcement of our open-desk, organised regularly every two week.

 

2. Build and deploy custom analysis tools for projects requiring special developments.

Research endeavours to address original questions, for which analysis tools might be lacking or incomplete. The Image Analysis Hub aims at creating or implementing novel tools based on existing algorithms to address these questions, using skills in image analysis and software development. More than just developing the analysis tool, this activity often involves deriving a suitable analysis methodology, for which the facility expertise in microscopy and biophysics is key. Engineers work in close collaboration with users within the framework of a scientific project over medium or long durations. For projects whose effort would extend beyond typical facility usage or involve original research work, the project may be directed to the BioImage Analysis unit after a discussion with all parts.

 

3. Maintain an infrastructure for autonomous image analysis. Deal with complex tool deployments.

Data volume and modern analysis techniques may call for a computing power not always present in Pasteur labs. Providing open-access workstations unlock barriers to compute-intensive tools. They also act as the central sharing points for commercial softwares, making them available to the whole campus. Finally, some specialized tools require special deployment efforts, e.g. to make such a tool able to exploit the HPC infrastructure of the Institut Pasteur.

 

4. Develop original and innovative software tools for image analysis, whose scope exceed user projects.

Software development and image analysis skills of the facility can be leveraged to build ambitious software tools shipping innovative technologies. These tools exceed the scope of single projects and address the unarticulated needs of the Pasteur community and their creation is part of the development activity of the facility.

Services on this Facility

Service

Image Data Handling

Facility

IMAG’IC (Institut Cochin photonic imaging facility)

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Facility: IMAG’IC (Institut Cochin photonic imaging facility)

Head: Pierre Bourdoncle

u1016-imagic@inserm.fr
Institut Cochin, Rue Mechain, Paris, France

The Institut Cochin photonic imaging facility (IMAG’IC), which has the Gis IBiSA, France-BioImaging and ISO 9001 labels, is under the scientific direction of Florence Niedergang and under the responsibility of the engineer Pierre Bourdoucle.
In the center of Paris, the platform has 15 acquisition systems and 3 stations for analysis and image processing, spread over 130 m². Any person working in a public laboratory (EPST, University) or private company can benefit from help or training to become autonomous to work on all microscopes managed by the platform.
In parallel, image restoration by 3D deconvolution, image quantification, database,  3D printing, vibratome sectioning of thick tissues and tissue clarification are also now proposed to our users.

Services on this Facility

Service

Image Data Handling

Service

Microscopy Technologies

Facility

PIBBS – MARS & AFM Facilities @CBS

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Facility: PIBBS – MARS & AFM Facilities @CBS

Scientific directors: Christine Doucet (MARS) & Luca Costa (AFM)

doucet@cbs.cnrs.fr
Centre de Biochimie Structurale, 29 Rue de Navacelles, 34090 Montpellier, France

PIBBS-MARS & AFM comprises two facilities :

  • The AFM facility is the only one in the FBI Infrastructure to provide access to state-of-the-art Atomic Force Microscopes, including a custom built high-speed AFM.
  • The MARS facility is devoted to cutting-edge optical microscopies such as Single Molecule Localization Microscopy, smFRET, PIE-FCCS, 2-photons FCS, single particle tracking, etc… The MARS R&D division, closely associated to two R&D teams, is in charge of implementing and developing new custom
    advanced microscopies (such as STED-FCCS, 2foci-FCS or multifocal microscopy) before their transfer to the facility.

Moreover, the AFM and MARS facilities and staff work closely together to develop and transfer new correlative imaging modalities, such as AFM / Superresolution or AFM / Confocal (FLIM, spFRET).

Users are assisted by dedicated research engineers and scientific coordinators to define the best approach, experimental design, help in data acquisition and analysis.

http://www.cbs.cnrs.fr/index.php/fr/fluorescence

Microscopy systems available @PIBBS

Services on this Facility

Service

Microscopy Technologies

Facility

H2P2 (Histo pathology High precision)

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Facility: H2P2 (Histo pathology High precision)

Head & CoHead: Alain Fautrel, Nicolas Mouchet, Bruno Turlin and Marie-Dominique Galibert

H2P2@univ-rennes1.fr
2 Avenue du Professeur Léon Bernard, 35000 Rennes, France

The H2P2 platform performs histology work on human, animal and plant tissues. The facility is equipped with last generation devices to increase analysis reproducibility and ensure rapid automatic processing. We produce Tissues Micro Array (TMA) that can group hundreds of tissulars spots on a single microscope slide. We have developed a thorough expertise in immuno-labeling (more than 1000 Ac in our catalog) as well as multiplex staining, a technique that can highlight up to 6 different proteins per slide, fluorescence or chromogenic. Since 2021, with the CELLDive technology we are able to visualize up to 60 markers on the same sample. To visualize slides we offer several options: epifluorescence microscope, virtual slides from a Hamamatsu scanner with fluorescence and a new generation confocal scanner (3D-Histech) with seven channels in fluorescence.  This latter technology gives the opportunity to scan thick tissues (300µm) after clearing. Slides are analysed in 2D using Halo, an image analysis platform/software (with machine learning) for quantitative tissue analysis in digital pathology.  We perform 3D images routinely and advanced analysis reconstruction with Amira. We also developed extensive expertise in laser capture microdissection, allowing single cells capture. We are developing in situ molecular technologies, as Raman micro spectroscopy imaging on biological samples with statistical analysis of obtained spectra.

Services on this Facility

Service

Microscopy Technologies

Facility

MicroPICell (Tissue and cell imaging)

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Facility: MicroPICell (Tissue and cell imaging)

Head: Perrine Paul-Gilloteaux, Emmanuel Scotet

perrine.paul-gilloteaux@univ-nantes.fr
8 Quai Moncousu, 44000 Nantes, France

MicroPICell is an imaging facility specialized in sample preparation (histology), cellular and tissular imaging (photonic microscopy) and data processing and analysis (bioimage analysis). The facility is located within the precinct of the Hotel Dieu hospital, Nantes University. The platform is affiliated to the Structure Federative de Recherche UMS INSERM 016/CNRS 3556/Nantes University and teamed up with Nikon Instrument society and the APEX veterinary facility to create the Center of Excellence Nikon Nantes in 2016. The MicroPICell facility offers a complete integrated cellular imaging service to all users after analysis of the feasibility of their projects. The applications range is then very large, for example cancer research and immunology, regenerative medicine or stem cells research. It is organized in 3 main services: histology, photonic microscopy, image data management and analysis, all these services working closely together on users projects.

Services on this Facility

Service

Image Data Handling

Service

Microscopy Technologies

Facility

MRIC (Microscopy Rennes Imaging Center)

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Facility: MRIC (Microscopy Rennes Imaging Center)

Head: Marc Tramier, Claude Prigent

marc.tramier@univ-rennes1.fr
2 Avenue du Professeur Léon Bernard, 35000 Rennes, France

The platform provides regulated access to imaging systems, as well as scientific and technical assistance in the design of projects and experiments. Proposed techniques are: epifluorescence, video microscopy, confocal, spinning disk, multiphoton, lightsheet, TEM, cryo-electron microscopy, high pressure freezing, tomography, immuno-electron microscopy.
Backed by research teams, the platform also has a strong R&D activity dedicated to the design of prototype microscopes. Finally, MRic provides training to microscopy techniques.

Services on this Facility

Service

Microscopy Technologies

Facility

Imaging and Cytometry Platform (PFIC) – Institut Gustave Roussy

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Facility: Imaging and Cytometry Platform (PFIC) – Institut Gustave Roussy

Director: Pr. Jean-Yves SCOAZEC

jean-yves.scoazec@gustaveroussy.fr
114 Rue Edouard Vaillant, Villejuif, France

The Imaging and Cytometry Platform (PFIC) is one of the 9 scientific Platforms of the UMS AMMICa of Gustave Roussy, one of the first European comprehensive cancer center, located in the south of Paris.
Supporting basic and clinical research programs on cancer, the PFIC is a service, training and R&D center at the interface of basic, translational and clinical research.
The PFIC provides research and industry with an open center of expertise in multi-scale photonic imaging from molecular to tissue, and from animal models to the human. Run by 9 engineers from which 5 dedicated to imaging, the PFIC is organized into specialized units to offer expertise:

  • In confocal and multiphoton imaging together with the combined techniques TIRF, live SR, FRAP, FRET, photoconversion, for the study of dynamic interactions at high resolution.
  • In complex multidimensional dynamic imaging in living organs, 3D-organoid models, high resolution intravital imaging on small animal and whole animal imaging.
  • In transfer of photonics into the clinic (New contrast, NIR and confocal)
  • In flow, spectral and mass cytometry and high throughput cell sorting and cloning
  • Bioinformatics expertise for data processing and quantification

The PFIC is also strongly involved, with industrial partners, in innovative developments in new optical devices, new fluorescent probes and specific requests for clinical transfer of photon imaging.

Microscopy systems available @PFIC

Services on this Facility

Service

Microscopy Technologies

Facility

MORPHOSCOPE / Polytechnique bioimaging facility

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Facility: MORPHOSCOPE / Polytechnique bioimaging facility

Scientific Director: Emmanuel Beaurepaire

emmanuel.beaurepaire@polytechnique.edu
École Polytechnique, Route de Saclay, Palaiseau, France

The Morphoscope / Polytechnique BioImaging Facility received the IBiSA labelled in 2019. It is hosted and operated by the Laboratory for Optics & Biosciences (LOB) at Ecole Polytechnique, one of the founding members of the France BioImaging infrastructure. The Morphoscope facility results from a major equipment investment grant initiated in 2013 (Equipex Morphoscope2 project). It is based on the expertise of the LOB Advanced Microscopies group (9 tenured scientists, 1 tenured research engineer, 1 zootechnician, students, and access to LOB electronics & mechanics workshops). One important specificity of this platform is its emphasis on technology development and methodological innovation. In particular, the host team is a world leader in multiphoton microscopy of tissues, and the platform hosts both state-of-the- art commercial systems and lab-built systems based on cutting-edge technologies.
Imaging equipment is organized along three complementary needs:

  •  deep tissue imaging with multi-contrast nonlinear microscopy;
  • fast imaging of semi-transparent samples using light-sheet excitation microscopy;
  • super-resolution optical microscopy.

In addition, we have an expertise in large-volume bioimage informatics (e.g. managing & processing 3D images with >10^10 voxels)
We can provide the following:

  • Case study, expertise, and technological innovation in cell and tissue imaging.
  • Tissue imaging:
    • multicontrast multiphoton microscopy: 2PEF, SHG, THG, polarimetry, FLIM, CARS, multicolor 2-photon through wavelength mixing;
    • deep-tissue three-photon microscopy (Light Sci App 2018);
    • large volume multicolor microscopy of uncleared tissue ex vivo (ChroMS, multicolor 2P integrated with automated serial cutting, Nat Commun 2019);
  • Fast imaging:
    • standard and 2-photon light-sheet microscopy (Nat Methods 2014).
  • Super-resolved optical imaging:
    • TIRF-SIM microscopy.
Installed equipment:

Application-oriented setups (access through collaborations or reservation):

  • Multimodal/multicolor multiphoton microscope (2PEF, SHG, THG) – LaVision Biotec, Trimscope-II equipped with three femtosecond beams.
  • Super-resolution SIM / TIRF microscope – GE Healthcare, DeltaVision OMX SR.
  • Confocal microscope (FRAP, white light laser, resonant scanner) – Leica, TCS SP 8X.
  • Multi-view light-sheet microscope – Luxendo-Bruker, MuVi-SPIM.

Methodology-oriented setups (collaborative access):

  • Multimodal multiphoton microscope (2PEF, SHG, THG, FLIM, CARS, polar.) – Lab-built.
  • Multicolor 2PEF microscope (wavelength mixing, brainbow) – Lab-built.
  • 3-photon/THG microscope – Lab-built.
  • Two-photon light-sheet microscope – Lab-built.

Zebrafish facility. Capacity 6000 fish.
Secured image server with an OMERO installation (70 TB).
One GPU compute server with NVidia v100x3
Several image processing/analysis workstations, including 3 Imaris licences.

Microscopy systems available @Morphoscope

Services on this Facility

Service

Microscopy Technologies

Facility

Genethon’s Imaging Cytometry platform (ImCy)

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Facility: Genethon’s Imaging Cytometry platform (ImCy)

Scientific Director: Daniel STOCKHOLM

Daniel STOCKHOLM
Généthon, Rue de l'internationale, Évry-Courcouronnes, France

The imaging and Cytometry facility is part of Généthon, which is a pharmaceutical organization specialized in understanding rare diseases and designing new approaches of therapy, mostly gene transfer. The imaging and Cytometry facility offers services in imaging and cytometry, acquisition and analysis. The facility organizes its activity around 3 main missions: services, training, Research and Development.
The facility interacts with different partners:

  • inner departments of Genethon (5 R&D teams, vector production unit, technical development unit ; preclinical evaluation department)
  • Genethon belongs itself to a public interest group named Genopole, which gathers Start-up, companies, facilities, institutes and public laboratories, and promote their activity and research. Consequently, the facility has strong interaction with Genopole partners.

The facility is open to any user outside Genopole, and is currently working with the CEA, the institute of myology, the “Institut de Recherche Biomédial des armées (IRBA)” etc.

Scope of activity: The facility concentrates on quantitative imaging of muscles and neuromuscular disease.

Microscopy systems available @ImCy

Services on this Facility

Service

Microscopy Technologies

Facility

NeurImag

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Facility: NeurImag

Scientific Director: Lydia Danglot

neurimag.ipnp@inserm.fr
102-108 Rue de la Santé, 75013 Paris, France

NeurImag is a service and R&D Cell and Tissue imaging core facility of the Institute of Psychiatry and Neuroscience of Paris (IPNP, INSERM U1266 – Université de Paris) since October 2017.

It is divided in :

  • Imaging services using photonic microscopy,
  • Image analysis service providing « home made analysis solutions » through programming using either Icy, iLastik, ImageJ and/or MatLab.
  • Primary cell culture services that provide neuronal cells, organoïds and tissue to solve biological questions through live and super-resolution imaging.

To groundwork our scientific operation, the daily management is divided into three interconnected services under the single management of a scientific director, Lydia Danglot (Inserm, “Chargé de Recherche” in T. Galli research team, Ph.D. in Neurosciences). The daily management of the operations are coordinated by (1) David Gény (Inserm, “Ingénieur d’études”, Master in Imaging Methods and Technology) and Philippe Bun (Inserm, “Ingénieur de recherché”, Ph.D. in Biophysics) for the Advanced Light Imaging and Data Analysis service, (2) and Julie Nguyen (Inserm, “Ingénieur d’études”, Master in Biochemisty and Cell Biology) for the Primary Cell Culture service.

NeurImag manages 7 light microscopy systems for (A) the observation of biological macromolecular structures (full field) with very high spatial (3 confocal, 1 Airyscan confocal,  1 super-resolution SIM and 1 3D-STED and STED-FCS) and temporal (spinning-disk) resolution or high molecular localization precision (2 super-resolution microscope for PALM, SPT and 3DSTORM) correlated respectively with high speed Airyscan or swept-field confocal (SFC), (B) monitoring macromolecular dynamics and interaction within cells and/or living organism with minimal phototoxicity (full field, spinning-disk and fast Airyscan confocal) and (C) spectroscopy approaches for monitoring intracellular and molecular dynamics using light manipulation (spinning-disk with laser ablation and FRAP addons) and fluorescent lifetime decay measurements (fast-FLIM confocal) respectively. NeurImag also provides 3 workstations directly connected to microscope computers for image processing and data analysis using free- and commercial software such as ICY, ImageJ, Huygens, iLastik, Imaris, Neurolucida, Volocity, Zen Blue (Zeiss), SRX (Bruker) and MatLab.
The NeurImag cell and tissue culture services offers a unique service for biological sample preparation ranging from cells (primary culture of hippocampal/cortical neurons or glial cells, organoïdes, cells lines and tissues) with the optimization of immunofluorescence labeling or transfecting protocols to the management of human biological samples from the Pathology department of GHU-Paris/Sainte-Anne Medical Center, located on the same campus. The service is equipped with 6 biosafety level2-culture rooms including 15 Class II A2 biosafety cabinet, 18 CO2 incubators, 6 bench top centrifuge, 5 light microscope and one fluorescent microscope for a quick cell culture/transfection check. As an example, internal and external teams can buy weekly, plates of neurons seeded on glass coverslips to directly proceed for imaging or transfection.
Since Neuroscience is a major research topic at IPNP, the NeurImag Imaging Facility addresses imaging techniques related to issues faced in this field. Imaging techniques currently available cover a wide range of spatiotemporal resolution, ranging from video-microscopy, super-resolution imaging (PALM, STORM, STED 3D and SIM), sample preparation and quantitative image analysis. If you wish to discuss about the potential and decisive contribution of imaging techniques to your research project, do not hesitate to contact us.

List of system and services available

  • Deconvolution widefield microscopy
  • Videomicroscopy and slide scanner system
  • Laser scanning confocal microscopy (LSCM) + Gated detectors + White Light Laser
  • Spinning disc confocal system +Fast 2 colors GEMINI module
    Swept-field confocal system
  • Total internal reflection fluorescence microscopy (TIRF)
  • Fluorescence Correlation Spectroscopy (FCS)
  • Fluorescence Cross-Correlation Spectroscopy (FCCS)
  • Fluorescence lifetime Imaging microscopy (FLIM)
  • Fluorescence resonance energy transfer (FRET)
  • Fluorescence recovery after photobleaching (FRAP)
  • Laser ablation and Photon uncaging
  • Structured Illumination Microscopy (SIM)
  • Photoactivated localization microscopy (PALM)
  • STimulated Emission Depletion microscopy (STED) +/- Fluorescence Correlation Spectroscopy module
  • Stochastical Optical Reconstruction Microscopy (STORM) with 3D biplane module
  • Primary cell culture preparation + optimization on request/demand
  • Sample preparation (transfection, Immunostaining, 3D cultures)
  • Image Data Processing and Analysis +custom made solution
  • Workstations for data analysis (commercial softwares)

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Microscopy Technologies

Facility

Imachem – Collège de France

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Facility: Imachem – Collège de France

Scientific Director: Olivier Espeli

olivier.espeli@college-de-france.fr
11 Place Marcelin Berthelot, Paris, France

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Facility

IMM Microscopy Core Facility

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Facility: IMM Microscopy Core Facility

Scientific Director: Pr. James Sturgis

sturgis@imm.cnrs.fr
31 Chemin Joseph Aiguier, 13009 Marseille, France

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Microscopy Technologies

Facility

InMAGIC (INMED Imaging Center)

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Facility: InMAGIC (INMED Imaging Center)

Head: François Michel

francois.michel@inserm.fr
INMED, Marseille, France

InMagiC (INMED iMAGing Center) is the microscopy platform of the Institute of Neurobiology of the Mediterranean: INMED in Marseille on the Luminy campus.
The platform is under the scientific direction of Rosa COSSART and under the responsibility of the engineer François MICHEL rosa.cossart@inserm.fr / francois.michel@inserm.fr

INMAGIC gathers in one place the multi-scale study tools necessary to study the development and the physio-pathological functioning of the central nervous system.
These tools cover the scales of observation from the whole animal (binocular loupes) to the dynamic morphology of neuronal contacts (synapses) thanks to widefield, confocal and multiphoton microscopes.
In addition, the platform provides a large number of training courses at all levels, both theoretical and practical, for all audiences (students, engineers, researchers, etc.).

The strong and original points of our structure are:

  • A space dedicated to the techniques of tissue clearing and the acquisition of these samples by an ultramicroscope (light sheet) in platform access, as well as the expertise of the engineer in charge (active member of the GT transparencies of the RTMFM);
  • The use of the multiphoton microscopy for the fast measurement (10-20 Hz) of the neuronal activity in vitro and in vivo on large populations of cells (up to more than 500 simultaneous cells).

Two high performance analysis stations are also available to all users. They include free and commercial software dedicated to analysis such as FIJI, ICY, IMARIS, Neurolucida360, Matlab…

Finally, the platform is a laureate of the PIA Equipex + 2020 and in this context the availability of tools beyond the state of the art in minimally invasive in vivo imaging will soon be open to the community.
These new tools will be commercial with industrial co-developments: a 3-photon excitation microscope, an ultra-fast AOD scanning microscope, a 2-photon endoscope or in academic development with the collaboration of the Fresnel Institute such as an ultra-thin endoscope and a deep recording station by photo-acoustics.

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Facility

QuESt (Quantum Efficiency Strasbourg)

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Facility: QuESt (Quantum Efficiency Strasbourg)

Head: Ludovic Richert & Bertrand Vernay

ludovic.richert@unistra.fr , vernayb@igbmc.fr
Illkirch-Graffenstaden, France

The QuESt imaging facility combines the microscopy resources of the Institut de Génétique et Biologie Moléculaire (IGBMC) and the Laboratoire de Bioimagerie et Pathologies (PIQ). The two laboratories are located on the Illkirch bio-campus, just 10 minutes’ walk from each other. QuESt has held the IBiSA label since 2014. QuEst offers a range of instruments for multi-scale imaging, from the molecule to the whole animal. The ICI (Imaging Center IGBMC) component located at the IGBMC specialises in imaging the dynamic processes of living organisms at the molecular, cellular and whole organism levels. Researchers can analyse, in an integrated manner, their study models at different resolutions, ranging from the finest cellular structures to the complex functioning of organs in vivo. The PIQ (Plateforme d’Imagerie Quantitative – Quantitative Imaging Platform), located in the Faculty of Pharmacy, has a specific focus on quantitative molecular microscopy methods. In addition to commercial instruments, the PIQ-QuESt develops its own state-of-the-art instruments.

Microscopy systems available @QuESt

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Microscopy Technologies

Facility

Plateforme d’Imagerie Cellulaire de l’IBMP

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Facility: Plateforme d’Imagerie Cellulaire de l’IBMP

Head: Jerome Mutterer & Mathieu Erhardt

jerome.mutterer@cnrs.fr & mathieu.erhardt@ibmp-cnrs.unistra.fr
Plateforme d’Imagerie Cellulaire Institut de Biologie Moléculaire des Plantes 12, rue du Général Zimmer 67084 STRASBOURG Cedex

The microscopy facility was the first technology platform established in the IBMP in 1998. Its scientific programme aims at understanding the expression of plant or animal genes over space and time at various levels. Microorganisms or biomaterials studied by partner research units are other topics of interest. Our facility follows official guidelines for « Plates-Formes Technologiques du Vivant » and has received RIO 2001, 2004 and 2006 labels. It’s part of the larger PIC.sc Strasbourg Centre Cell Imaging Facility that allows sharing devices and knowledge from several research units from CNRS, INSERM, UNISTRA. Our missions include assisting research from IBMP and partner research units, developing and implement new imaging technologies, training our user base and beyond, getting involved in microscopy education and science popularization.

Microscopy systems available @Plateforme d’Imagerie Cellulaire de l’IBMP

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Microscopy Technologies

Facility

Plateforme Imagerie In Vitro @INCI

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Facility: Plateforme Imagerie In Vitro @INCI

Head: Sylvette Chasserot-Golaz (LM) & Frank Pfrieger (EM)

chasserot@inci-cnrs.unistra.fr & Frank.Pfrieger@unistra.fr
8 Allée du Général Rouvillois, 67000 Strasbourg, France

The platform is attached to ITI Neurostra. It is located at the Institut des Neurosciences Cellulaires et Intégrées (INCI) and managed administratively by the CNRS UAR 3156 headed by P. Darbon.
The expertise of the in vitro imaging platform applies to the study of biological materials, tissues and isolated cells on a structural and ultrastructural scale. It extends to the immunocytochemical visualisation of molecules and the phenotypic detection of gene expression.
The platform is involved in a wide variety of interdisciplinary projects (biology, chemistry, agronomy, medicine). Around two-thirds of users come from the CNRS INCI UPR3212 (6 groups), with the remainder coming from other Strasbourg institutes (IBMC, IBMP, ISIS, IPHC, ECPM, CRBS, etc.).
A number of developments have taken place in recent years, including cryofixation (Wohlwend system) and super-resolution microscopy (Stellaris 8 confocal microscope with a STED module).

Microscopy systems available @Plateforme Imagerie In Vitro INCI

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Microscopy Technologies

Facility

PI2 (Plateforme d’imagerie de l’I2CT)

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Facility: PI2 (Plateforme d’imagerie de l’I2CT)

Head: Jean-Daniel Fauny

jd.fauny@ibmc-cnrs.unistra.fr
Institut de Biologie Moléculaire et Cellulaire 2, Allée Konrad Roentgen - 67 084 Strasbourg Cedex - France

The PI2 imaging technical platform belongs to the UPR3572 research unit: I2CT (Immunology, Immunopathology and Therapeutic Chemistry) of the IBMC (Institute of Molecular and Cellular Biology) in Strasbourg. The platform has i) sample preparation tools, ii) microscopy/imaging tools and iii) image processing and analysis tools. The platform offers workflows involving these 3 stages in order to answer the biological questions raised by scientists. The platform is part of the local RISEst network (Réseau d’Imagerie Strasbourg grand Est) and works in close collaboration with the other platforms in the network.

Microscopy systems available @PI2

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Microscopy Technologies

Facility

PIC-STRA (Plateforme d’Imagerie du CRBS – STRAsbourg)

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Facility: PIC-STRA (Plateforme d’Imagerie du CRBS – STRAsbourg)

Head: Pascal Kessler

Pascal.Kessler@unistra.fr
Centre de Recherche en Biomédecine de Strasbourg 1 rue Eugène Boeckel - CS 60026 - 67084 Strasbourg Cedex

PIC-STRA aims to support the 10 CRBS research units, as well as external teams from both the academic and private sectors. Opened in October 2020, this 350 m2 imaging platform provides users with around ten imaging systems (stereomicroscopes, wide-field and confocal single- and multiphoton microscopes with super-resolution module) for multi-scale observation, from whole small animals to sub-cellular details. It provides various solutions for the observation of fixed and living samples (videomicroscopy) and is equipped for image processing and analysis (IMARIS, Fiji/ImageJ, ICY, iLastik). The platform is part of the local RISEst network (Réseau d’Imagerie Strasbourg grand Est), is in the process of obtaining CORTECS and IBISA (STrasbourg Centre) accreditation and works closely with the other platforms in the network.

Microscopy systems available @PIC-STRA

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Microscopy Technologies

Facility

Plateforme de Microscopie confocale @IS2M

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Facility: Plateforme de Microscopie confocale @IS2M

Head: Tatiana Petithory

tatiana.petithory@uha.fr
15 Rue Jean Starcky, Mulhouse, France

The ISO 9001 certified platform consists of 2 systems:

  • Zeiss Axio Imager M2 LSM 800 confocal upright microscope with PI XY motorized piezo stage, 2 PMTs and an AiryScan super resolution module The excitation wavelengths available on the equipment are 405nm, 488nm, 561 nm, 640 nm. An OKOLAB incubation chamber maintains a stable temperature and CO2 level in the microscope for live image acquisition. This equipment allows the acquisition of topography information by reflection and fluorescence simultaneously.
  • Inverted confocal microscope Spinning disk CSU W1: The stand is an Eclipse Ti2-E Nikon equipped with a motorized XY stage and a piezzo Z-stage, the “Perfect Focus” focus maintenance system and a “water dispenser immersion”. The confocal spinning disk is the Yokogawa mono-camera SD CSU-W1 mono-disk (50µm), the Oxxus excitation laser source has 4 wavelengths 405-488-561-640 nm. The sCMOS Hamamatsu Orca Flash 4.0 camera complements this detection equipment as well as a thermostated and CO2 OKOLAB incubation chamber with different insert sizes. An off-line station allows the analysis of images with the software ZEN blue, NIS-AR, FiJi, ICY and Imaris and to manipulate large files. A reservation system has been also set up.

Microscopy systems available @IS2M

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Facility

Toulouse Reseau Imagerie (TRI)

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Facility: Toulouse Reseau Imagerie (TRI)

Head: Olivier GADAL

tricontact@genotoul.fr
Center for Integrative Biology, Rue Marianne Grunberg-Manago, Toulouse, France

Toulouse Réseau imagerie (TRI) platform is a large multisite platform, federates all shared imaging resources in biology lab in Toulouse Area. TRI offers, through 4 fields of expertise which are photonic microscopy, electron microscopy, cytometry-cell sorting and image processing and analysis, the visualization of biological functions, from the nanometric scale to the whole organism.

The missions of the platform are threefold:
1- To provide researchers expertise and cutting edge technology in the field of :
• Mecano-biology
• Molecular and single cell characterization
• Whole organism, including intra-vital imaging
• Image analysis, signal treatment and modelisation
2- To constitute a framework for reflexion and exchanges in this very rapidly evolving field.
3- To contribute to the formation of researchers in all methods related to microscopy.
TRI platform is ISO9001-NFX50-900 certified and IBiSA facility labeled.

Microscopy systems available @TRI

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Microscopy Technologies

Facility

PRIMACEN/Cell Imaging platform of Normandy

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Facility: PRIMACEN/Cell Imaging platform of Normandy

Head: Ludovic Galas

ludovic.galas@univ-rouen.fr
PRIMACEN, CURIB, Université de Rouen, Rue Lucien Tesnière, Mont-Saint-Aignan, France

Located in Rouen, PRIMACEN, the cell imaging facility of Normandy (1000 m2) is integrated since 2022 in HeRacLeS (Univ. Rouen Normandy, Inserm US51, CNRS UAR2026). To achieve its service offering and R&D objectives, PRIMACEN proposes a continuum with 3 pillars thanks to complementary skills in cell biology-histology, instrumentation-quality control and data processing. In tight connection with animal (rodent/marine models) and plant facilities, the first transversal pillar involves living and fixed sample preparation including labeling, for advanced light and electron microscopies. Then, appropriate resolutions are proposed to users and collaborators through multi-scale and multi-modal imaging including LSM and 2P, WF/confocal micro/macroscopy, TIRFM, FLIM-STED imaging, cryo-FLIM/confocal and TEM/cryoTEM microscopies. To finally help users in their scientific projects, image processing and analysis (3D modeling, ImageJ macros, AI…) are available on highly performing working stations.

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Microscopy Technologies

Facility

Lyon multiscale imaging center (LyMIC)

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Facility: Lyon multiscale imaging center (LyMIC)

Scientific Director: Jean-Louis Bessereau

jean-louis.bessereau@univ-lyon1.fr
8 Avenue Rockefeller, Lyon, France

Lyon Multiscale Imaging Center is a microscopy facility opened to academic research and industry. It federates 3 imaging centers in the Lyon area and provides multi-scale imaging tools including light and electron microscopy:

  • the PLATIM, located at the Ecole Normale Supérieure de Lyon and at Lyon-Sud Medical University, offers a wide range of light microscopy techniques ranging from fully automated video-microscopy, confocal and two-photon microscopy. The PLATIM accounts also for a platform of atomic force microscopy and microindentation for acquiring high resolution 3D topographies and for measuring micro/nano-mechanical properties.
  • the Centre Technologique des Microstructures CTµ, located on the La Doua campus, is mainly an electron microscopy facility that handles multi-disciplinary projects at the interface between biology, chemistry and physics. the CTµ provides access to a wide range of scanning and transmission electron microscopy techniques, and masters cryomethods for sample preparation and observation.
  • the East Lyon imaging center (CIQLE) is located in the Rockefeller Medical University. It provides access to wide-field and confocal light microscopy and transmission electron microscopy for the bio-medical research community.

Machines can be operated independently by the users after appropriate training. Users can also benefit partial or full assistance for their projects. LyMIC provides training sessions for groups or individuals.

The team is watching technology progress and implement new techniques to provide state-of-the-art tools.

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Microscopy Technologies

Facility

Imagerie des sciences du vivant (ISDV)

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Facility: Imagerie des sciences du vivant (ISDV)

Scientific Director: Yves Usson

yves.usson@univ-grenoble-alpes.fr
Faculté de Médecine et Pharmacie - Université Grenoble Alpes, Avenue des Maquis du Grésivaudan, La Tronche, France

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R&D team

LOB

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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.

R&D team

BioEmergences

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R&D team: BioEmergences

Team Leader: Nadine Peyréras

nadine.peyrieras@cnrs.fr
Université Paris-Sud, Rue Georges Clemenceau, Orsay, France

The team investigates morphogenetic processes in morphogenesis in Metazoans. We focus on the integration of cellular, molecular and genetic processes based on long-term 3D+time imaging of developing organisms in normal and perturbed conditions, data reconstruction and quantitative analysis. Methodological developments include: assisted microscopy based
on machine learning strategies to optimize live imaging conditions by multiphoton point laser scanning microscopy and light sheet microscopy, automated image processing and quantitative data analysis, interactive visualisation for cell lineage data validation, correction and analysis.

Expertise of the Team:

  • Machine learning for assisted microscopy and image processing
  • Optimization for in vivo and in toto 3D+time imaging by multiphoton point laser scanning microscopy and light sheet microscopy of developing organisms (metazoans an plants)
  • Data management, image processing workflow, interactive visualisation

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R&D team

MOSAIC Group @Fresnel Institut

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R&D team: MOSAIC Group @Fresnel Institut

Head: Hervé Rigneault

herve.rigneault@fresnel.fr
Institut Fresnel, Avenue Escadrille Normandie Niemen, Marseille, France

The Mosaic group of the Fresnel Institute headed by H. Rigneault has been involved for almost a decade in developing dedicated optical instruments for biological imaging. Among other, the team has developed together with CIML the “FCS diffusion law” approach in Fluorescence Correlation Spectroscopy that has been successfully applied to the cell membrane. More recently single particle tracking using multiple targets have proved to be powerful to distinguish confinement zone at the cell membrane and Holographic Optical Tweezers shows potential application into TCR/MHC control. Phase control for micro-manipulation and imaging is an active field of research at Mosaic. Since 2002, the Mosaic group has been involved in coherent Raman microscopy and nonlinear imaging and was the first in France to build and develop a CARS microscope. One of the group world recognized expertise is in polarization resolved fluorescence and nonlinear microscopy that has proved to be able to retrieve molecular order in cell and tissue imaging. The group is now also involved in the development of nonlinear imaging using endoscopes using innovative microstructured optical fibers. Another active field of research is fluorescence enhancement at the nanoscale using metallic nano-antenna that have the ability to perform dynamic analysis on time and spatial scales unreachable with far field optics.

R&D team

Membrane dynamics and lymphocyte signaling Team @CIML

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R&D team: Membrane dynamics and lymphocyte signaling Team @CIML

Head: Didier Marguet

marguet@ciml.univ-mrs.fr
C.I.M.L., Marseille, France

Founded in 1976, the Centre d’Immunologie de Marseille Luminy (CIML) is a research institute internationally renowned in its discipline. From worm to man, from molecule to the whole organism, from physiology to pathology, the CIML addresses, over numerous models and scales, all fields of contemporary immunology: the genesis of different cell populations, their patterns of differentiation and activation, their implication in cancer, infectious and inflammatory diseases and the mechanisms of cell death. At CIML, Marguet team aims at understanding the role of membrane lateral dynamics and organization in T lymphocyte signaling, by analyzing the molecular interaction/association events at high spatial-temporal resolutions. A special emphasize is made at examination of the molecular dynamics in the plasma membrane to initiate and to integrate extracellular stimuli. In this context, Marguet team develops analytical methods based on the combination of single molecular sensitive detection approaches such as fluorescence correlation spectroscopy (FCS) and derivatives, of single particle tracking with optical tools allowing to manipulate the biological samples such as dynamic holographic optical tweezers.

R&D team

Physical approaches to cell dynamics and tissue morphogenesis Team @IBDM

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R&D team: Physical approaches to cell dynamics and tissue morphogenesis Team @IBDM

Team Leader: Pierre-François Lenne

pierre-francois.lenne@univ-amu.fr
IBDM, Avenue de Luminy, Marseille, France

The Developmental Biology Institute of Marseille (IBDM) is an international and interdisciplinary research institute oriented towards developmental biology and pathologies. The research activity is at the crossroads of development, neurobiology, cell biology, biophysics and genetics. The general theme of IBDM is to understand how the instructions encoded in the genome are translated to build structures (cells, tissues, organs) that perform specific functions, and how these processes are regulated and integrated in the whole organism. There are links between developmental biology and diseases such as cancer, neurodegenerative and genetic diseases. One of the priorities of IBDM is to foster interdisciplinarity through the integration of new and original approaches that create conceptual and technical interfaces. At IBDM, Lenne team aims at determining how (1) mechanical and (2) physical interactions are organized at cell surfaces in vivo and (3) how these interactions are processed to produce cell and tissue responses. To tackle these questions, we focus on two aspects of tissue morphogenesis, namely cell polarization and force transmission in fields of cells. We are using Drosophila and C. Elegans as systems to address questions (1-2) and question (3), respectively. The originality of our project relies in the integration of both physics and experimental biology to study quantitatively tissue morphogenesis.

R&D team

LP2N

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R&D team: LP2N

Head: Philippe Bouyer

philippe.bouyer@u-bordeaux.fr
Institut d’Optique d’Aquitaine, Rue François Mitterrand, 33400, Talence, France

Bordeaux Nanophotonics

The “Nanophotonics” group research activities aim at understanding, mastering and using light-matter interactions at the nanometer scale. For this purpose, the group develops ultra-sensitive optical nanoscopy techniques for the detection of individual nanoscale objects, perform the spectroscopy of their electronic excitations, and explore their applications in physics and biophotonics.

NanoBioMicroscopy

The general ambition of the team is at the crossroad of nanoscience, imaging and biology through the design and study of innovative optically active synthetic nanostructures as well as the investigation of complex and dynamic biological systems at the nanoscale. One of our focus is to work with living biological tissues.

BioImaging & OptoFluidics

The majority of our samples of interest are engineered, and more specifically, generated using the Cellular Capsule Technology (CCT), which was invented and patented in the lab and led to the creation of a startup company (TreeFrog Therapeutics). The CCT relies on the use of 3D-printed microfabricated or microfluidic and allows to produce organoids encapsulated in hollow alginate spherical or tubular micro compartments. These multicellular aggregates are highly relevant to model disease and in regenerative medicine, but they are challenging to image in live conditions, without labelling or in a high throughput format. We thus develop imaging and environmental set-ups dedicated to their observation, in conditions that are dictated by the biological or medical question.

R&D team

IINS

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R&D team: IINS

Head: Daniel Choquet

Centre Broca Nouvelle-Aquitaine, Rue Albert Marquet, Bordeaux, France

Choquet team

The team develops several research topics, combining neuroscience, imaging, chemistry and protein
engineering in order to unravel the dynamics and nanoscale organization of multimolecular receptor
complexes and their functional role in glutamatergic synaptic transmission. We develop 3 main
research axes to understand the interplay between AMPA type glutamate receptor nanoscale
dynamics, synaptic plasticity and memory formation in the healthy and diseased brain: 1) dynamics
and physical-chemistry of the macro-molecular complexes of the synapse, 2) nano-scale organization
and dynamics of synaptic proteins and membrane trafficking, 3) impact of the dynamic of synapse
organization on synaptic physiology.

Groc team

We specifically investigated the trafficking and function of the NMDA receptor (NMDAR), as well as dopamine receptors, since their physiological activity is central for the maturation of networks, synaptic plasticity, learning and memory, and is currently one of the most studied targets for neuropsychiatric disorders. Indeed, a deficit in NMDAR signaling in the brain is currently proposed as the core molecular dysfunction of brain circuits in psychotic disorders. The team contribution to the field has been to demonstrate that i) these receptors are highly dynamic at the surface of neurons, ii) the dynamics is regulated by intracellular, transmembrane, and extracellular interactors, iii) their dynamics is essential for activity- and hormone-dependent synaptic plasticity and associative memory, and iv) this surface dynamics is strongly dysregulated in psychotic disorders (e.g. autoantibodies). Our discoveries were possible thanks to interdisciplinary efforts, in which for instance we developed single nanoparticle tracking in live brain tissue to define receptor behavior and the extracellular space ex vivo.

Naegerl team

The team develops and applies advanced super-resolution microscopy approaches to study the
molecular and cellular mechanisms of cell-to-cell communication and its dynamics in the mammalian
brain, using the mouse as a model system. Notably, we invented super-resolution shadow imaging
(SUSHI) to visualize the extracellular space of the brain in the living state. 

Sibarita team

It is an interdisciplinary team composed of physicists, computer scientists and bioengineers having a strong interest in biology. The team is developing cutting edge quantitative imaging and analysis techniques to decipher protein organization and dynamics with high spatial and temporal resolution and high content screening context. Recent developments include analysis software for single molecule-based super-resolution microscopy (SMLM), innovative single objective light-sheet microscopy, SMLM-based high content screening platform and correlative STED-SMLM super-resolution platform. The Quantitative Imaging of the Cell has an important academic and industrial transfer technology activity.

Giannone team

Our goal is to decipher at the molecular level the spatiotemporal and mechanical mechanisms controlling the architecture and dynamics of motile structures. Exploration of these new dimensions requires an innovative and multidisciplinary approach combining cell biology, biophysics, biomechanics, super-resolution microscopy, single protein tracking and quantitative image analysis.

Studer team

This team is a joint research lab between IINS and the company Alvéole (www.alveolelab.com). By joining their research efforts in a joint research laboratory (JRL), Alvéole and IINS expect to become key players in the development of human in vitro models for fundamental research, disease modeling and drug testing. The team develops instruments and methods to prototype and image advanced in vitro cellular models.

Perrais team

The team studies the nanostructure of exocytosis and endocytosis sites at synapses, the cellular and molecular mechanisms of endocytosis. We extend the topic to diverse synapse types (glutamate, dopamine…) and how these processes are affected in early stages of neurodegenerative diseases (synucleinopathies). We develop new probes (pH sensors) to detect exo- and endocytosis events at the highest resolution possible. We also develop fluorescence-based strategies to purify synaptosomes for cellular and molecular omics analyses.

Thoumine team

The team investigates then mechanisms of synapse assembly in neuronal culture systems with a focus on the role of adhesion molecules, using a combination of experimental approaches ranging from single molecule imaging to optogenetics and electrophysiology. Recent developments include the design of small fluorescent probes for super- resolution imaging of synaptic adhesion molecules (Chamma et al., Nat Comms 2016), the release of a simulator of single molecule dynamics for fluorescence live-cell imaging (Lagardère et al., Sci Reports, in press), and the optogenetic stimulation of phosphotyrosine pathways for the control of synapse differentiation (Letellier et al., eLife 2020).

R&D team

Institut Pasteur – BioImage Analysis Team

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R&D team: Institut Pasteur – BioImage Analysis Team

Head: Jean-Christophe Olivo-Marin

jean-christophe.olivo-marin@pasteur.fr
Institut Pasteur, Rue du Docteur Roux, Paris, France

The scientific project of the BioImage Analysis (BIA) unit is to develop image analysis and computer vision tools for the processing and quantification of multi-channel temporal 3D sequences in biological microscopy. The topics are centered about the development of new algorithms for multi-particle tracking, deformable models, mathematical imaging and spatial distribution analysis. The group has produced powerful tools for spot detection and counting in real-time imaging of virus and genes, movement and shape analysis in 3D+t microscopy and cell growth analysis. These methods and algorithms have now been regrouped under the open-source and free platform Icy (http://icy.bioimageanalysis.org), which provides a comprehensive framework for extended reproducible research in bioimage informatics. They have been instrumental for the successful achievement of a large number of collaborative biological projects.

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R&D team

Bioimage Informatics IPDM

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R&D team: Bioimage Informatics IPDM

Head: Perrine Paul-Gilloteaux

Institut Curie - Pavillon Trouillet-Rossignol, Rue d'Ulm, 5e Arrondissement, France

Institut Curie is active in image databases and management. The PICT imaging facility is engaged since 2011 with the Strand Life Sci. company in the development of the CID (Curie Image Database)/iManage (supported by Paris-Centre Node). The CID is linked to the “Curie Image Data center” (2x 100Tb Storage equipment and cluster for image processing and analysis). Since December 2013 CID is open to all FBI users of the PICT, under demand and common rules of imaging platforms (web client). iManage is the commercial version (with licensing), offering support to labs, to install and adapt CID on their own microscopy, at their own sites. Plugins to access the CID from Icy (Institut Pasteur) are developed and published on the central repository of Icy. An interface to interoperate with the servers at Institut Curie is under development. Integration of software developed in collaboration with Inria-Serpico (http://mobyleserpico.rennes.inria.fr/) such as ND-SAFIR, Hullkground are now integrated in the CID for automated treatment. Institut Curie, specifically with Serpico’s Team@Inria-Rennes, also develops new algorithm solutions for dynamic events detection and classification, sub-diffraction light microscopy and CLEM approaches.

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R&D team

Inria-Curie SERPICO/STED

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R&D team: Inria-Curie SERPICO/STED

Head & CoHead: Charles Kervrann & Jean Salamero

charles.kervrann@inria.fr
Inria Rennes - Bretagne Atlantique, Avenue Général Leclerc, Rennes, France

The Serpico team provides computational methods and mathematical models to automatically extract, organize and model information present in temporal series of images as they are obtained in multidimensional light and cryo-electron microscopy. In the field of membrane traffic, Serpico addresses the following themes in close collaboration with Curie Institute: image superresolution and image denoising to preserve cell integrity (photo-toxicity vs exposure time), information extraction from images and videos in multidimensional microscopy for molecular interaction analysis, spatiotemporal modeling of molecular species and multi-scale architectures, computational simulation and modeling of membrane transport at different scales. In collaboration with UMR 144 and PICT at Institut Curie, the members of Serpico participate in several joint projects (PhD and post-doc supervision, industrial contracts…). They have proposed user-friendly algorithms for processing 3D or 4D data. Other projects are related to instrumentation in microscopy including computational aspects (SERPICO@Mobyle web service) and data management (CID iManage) on the reconstruction and enhancement of images related to subdiffraction light microscopy and multimodal approaches.

Services on this R&D team

Service

Image Data Handling

R&D team

ENS Chemistry

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R&D team: ENS Chemistry

Head: Ludovic Jullien

École Normale Supérieure, Rue d'Ulm, Paris, France

ENS Chemistry facility gathers instruments devoted to the characterization and purification of optical probes and actuators by means of various spectrometries (UV-Vis absorption, fluorescence emission) and chromatographies (capillary electrophoresis, HPLC analytical or preparative), installed on 100 m² at ENS Chimie. Access is provided to external users with technical and conceptual assistance from the 8 permanent members involved in FBI. The originality of ENS Chimie is the close collaboration between the characterization facility making available established approaches to the biological community and a research team involved in the development of state of the art chemical technologies for the optical control and reading out of living systems. The ultimate goal is to provide access and training to these emerging techniques and methods for the realization of competitive biological projects.

Services on this R&D team

Service

Bioprobes

R&D team

Mechanisms of DNA segregation and remodelling Team @CBS

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R&D team: Mechanisms of DNA segregation and remodelling Team @CBS

Head: Group Leader: Marcelo Nollmann

nollmann@cbs.cnrs.fr
Rue Serge Reggiani, Montpellier, France

We develop single-molecule and advanced microscopy methodologies to investigate the mechanisms underlying DNA segregation and remodeling in live cells.

Our current research projects:

  • DNA organization and segregation in bacteria
  • Eukaryotic DNA structure
  • Molecular Motors
  • Single-molecule & advanced optical microscopies
R&D team

Integrated Biophysics of Membranes Team @CBS

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R&D team: Integrated Biophysics of Membranes Team @CBS

Group Leaders: Emmanuel Margeat & Pierre-Emmanuel Milhiet

Emmanuel.Margeat@cbs.cnrs.fr
Centre de Biochimie Structurale, Rue de Navacelles, Montpellier, France

Our research aims at characterizing macromolecular complexes governing major biological processes, focusing on transcription regulation, signaling and remodeling of biological membranes. To achieve these goals, we develop, combine and use advanced single molecule biophysical methods (such as atomic force and fluorescence microscopies), as well as DNA nanotechnology.

Research:

Structure and dynamics of nucleoproteic and membrane assemblies

Structure and dynamics of membrane assemblies

R&D team

CeDRE (Cell Division Reverse Engineering)

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R&D team: CeDRE (Cell Division Reverse Engineering)

Head: Jacques Pécréaux

jacques.pecreaux@univ-rennes1.fr
2 Avenue du Professeur Léon Bernard, 35000 Rennes, France
The CeDRE team, led by Jacques Pécréaux (CRCN CNRS) is multidisciplinary, teaming up biologists, physicists and mathematicians. They are interested in mechanical aspects of cell division to understand its dynamical aspects and ultimately the extra-ordinary faithfulness of mitosis. Therefore, the team finely quantifies biological phenomena to recapitulate the results using physical models. In particular, the team performs advanced data analysis and modelling. It includes the fine tracking of spots like the tips of the microtubule, or super-resolution positioning of the centrosomes at a high frame rate (tens of frames per sec.). The obtained tracks are analysed statistically (for example, to classify the dynamics, reduce the dimension using PCA) or using Fourier spectral analysis to fingerprint the underlying mechanisms. To take full advantage of this data analysis, we model the sub-cellular mechanics during mitosis, in particular, the one grounded on microtubules, molecular motors and associated regulators on the one hand. On the other hand, we use agent-based simulations, especially cytosim, to screen for the variety of behaviours without solving the analytical equations. Finally, the team contributes to developing autonomous microscope by enslaving the driving of the microscope to on-the-fly analysis of acquired images, in particular using machine and deep learning.
R&D team

SIMS @LS2N

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R&D team: SIMS @LS2N

FBI contact in the Team: Jérôme IDIER

jerome.idier@ls2n.fr
1 Rue de la Noë, 44300 Nantes, France

The SIMS Group (Signal, Image and Sound) develops its research in the field of statistical signal and image processing. Tackling ill-posed inverse problems such as deconvolution and diffraction tomography is one of our main fields of expertise. We also focus on computational imaging issues, relying on mathematical tools from both optimization and Bayesian simulation fields. The optimal co-design of computational imaging systems is among our growing topics of interest, with the viewpoint of information theory. In the area of fluorescence microscopy, we investigate the superresolution capacity of random illumination microscopy, in collaboration with Institut Fresnel (Marseille) and the Centre for Integrative Biology (Toulouse).

Expertise of the Team:

  • Inverse problems
  • Computational imaging
  • Machine learning
R&D team

MFQ (Microscopie de Fluorescence Quantitative)

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R&D team: MFQ (Microscopie de Fluorescence Quantitative)

Head: Marc Tramier

marc.tramier@univ-rennes1.fr
2 Avenue du Professeur Léon Bernard, 35000 Rennes, France

The team aims at developing techniques and methodologies in fluorescence microscopy to study dynamics of protein-protein interactions and biochemical activities in live sample. Team approaches are mainly driven by methodological and technological development, its transfer and its applicability in biology to answer relevant new questions. Recently, the team is investigating the possibility to implement smart and autonomous microscopy approches to be able to develop robust and automated high content microscopy pipelines of cutting-edge methods such as F-microscopy or photoperturbative experiments.

R&D team

NanoBio Team @ ISMO (CNRS/ Univ. Paris Saclay)

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R&D team: NanoBio Team @ ISMO (CNRS/ Univ. Paris Saclay)

Head: Sandrine Lévêque-Fort

sandrine.leveque-fort@u-psud.fr

The Imaging group within the Nanobio team is composed of 8 people, with 1 CNRS researcher, 1 MCF, 4 PhD students and 1 engineer on temporary contract. The team develop new fluorescence imaging microscopy modalities for live cell imaging, FLIM and super-resolution.

For most biological questions, it is essential to monitor in vivo and in real time the complex cellular machinery with extreme sensitivity and ultimate resolution. The fluorescence thus remains the tool of choice for specific monitoring in biology. Beyond imaging intensity to a specific location, fluorescence and its various spectroscopic properties can be used to locally probe its environment or reveal interactions. The photophysical properties of fluorophores are the basis of recent developments, which have enabled microscopy to turn into nanoscopy, exceeding the resolution limit imposed by diffraction, enabling the detection of single molecules with nanometer resolution. This level of resolution allows to consider the study of biological systems at a scale unprecedented in optical microscopy. The developments of the team aim to correlate functional and structural 3D information in different biological applications. In particular we develop different strategies to take advantage of supercritical angle fluorescence (SAF) emission and also introduced a time approach to localize single molecule in structured excitation (ModLoc)

R&D team

OV cytology and imaging (OV-CI)

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R&D team: OV cytology and imaging (OV-CI)

Head of the facility: Lionel Gissot

Lionel.gissot @inrae.fr
Allée des Paons, 78000 Versailles, France

The OV-Cytology and Imaging Team (OV-CI) is part of a multi-level IBISA plant phenotyping facility named “Observatoire du Végétal (transcriptome, proteome, metabolome, but also cell and tissue organization). It is hosted at the INRAE at the Institut Jean-Pierre Bourgin (Saint-Cyr l’Ecole) near Versailles, in Ile de France-Sud, and is associated with the University Paris-Saclay.

The OV-CI team is animated by 8 permanent people (full or part-time), with 1 INRAE researcher, and 7 INRARE engineers. The OV-CI team is mainly devoted to take up challenges in plant Imaging.
It provides new methods, protocols, or devices/equipment in BioImaging necessary to tackle the plant front science. Recent developments include a workflow for live meristem imaging, microfluidic devices for roots imaging, specific configuration for plant vertical fluorescence imaging to study tropism, sensors and growth monitoring, etc.

R&D team

Learning Meaningful Representations of Life

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R&D team: Learning Meaningful Representations of Life

Team Leader: Paul Villoutreix

paul.villoutreix@univ-amu.fr
Faculty of Sciences of Luminy, 163 Avenue de Luminy, Marseille, France

The team has close links with the Turing Center Multi-engineering platform where 3 engineers are specialized in image processing, database management and software development. The team develops inference
methods and machine learning tools for developmental biology, with the aim of understanding the relationships between morphogenesis and cell differentiation trajectories by bridging microscopy and single cell-omics.

Three expertise of the Team
  • Image processing
  • Machine learning
  • Single cell omics
R&D team

ICAR Research-Team @LIRMM

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R&D team: ICAR Research-Team @LIRMM

FBI Contact: Emmanuel Faure

emmanuel.faure@lirmm.fr
Building 5 - 860 rue de St Priest 34095 Montpellier

The ICAR Research-Team develops research themes combining the interaction and processing of visual data such as 2D, 3D, videos or nD+t image sequences and 3D meshes. The team is structured according to 3 research axes: Analysis & Processing which is focused on new low-level processing techniques of visual information, Multimedia Security which is interested in securing visual data and Modeling & Visualization which aims at representing large and complex visual data sets.

Expertise of the Team

  • The Analysis & Processing axis is interested in new low-level information processing techniques to improve the information perceptible in the image and to take into account, within the same theoretical framework, the imprecise, uncertain and incomplete (the different types of error in
    visual data processing).
  • The Multimedia Security axis is interested in the security of visual data. In order to ensure this security, coding algorithms are developed combining tattooing, steganography, forensics, encryption and authentication and often requiring robustness to compression.
  • The objective of the Modeling & Visualization axis is to model large sets of complex data (in dimension and nature) in order to allow intuitive visualization or to manipulate these data to extract knowledge from them.
R&D team

Unit of Synapse and Circuit Dynamics @Institut Pasteur

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R&D team: Unit of Synapse and Circuit Dynamics @Institut Pasteur

Team Leader: David DiGregorio

david.digregorio@pasteur.fr
Institut Pasteur, Rue du Docteur Roux, Paris, France

The Synapse and Circuit Dynamics (SCD) team is composed of 12 people, with 1 CNRS researcher, 1 Institut Pasteur researcher in optics, 1 Institut Pasteur engineers (IR) in optics, 6 post-docs, 1 student and 1 technician. The optics part of the team is pursuing STED nanoscopy developments specifically tailored to the needs of neurobiology studies and is dedicated in particular to the development of an upright microscope design for two-photon excitation STED towards deep brain imaging. The Unit is also partner on a grant for
the dissemination of a design of a random access acousto-optic scanning two-photon microscope in collaboration with Dr. Angus Silver (UCL). The laboratory has also pioneered methods for fast calcium imaging (spot detection, Nakamura et al. 2015) voltage dye imaging, and photolysis of neurotransmitter (uncaging, DiGregorio et al. 2007; Tran Van Minh et al. 2020).

  • David DiGregorio is currently the director of the shared 2-photon imaging facility for the Neuroscience Department. SCD team member, Dr. Ruckerl manages the training and usage of the microscopes, while Dr. Moneron provides advice and design suggestions. There are three 2-photon microscopes (2 of which are embedded in a BSL2 animal facility).
  • The SCD also established the first fluorescence microscopy course (since 2016) at Institut Pasteur and continues to direct this course.
  • The SCD team is currently engaged in a project to install a small footprint 2-photon microscope in a BSL3 facility for imaging live infected animals, and in particular those mice infected with SARS-CoV2.
R&D team

Complex Media Optics @Laboratoire Kastler-Brossel

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R&D team: Complex Media Optics @Laboratoire Kastler-Brossel

Team Leader: Sylvain Gigan

sylvain.gigan@lkb.ens.fr
France, Paris, Rue Lhomond, KASTLER BROSSEL LABORATORY

The team is concerned with developing novel optical imaging methods using scattered light. This includes methods for deep imaging in the multiple scattering regime, super-resolution and non-linear coherent and incoherent microscopies.
Expertises of the Team:

  • Imaging in the multiple scattering regime
  • Super-resolution
  • Computational imaging for fluorescence and Raman
R&D team

Dynamic Control of Signaling and Gene Expression @Institut Curie

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R&D team: Dynamic Control of Signaling and Gene Expression @Institut Curie

Team Leader: Pascal Hersen

pascal.hersen@curie.fr
11 Rue Pierre et Marie Curie, Paris, France

The team is a pioneer of Cybergenetics, which aims at controlling biological systems in real time thanks to computercontrolled feedback loops fed by real time image analysis and driven by microscopy automation. We are developing novel software solutions to enable smart microscopy applications.

Expertise of the Team

  • Smart microscopy
  • Dynamic control of living systems
  • Microfluidics for biology
R&D team

Biology of Phagocytes, Infection and Immunity @Institut Cochin

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R&D team: Biology of Phagocytes, Infection and Immunity @Institut Cochin

Team Leader: Florence Niedergang

florence.niedergang@inserm.fr
Institut Cochin, Rue Mechain, Paris, France

We focus on the functions of phagocytic cells in normal and infected conditions. We have developed dedicated imaging techniques to monitor with high spatial and temporal resolution the mechanims of capture and degradation by phagocytic cells, their impact on immune responses and their alterations by viral infections, which can lead to the development of bacterial co-infections or uncontrolled inflammation.

Expertise of the Team

  • TIRF microscopy with dedicated analysis of phagosome closure assay in three dimensions on living cells
  • TFM adapted for living and phagocytosing cells (collaboration with M Balland, LiPhy, Grenoble)
  • New FRET probes to analyse receptor clustering on living cells (collaboration with J Fattaccioli, ENS and Institut Pierre Gilles de Gennes, and Jean-Maurice Mallet, ENS Paris, programme 80 PRIME CNRS and ANR 2021-2024).
R&D team

Molecular Motors @iBENS

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R&D team: Molecular Motors @iBENS

Team Leader: Terence Strick

strick@bio.ens.psl.eu
Institut de Biologie de l'Ecole Normale Superieure IBENS, Rue d'Ulm, Paris, France

The team develops high-resolution systems for nanomanipulation and imaging of single molecules, with a focus on analysis of DNA metabolic processes such as gene expression and DNA repair. Recent developments include the synthesis of molecular DNA scaffolds for the generic study of protein-protein and drug-protein interactions in real-time and at single-molecule resolution.

Expertise of the Team

  • Single-molecule experimentation (single-molecule nanomanipulation, single-molecule fluorescence)
  • Biochemistry
  • Optics
R&D team

Imaging and Modeling Unit @Institut Pasteur

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R&D team: Imaging and Modeling Unit @Institut Pasteur

Team Leader: Christophe Zimmer

czimmer@pasteur.fr
Institut Pasteur, Rue du Docteur Roux, Paris, France

The team develops experimental and computational imaging and modelling approaches for cell biology and microbiology, with a focus on single molecule localization microscopy, deep learning, chromatin organization and spatial transcriptomics.

Expertise of the Team

  • Single molecule localization microscopy (optics and computational image reconstruction)
  • Deep learning (applications to biological and medical imaging)
    RNA-FISH and quantitative analysis
R&D team

RNA biogenesis @IGH

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R&D team: RNA biogenesis @IGH

Team Leader: Edouard Bertrand

edouard.bertrand@igh.cnrs.fr
Institute of Human Genetics, Rue de la Cardonille, Montpellier, France

Our group has strong interests in gene expression mechanisms, from transcription to translation. While we are interested in the regulation of these processes and their functional consequences, the big question that moves us is to understand how they occur in the context of a living cell.

Indeed, cells are not only the individual units where gene regulation takes place, but they are also incredible objects: if we consider RNA and proteins, a typical cell contains several hundreds of thousands of different molecular species, with some present in millions of copies per cell while others in only few. In order to function with such a high complexity within a crowded molecular environment, cells rely on two main tools: (i) chaperones specialized in the control of molecular interactions; (ii) a remarkable degree of spatial organization, which also allows a high plasticity and a high dynamics of molecules. It is to get insights into these very fundamental questions that we first developed tools to image single mRNAs in live cells. With these tools in hands, and others that we developed later, we aim at imaging the basic mechanisms of gene expression directly in living cells, thereby providing a renewed vision of these fundamental processes.

Our strategy is to invest in methodological developments to access and image new facets of gene expression, usually at the levels of single molecules. These developments are mostly focused on imaging RNA metabolism and they are guided by our current scientific questions.

Methodological developments require multidisciplinary approaches, and we have therefore developed a stable network of collaborators who complement our own expertise. This includes the groups of: (i) C. Zimmer and F. Müller (Pasteur Institute, Paris; https://research.pasteur.fr/en/team/imaging-and-modeling/), a physicist team with a great expertise in image analysis; (ii) T. Walter (Curie/Ecole des Mines; Paris; http://members.cbio.mines-paristech.fr/~twalter/), an applied mathematician expert in high-content microscopy and in complex, high-dimensional dataset analysis; (iii) O. Radulescu (Montpellier University; https://systems-biology-lphi.cnrs.fr/), a mathematician expert in modeling biological processes. More recently, we initiated collaborations with chemists to develop novel RNA probes and biosensors.

Our group works in three main areas: transcriptional and translational regulation, as well as chaperone-mediated control of molecular interactions.

R&D team

Decision and Bayesian computation Team @Institut Pasteur

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R&D team: Decision and Bayesian computation Team @Institut Pasteur

Team Leader: Jean-Baptiste Masson

jbmasson@pasteur.fr
Institut Pasteur, Rue du Docteur Roux, Paris, France

The lab is focused on the algorithms and computation selected by evolution to perform biological decision-making. We address this topic with an interdisciplinary approach mixing statistical physics, Bayesian machine learning, information theory and various experimental biological setups. We are pursuing 4 research axis:

  • Probabilistic pipelines and Artificial Intelligence to probe single biomolecule random walks
  • Decision-making of biological system
  • Amortized inference in Virtual Reality: DIVA + Genuage
  • Numerical Methods for temporal networks

Expertise of the Team:

  • Probabilistic pipelines for microscopy data analysis
  • Virtual reality and augmented reality applied to visualisation and analysis
  • Bayesian Inference, amortised inference and physics-based Bayesian induction.
R&D team

Computational bioimaging and bioinformatics @iBENS

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R&D team: Computational bioimaging and bioinformatics @iBENS

Team Leader: Auguste Genovesio

auguste.genovesio@ens.psl.eu
Institut de Biologie de l'Ecole Normale Superieure IBENS, Rue d'Ulm, Paris, France

The team develops deep learning models and large scale image and data analysis algorithms. Applications range from basic research in developmental biology and neuroscience to drug discovery in collaboration with the pharma industry. We provide the source code of our methods with all papers we publish.

Expertise of the Team:

  • Deep learning
  • Image processing & analysis
  • Computational biology
R&D team

Data modeling and computational biology @iBENS

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R&D team: Data modeling and computational biology @iBENS

Team Leader: David Holcman

David.holcman@ens.fr

The team develops tools in modeling, simulation, data analysis in cell biology and medicine. Recent developments include new super-resolution SPTs analysis.

Expertise of the Team:

  • Modeling: biology at multiple scales.
  • Simulation: stochastic and deterministic
  • Data analysis: trajectories, EEG, electrophysiology data.
R&D team

Multifunctional molecular and hybrid nanomaterials @CEISAM

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R&D team: Multifunctional molecular and hybrid nanomaterials @CEISAM

Head: Eléna ISHOW

elena.ishow@univ-nantes.fr
2 Chemin de la Houssinière, Nantes, France

Nanomaterials nowadays occupy an indisputable place for their diagnostic and therapeutic potentialities, offering new paradigms in the field of medicine in terms of follow-up, safety and personalized treatments. Due to the complexity of the biological environment, mastering the synthesis and understanding the interplay between nanomaterials and biological entities, especially cells, is an imperative need to overcome numerous pitfalls related to toxicity, chemical instability, undesirable targeting, diagnostic artefacts and bioaccumulation, to cite only the major ones.

To this aim, we have been developing for several years multimodal nanoassemblies, originally based on small-molecule photoactive materials, self-assembled as a platform and comprising functional inorganic nanoparticles to bridge the gap from in cellulo to in vivo investigations. Their versatile fabrication offers straightforward architectural tunability, allowing us to decipher their in cellulo interactions.

R&D team

Microscopic Imaging & Image Treatment team @IRIMAS

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R&D team: Microscopic Imaging & Image Treatment team @IRIMAS

Head: Olivier Haeberlé

olivier.haeberle@uha.fr
Institut de Recherche en Informatique, Mathématiques, Automatique et Signal IRIMAS UR UHA 7499 Equipe IMTI - IUT de Mulhouse, 61 rue Albert Camus, 68093 Mulhouse Cedex

IMTI team develops innovative microscopes to image unlabeled samples. Such systems achieve 3D refractive index distribution measurements at cellular level, with twice-improved resolution compared to conventional optical microscopes. We have achieved several premieres in the domain: 

2009: world-first TDM with improved resolution: 130 nm, world record at that time (Opt. Lett. 34, p. 79 (2009)). 

2010: world-first images in correlative TDM-Fluorescence microscopy (J. Biophoton. 3, p. 462 (2010)). 

2010: world-first dual transmission-reflection TDM images (J. Mod. Opt. 57, p. 740 (2010)). 

2014: world-first high lateral resolution/high longitudinal precision profilometry (Appl. Opt. 53, p. 748 (2014)). 

2017: world-first improved and isotropic resolution TDM images (≈180 nm in 3D, distinguishing absorption and refraction. This achievement was awarded the cover of Optica, April 2017 (Optica 4, p. 460 (2017)). 

2019: world-first experimental mirror-assisted TDM images (albeit in simplified configuration) (J. Opt. Soc. Am. A 36, COF1 (2019)).

R&D team

Biophotonics of molecular and cellular interactions team @LBP

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R&D team: Biophotonics of molecular and cellular interactions team @LBP

Head: Yves Mély

yves.mely@unistra.fr
Faculté de Pharmacie - Université de Strasbourg, 74 Route du Rhin, Illkirch, France

The highly multidisciplinary Biophotonics team develops fluorescence-based imaging techniques and innovative probes, in order to apply them for solving key questions related to the molecular and cellular functions and interactions of viral and epigenetic proteins with their nucleic acid targets. The physicists and engineers of the team have implemented and developed home-made microscopy set-ups, which are regularly upgraded and optimized for new applications and projects. The team implemented in 2003 one of the first two-photon FLIM/FCS microscopes in France. Later, the team developed a high resolution 3D dSTORM/PALM microscope and a STED microscope with cw laser. In order to track and image UCNPs, an anti-Stokes wide-field for SPT and an anti-Stokes luminescence lifetime confocal microscope were developed. More recently, a spectral PAINT (sPAINT), a light sheet single molecule microscope and a single molecule UV microscope were developed. These instruments are accessible to the community through their integration into the platform PIQ-QuESt (IBISA).

R&D team

Nanochemistry and Bioimaging team @LBP

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R&D team: Nanochemistry and Bioimaging team @LBP

Head: Andrey Klymchenko

andrey.klymchenko@unistra.fr
Faculté de Pharmacie - Université de Strasbourg, Route du Rhin, Illkirch-Graffenstaden, France

The team develops multifunctional fluorescent molecules and nanoparticles for biomolecular detection and imaging. We developed i) solvatochromic probes for ratiometric and super-resolution imaging of plasma membrane organization and cell polarity mapping, and ii) fluorogenic membrane probes operating from green to near-infrared range for imaging cells, tissues and organoids by advanced microscopy techniques. We also introduced environment-sensitive fluorogenic probes for imaging G protein coupled receptors and intracellular RNA. We also developed dye-loaded fluorescent polymeric nanoparticles (NPs) 100-fold brighter than quantum dots of similar size. They were successfully applied for single-particle tracking in cells and mice brains by intravital microscopy. Using NPs of different colors, we introduced a technique for barcoding of living cells. These NPs were also used as light-harvesting nanoantennas to prepare biosensors for cancer diagnostics and fluorescence in situ hybridization (FISH) for intracellular RNA imaging.

R&D team

Photonic Instruments and Processes, ICube laboratory @ICube

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R&D team: Photonic Instruments and Processes, ICube laboratory @ICube

Head: Sylvain Lecler

sylvain.lecler@unistra.fr
300 Boulevard Sébastien Brant, Illkirch-Graffenstaden, France

The IPP team (Photonic Instruments and Processes, ICube laboratory) has a long-standing expertise in microscopy and coherent imaging, as well as diffuse optics for surgical guidance. In particular, the team develops full-field OCT (scanning interference microscopy), endoscopic OCT, digital holography, hyperspectral imaging and quantitative phase imaging for biomedical application. Moreover, the team has a particular interest in multimodal imaging and contrast for example spectroscopy, elastography and Doppler imaging. The team has also more recently started work on fluorescence imaging, and in particular light-sheet microscopy for high-throughput imaging of live biomedical samples, based on the single-objective Oblique Plane Microscopy technique. The strategy of the team is to tackle biomedical questions with optical imaging with a multiscale approach from cellular scale to the organ scale.

R&D team

Large complexes involved in transcription and translation team @IGBMC

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R&D team: Large complexes involved in transcription and translation team @IGBMC

Head: Bruno Klaholz

klaholz@igbmc.fr
Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.

As part of the Integrated Structural Biology platform at the Centre for Integrative Biology (hosting the national and European Infrastructures FRISBI, Instruct-ERIC and iNEXT-Discovery), and our research group at CBI/IGBMC we have recently done a series of developments in super-resolution fluorescence microscopy to facilitate single molecule localization microscopy (SMLM) analysis with the aim of integrating structural data generated through crystallography, cryo-EM, cryo-ET and FIB towards the cellular level (Biol Cell., 2017). We developed an integrated software for image reconstruction, drift & chromatic aberration correction, co-localization, resolution estimation (SharpViSu; Bioinformatics 2016), segmentation & clustering of labeled complexes [ClusterViSu;4], including 3D analysis and segmentation of SMLM data using Voronoi diagrams [3], as summarized in a book chapter [1]. Our latest development comprises a spectral demixing method which facilitates co-localization of proteins in SMLM (https://doi.org/10.1101/2021.12.23.473862).

R&D team

Synthèse Pour l’Analyse (SynPA) team @IPHC

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R&D team: Synthèse Pour l’Analyse (SynPA) team @IPHC

Head: Loïc Charbonnière

l.charbonn@unistra.fr
25 Rue Becquerel, Strasbourg, France

The team is dedicated to the synthetic development of new tools for analytical and imaging applications. We notably develop luminescent labels for microscopy imaging and bio-analytical applications such as luminescence based assays. The team has a strong background in synthetic organic chemistry applied to the design of lanthanide based luminescent labels. Thanks to the spectral and temporal signature of lanthanide elements, the probes have exceptional characteristics such as very long lived excited states, line-like emission spectra and large pseudo Stokes’ shift. The main scientific axes related to the project are the design of luminescent probes displaying upconversion at the molecular and supramolecular level and the optimization of lanthanide based nanoparticles for time-resolved luminescence microscopy. Regarding upconversion, our molecular approach is expected to remove the troubles associated with the use of nanoparticles (biotoxicity, reproducibility,…) while profiting from the spectroscopic advantages of the anti-Stokes process. For lanthanide based nanoparticles, the displacement of the excitation wavelength towards the visible region will provide strong perspectives for luminescence microscopy and flow cytometry. Our team is fully equipped for organic and inorganic synthesis as well as for the spectroscopic characterization of the luminescent objects with UV-Vis-NIR absorption spectrometers and UV-Vis-NIR emission spectroscopy (up to 1600 nm) in the steady-state and time-resolved modes.

R&D team

Laboratory of Membrane Biology

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R&D team: Laboratory of Membrane Biology

Head: Jean-Jacques Bessoule

jean-jacques.bessoule@u-bordeaux.fr

Plasmodesmata mediated intercellular communication

The team studies the function of organelle tethering in plant cell to cell communication via plasmodesmata pores, and develops tools and methods to 1) image these structures at a nanometer resolution 2) measure cell-cell trafficking in a non-invasive way in planta. Plant samples present cytological particularities (auto-fluorescent components, presence of cell wall, large cells with an important vacuole compartment, air flats) that require developments for high-resolution microscopy approaches. Recent developments include the adaptation transmission electron tomography to reveal plasmodesmata ultrastructure at unprecedented resolution.

Autophagy

The ‘autophagy’ team was recently created within the Laboratoire de Biogenèse Membranaire. The team studies the function of lipids in the formation of the autophagy vesicles in plant cells, the autophagosomes. The team combines biochemistry and imagery to decipher the nature, dynamics and lateral heterogeneity of lipids within autophagosome membranes.

R&D team

Engineering for Life Sciences and Applications (ELiA) @ LAAS

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R&D team: Engineering for Life Sciences and Applications (ELiA) @ LAAS

Head: Laurent Malaquin

laurent.malaquin@laas.fr
7 Avenue du Colonel Roche, Toulouse, France

3D printing and 3D Bioprinting applied to biodetection.
Development of 3D microenvironment as models for cell culture and cancer study.

Topics: Microenvironement for cell culture, tissue engineering, cancer diagnosis, microphysiological systems.
Skills: Microfluidics, 3D printing, Bioprinting, Self assembly, Biopatterning

R&D team

Micro-Nanofluidics for Life and Environmental Sciences @ LAAS

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R&D team: Micro-Nanofluidics for Life and Environmental Sciences @ LAAS

Head: Pierre Joseph

aurelien.bancaud@laas.fr ; morgan.delarue@laas.fr
7 Avenue du Colonel Roche, Toulouse, France

Development of microfluidic confining culture chambers, in order to study the impact of spatial confinement. Adapted to mechano-biology and allowing well-defined microenvironment.

R&D team

Chromatin and gene expression @ MCD-CBI

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R&D team: Chromatin and gene expression @ MCD-CBI

Head: Kerstin Bystricky

Kerstin.bystricky@univ-tlse3.fr
Center for Integrative Biology, Rue Marianne Grunberg-Manago, Toulouse, France

The team develops original systems to fluorescently label and track DNA (ANCHOR technology – NeoVirtech SAS) in real time at nanoscale resolution to understand physical principles underlying regulation of gene expression and DNA repair, in cellular plasticity and tumorigenesis.

R&D team

Phagocyte architecture and dynamics @ IPBS

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R&D team: Phagocyte architecture and dynamics @ IPBS

Head: Christel Vérollet & Renaud Poincloux

christel.verollet@ipbs.fr ; renaud.poincloux@ipbs.fr
IPBS-Toulouse, Route de Narbonne, Toulouse, France

Expertise of the team: Combination of cuttin-edge techniques in optical and electron imaging, material science, cell mechanics and intra-vital imaging to elucidate how phagocytes, in particular macrophages and osteoclasts, interact with the extracellular matrix, to decipher the mechanisms of macrophage 3D migration.

R&D team

Dynamics and disorders of ribosome synthesis @MCD-CBI

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R&D team: Dynamics and disorders of ribosome synthesis @MCD-CBI

Head: Pierre-Emmanuel Gleizes

pierre-emmanuel.gleizes@univ-tlse3.fr
118 Route de Narbonne, Toulouse, France

3D-electron microscopy approaches and correlative microscopies at different scales, from single molecules to tissues. Strong expertise in molecular imaging by cryo-EM and single particle analysis

R&D team

Gut Protease Signals @IRSD

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R&D team: Gut Protease Signals @IRSD

Head: Nathalie Vergnolle

nathalie.vergnolle@inserm.fr
Place du Docteur Joseph Baylac, Toulouse, France

Expertise in 3D imaging of live and fixed organoids. Drug screening tests using morphological characterization of organoid cultures as readouts. Organization of an open platform for Organoid development.

R&D team

R&D LITC platform @CBI @TRI

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R&D team: R&D LITC platform @CBI @TRI

Head: Thomas Mangeat

thomas.mangeat@univ-tlse3.fr
118 Route de Narbonne, Toulouse, France

Dévelopment of the RIM technology (Random Illumination Microscopy). Development of low cost integrated optical technology.

R&D team

MAthématiques pour l’iMagerie BiOlogique (MAMBO) @ MCD-CBI

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R&D team: MAthématiques pour l’iMagerie BiOlogique (MAMBO) @ MCD-CBI

Head: Pierre Weiss

pierre.weiss@cnrs.fr
Centre de Biologie Intégrative (CBI), Rue Marianne Grunberg-Manago, Toulouse, France

The MAMBO team (MAthématiques pour l’iMagerie BiOlogique) is specialized in mathematics (optimization, learning, approximation, inverse problems) and in imaging (reconstruction and analysis). It has 2 main objectives: – Participate in the improvement of microscopy techniques (e.g. RIM, TIRF, SMLM, …) by refining their mathematical modeling and by building efficient reconstruction algorithms. – Participate in the analysis of the resulting images by developing (or using) tools to improve the quality of segmentation or classification in large volumes of data. In particular, it develops new artificial intelligence models to achieve its goals.

R&D team

Phagocyte architecture and dynamics @ IPBS

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R&D team: Phagocyte architecture and dynamics @ IPBS

Head: Christel Vérollet & Renaud Poincloux

christel.verollet@ipbs.fr & renaud.poincloux@ipbs.fr
IPBS-Toulouse, Route de Narbonne, Toulouse, France

Expertise of the team: Combination of cuttin-edge techniques in optical and electron imaging, material science, cell mechanics and intra-vital imaging to elucidate how phagocytes, in particular macrophages and osteoclasts, interact with the extracellular matrix, to decipher the mechanisms of macrophage 3D migration.

R&D team

Bioorganic Chemistry UMR-CNRS 6014 COBRA

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R&D team: Bioorganic Chemistry UMR-CNRS 6014 COBRA

Head: Xavier Franck

xavier.franck@cnrs.fr
1, rue Tesnière 76821 Mont Saint Aignan cedex, France.

Bioorganic Chemistry team (15 people) develops bioconjugation, surface modification, multi-step synthesis, to create biocompatible chemical tools to explore the complexity of living mechanisms. The team’s expertise ranges from organic synthesis to photophysics; aiming at the development and tailoring of 1) new organic fluorophores (either push-pull or ESIPT based with high Stokes shifts and solvatochromism), with a recognized know-how in cyanins, coumarins, rhodamins, indazoles or BODIPY fluorescent scaffolds, notably their NIR derivatives, for application in conventional, two photon and STED microscopy, 2) biodetection (proteins, DNA) techniques based on profluorescent or chemiluminescent probes, and 3) new chemobiology tools such as bioconjugation reactions (and click-chemistry type tools), chemical or photoreactive cross-linkers, photolabile groups. The team collaborates with industrial companies through Carnot I2C and with international collaborators through XL-Chem program.

R&D team

Endothelium, Valvulopathy, Heart Failure @INSERMU1096

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R&D team: Endothelium, Valvulopathy, Heart Failure @INSERMU1096

Head: Jeremy Bellien / Ebba Brakenhielm

ebba.brakenhielm@inserm.fr
22 Boulevard Gambetta, Rouen, France

The translational Cardiovascular Research team develops fluorescence-based 3D imaging techniques and intravital microscopy approaches, in order to apply them for solving key questions related to the molecular and cellular functions, notably related to inflammatory responses in hearts and vessels. The researchers and technicians of the team, in collaboration with PRIMACEN, have implemented and developed set-ups for macroconfocal lymphangiography, vascular thrombosis evaluations as well as light sheet imaging, which are regularly optimized for new applications and projects. The team implemented in 2016 the first cardiac lymphangiography in rodents. Later, the team developed approaches for light sheet 3D imaging. These protocols are accessible to the community through their integration into the platform PRIMACEN (IBISA).

R&D team

Epigenetics and pathophysiology of neurodevelopmental disorders – U1245

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R&D team: Epigenetics and pathophysiology of neurodevelopmental disorders – U1245

Head: Bruno Gonzalez

Bruno.gonzalez@univ-rouen.fr
22 Boulevard Gambetta, Rouen, Normandy, France

Team 4 of the Inserm research unit 1245 aims to characterize the contribution of neurovascular dysfunction in the pathophysiology of neonatal brain lesions while keeping in mind brain immaturity. Thereby, research projects paid attention to molecular, cellular and integrated processes leading to angiogenesis defects and neurodevelopmental consequences such as vessel-associated migration. The team’s research activity is deeply committed into translational research validated by patents and clinical protocols with the objective to develop diagnosis tools and neuroprotection strategies. To reach these objectives, the research team developed mouse perinatal models of white matter injury, in utero gain and loss of functions, and environmental models of fetal toxicity such as FASD. Endothelial and neuro-vascular dysfunctions are apprehended in the developing brains and retinas by imaging approaches (light sheet, FLIM-STED, time-lapse migration, in situ zymography, OCT) on ex vivo tissues (brain organotypic slices, cultured retinas). Image processing and analysis through notably machine learning is developed in partnership with several members of the Normandy FBI node.

R&D team

GlycoMEV axe 3 – UR 4358

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R&D team: GlycoMEV axe 3 – UR 4358

Head: Elodie Rivet / Muriel Bardor

elodie.rivet@univ-rouen.fr
CURIB, Rue Lucien Tesnière, Mont-Saint-Aignan, France

The GlycoMEV team (research axis 3) aims in understanding the biosynthesis and secretion of glycoproteins with a special focus on N-glycosylation in microalgae models. As in all Eukaryotes, N-glycosylation occurs in the endoplasmic reticulum and the Golgi apparatus, where numerous enzymes act step-by-step to build and transfer oligosaccharides named N-glycans on secreted proteins. To decipher the sequence and regulation of these events, it has recently developed cryopreparation methods and imaging technologies (i.e. TEM) enabling the characterization the microalgae cell morphology and to analyse the subcellular localisation of distinct molecular actors. Furthermore, the team has acquired expertise in molecular biology techniques specific to these models allowing the generation of strains expressing various proteins fused to fluorescent reporters. They have also developed strategies based on confocal/FLIM imaging to characterize the targeting mechanisms responsible for the localization of glycoenzymes in the Golgi apparatus

R&D team

UMR-S U1237 – PhIND – INSERM UNICAEN

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R&D team: UMR-S U1237 – PhIND – INSERM UNICAEN

Head: Denis Vivien

vivien@cyceron.fr
Cyceron, Boulevard Henri Becquerel, Caen, France

The “tPA and neurovascular disorders” team within the UMR-S U1237 – INSERM UNICAEN and GIS Blood and Brain @ Caen-Normandie Institute” (BB@C – INSERM – UNICAEN- CHU CAEN) is focused on a better understanding of the physiopathology of thrombosis/ischemic neurovascular disorders by developing and applying advanced methods (from molecular to multimodal cell and in vivo imaging). Mainly dedicated to live-cell imaging, we will provide access to dynamic imaging, super-resolution microscopy (STED). We developed innovative neuroimaging tools such as biocompatible nanoparticles, multimodal probes to detect vesicles trafficking, autophagy, neuronal activity, inflammation in the field of vascular disorders. Additionally, we used multiphoton imaging to observe in vivo vascular events including inflammation, diapedesis of immune cells within the parenchyma as well as microthrombosis. Functional ultrasound localization microscopy enables us to assess brain-wide neurovascular activity at a microscopic scale.

R&D team

UMR-I 02 SEBIO – Environmental Stresses and Aquatic Biomonitoring

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R&D team: UMR-I 02 SEBIO – Environmental Stresses and Aquatic Biomonitoring

Head: Céline Boulangé-Lecomte

frank.lefoll@univ-lehavre.fr
25 Rue Philippe Lebon, Le Havre, France

SEBIO is a research unit specializing in aquatic ecotoxicology with a significant experience in the development and validation of effect-based tools for monitoring and predicting environmental impact of chemicals. As experts in marine biology, SEBIO develops in vivo whole aquatic organism imaging approaches aimed at achieving breakthrough in methods and physiological data in seawater shrimps, bivalves and fish larvae. By using light-sheet microscopy, multi-modal imaging and 3D-reconstruction, these projects will decipher fine structures and detailed homeostatic regulations, in particular related to vascular anatomy, immune cell migration and blood/hemolymph tissue perfusion, regarding infection disease, intertidal cycle, osmotic stress and blood withdrawal for laboratory sampling. In relation with INERIS, technological transfers to European environmental agencies and water monitoring programs will rely on a network of reference laboratories, research centers and organizations for environmental risk assessment.

R&D team

Endothelium, Valvulopathy, Heart Failure @INSERMU1096

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R&D team: Endothelium, Valvulopathy, Heart Failure @INSERMU1096

Head: Jeremy Bellien / Ebba Brakenhielm

ebba.brakenhielm@inserm.fr
UFR Santé, 22 Bd Gambetta, 76000 Rouen, France

The translational Cardiovascular Research team develops fluorescence-based 3D imaging techniques and intravital microscopy approaches, in order to apply them for solving key questions related to the molecular and cellular functions, notably related to inflammatory responses in hearts and vessels. The researchers and technicians of the team, in collaboration with PRIMACEN, have implemented and developed set-ups for macroconfocal lymphangiography, vascular thrombosis evaluations as well as light sheet imaging, which are regularly optimized for new applications and projects. The team implemented in 2016 the first cardiac lymphangiography in rodents. Later, the team developed approaches for light sheet 3D imaging. These protocols are accessible to the community through their integration into the platform PRIMACEN (IBISA).

R&D team

BioBrillouin @Institut Lumière Matière, UMR CNRS 5306

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R&D team: BioBrillouin @Institut Lumière Matière, UMR CNRS 5306

Team Leader: Thomas Dehoux

thomas.dehoux@univ-lyon1.fr
10 Rue Ada Byron, Villeurbanne, France

We possess unique Brillouin microscopes  for imaging different cells and tissues at various scales:

  • VIPA-based interferometer functioning at 660nm for low phototoxicity. Enclosed in an environmental chamber for temperature and CO2 control. Applications include single cells, spheroids and more complex tissues/organisms. Possibility of 3D imaging.
  • Standard interferometer for application to mineralized tissues (teeth, bones, shells) and plant epidermises with sub-mm resolution, possibility to reconstruct dispersion curves for analysis of mechanical anisotropy.

We also possess the expertise to analyze, process and model the Brillouin data to obtain information on the mechanical properties (including anisotropy). Home-made microfluidic devices to mount the samples in special conditions (perfusion, mechanical compression, osmotic shocks…) can be engineered with the input of the Biophysics team. Standard microscopy is also available at the ILM (spinning disk, time lapse…)

Publications

  • Giulia Guerriero, Alexis Viel, Veronica Feltri, Alice Balboni, Guqi Yan, Sylvain Monnier, Giovanna Lollo and Thomas Dehoux, “Predicting nanocarriers’ efficacy in 3D models with Brillouin microscopy”, Nanoscale 15, 19255 (2023)
  • Guqi Yan, Sylvain Monnier, Malèke Mouelhi, and Thomas Dehoux, “Probing molecular crowding in compressed tissues with Brillouin light scattering”, PNAS 119, e2113614119 (2022). 
  • Laura Bacete, Julia Schulz, Timo Engelsdorf, Zdenka Bartosova, Lauri Vaahtera, Guqi Yan, Joachim Matthias Gerhold, Tereza Tichá, Camilla Øvstebø, Nora Gigli-Bisceglia, Svanhild Johannessen-Starheim, Jérémie Margueritat, Hannes Kollist, Thomas Dehoux, Scott A. M. McAdam, and Thorsten Hamann, “THESEUS1 modulates cell wall stiffness and abscisic acid production in Arabidopsis thaliana”, PNAS 119, e2119258119 (2022). 
  • T. Lainović, J. Margueritat, Q. Martinet, X. Dagany, L. Blažić, D. Pantelić, M. D. Rabasović, A. J. Krmpot, T. Dehoux, “Micromechanical imaging of dentin with Brillouin microscopy”, Acta Biomater. 105, 214-222 (2020)
  • J. Margueritat, A. Virgone-Carlotta, S. Monnier, H. Delanoë-Ayari, H. C. Mertani, A. Berthelot, Q. Martinet, X. Dagany, C. Rivière, J.-P. Rieu, and T. Dehoux, “High-frequency mechanical properties of tumors measured by Brillouin light scattering”, Phys Rev. Lett. 122, 018101 (2019)
R&D team

Liphy R&D team

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R&D team: Liphy R&D team

Team Leader: Aurélie Dupont

aurelie.dupont@univ-grenoble-alpes.fr
140 Rue de la Physique, Saint-Martin-d'Hères, France

The Liphy R&D team has a long experience in collaboration, joint-development and consulting in optic projects between physics and biology labs. Recently, our team developed a robust method to obtain absolute values of FRET from any epifluorescence microscope. The QuanTI-FRET method calibrates the experimental system and the fluorophore pair, allowing for absolute FRET efficiency and stoichiometry measurements in living cells. Current work focuses on skipping the calibration step with specific samples, hence offering a direct calibration on the sample of interest. This project has been partly funded by the SATT Linksium, an intellectual property has been registered on the software part and discussions are ongoing with private partners.

Another part of the team’s expertise is reflection interference contrast microscopy which allows the measurement of distances with nanometric precision in the vicinity of a reference surface, and to assess the surface functionalization in situ without staining (quantification, quality control). The combination with force application techniques such as flow chambers permits probing biomechanics through the simultaneous control of the force (applied) and the distance (measured). This is essential to study adhesions forces of different organisms: from bacteria to immune cells. The dedicated microscope is fully automated with temperature control, and the PI is currently working on the development of a user-friendly interface for biology-oriented projects. 

Both developments are unique in France.

R&D team

MICROcell-IAB R&D team

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R&D team: MICROcell-IAB R&D team

Team leader: Olivier Destaing

olivier.destaing@univ-grenoble-alpes.fr
5 Av. du Grand Sablon, 38700 La Tronche, France

Since 2010, we have developped and implemented numerous methods in optogenetics, and even chemogenetics, in order to have access to dynamics and reversible perturbations of key biological functions such as cell adhesion, cell signaling, transcription factors, inflammation, functions of immune cells and even metabolism. Our lab proposes to share this expertise to the FBI users through access for consulting and even direct collaboration. In the Rhonalpin node, our lab is focused on the coupling between optogenetics, biosensors and metabolism imaging through FLIM imaging. Indeed, we have developed a TIRF microscope presenting a module of FastFLIM imaging. Through the use of dark acceptors, this technology allows the users to extend the possibilities in terms of combining optogenetics, biosensors, metabolic imaging through ratiometric probes and classical multicolors TIRF imaging. Moreover, TIRF imaging allows long term live imaging with low levels of photoxicity. This is essential for metabolic imaging and preserving photon budget for FLIM imaging. In the future, this system will be coupled with a module of evanescent field patterning (EFP) in order to have a specific TIRF-mode illumination of only  a region of interest (microm scale).

Publications

1- An optogenetic approach to control and monitor inflammasome activation. Julien Nadjar, Sylvain Monnier, Estelle Bastien, Anne-Laure Huber, Christiane Oddou, Léa Bardoulet, Gabriel Ichim, Christophe Vanbelle, Bénédicte Py, Olivier Destaing*, Virginie Petrilli*. Recently accepted in Science Signaling. bioRxiv 2023.07.25.550490; doi: https://doi.org/10.1101/2023.07.25.550490

2-Optogenetic control of YAP cellular localisation and function. Toh PJY, Lai JKH, Hermann A, Destaing O, Sheetz MP, Sudol M, Saunders TE. EMBO Rep. 2022 Sep 5;23(9):e54401. 

3-Control of SRC molecular dynamics encodes distinct cytoskeletal responses by specifying its signaling pathway usage. Kerjouan A, Boyault C, Oddou C, Hiriart-Bryant E, Pezet M, Balland M, Faurobert E, Bonnet I, Coute Y, Fourcade B, Albiges-Rizo C, Destaing O. J Cell Sci. 2021 Jan 25;134(2):jcs254599.

4-β1A integrin is a master regulator of invadosome organization and function. Destaing O, Planus E, Bouvard D, Oddou C, Badowski C, Bossy V, Raducanu A, Fourcade B, Albiges-Rizo C, Block MR. Mol Biol Cell. 2010 Dec;21(23):4108-19.

R&D team

R&D Team PLATIM / RDP

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R&D team: R&D Team PLATIM / RDP

Team Leader: Gwyneth Ingram

gwyneth.ingram@ens-lyon.fr
46 Allée d'Italie, Lyon, France

Over the last ten years, the joint effort of the platform PLATIM and the laboratory of Plant Development and Reproduction (RDP) has developed a strong and recognized expertise in the imaging and quantification of cell mechanical properties in living plant issues. Specific pipelines have been developed to map and quantify:

1. Wall mechanical properties through direct measurements of key parameters such as wall stiffness, adhesion, and resistance to piercing, using AFMs and nano-indenters 

2. Cell hydrostatic pressure through stiffness measurements made using AFMs or nano-indenters and the subsequent application of physical models but also through the development of a nano-pressure probe (in progress).

In addition of the originality of these technological approaches in mecanotransduction, the interest of our R&D teams is to develop and support their evolution directly into the environment of an IBiSA core facility. Thus, the R&D Team PLATIM/RDP is one of the rare facilities in France to provide different and integrated mechanical evaluations for both plant and animal multicellular organisms.

Publications:

  • Bauer, A., Ali, O., Bied, C., Boeuf, S., Bovio, S., Delattre, A., Ingram, G., Golz, J.F. & Landrein, BSpatiotemporally distinct responses to mechanical forces shape the developing seed of Arabidopsis. (2024) EMBO J. https://doi.org/10.1038/s44318-024-00138-w
  • Creff, A., Ali, O., Bied, C., Bayle, V., Ingram, G. & Landrein, B. Evidence that endosperm turgor pressure both promotes and restricts seed growth and size. (2023) Nature Comm. https://www.nature.com/articles/s41467-022-35542-5
R&D team

R&D Team MEC @GIN

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R&D team: R&D Team MEC @GIN

Team Leader: Karin Pernet-Gallay

Karin.Pernet-Gallay@univ-grenoble-alpes.fr
Bâtiment Edmond J. Safra, 31 Chem. Fortuné Ferrini, 38700 La Tronche, France

The development occurring in the platform MEC is tighly associated with joint effort with the “platform of nanocaractérisation” (PFNC) from CEA, leading to have a unique expertise in 3D electron microscopy of large tissue volumes reaching tens of thousands of cubic micrometers at the nanometer scale. This is essential to analyze rare events and true 3D morphological details in neurobiology to study finely cell connectivity, the characterization of membrane structures in chloroplasts from algae and plants, or to study nanoparticles toxicity. Indeed, EM stacks are acquired with much less efforts than by serial sectioning and in a relatively short time (preparation of the sample 3 days, acquisition of the stack 1 day due to high quality stabilization of the samples) new biological questions of interest to the FBI community can be addressed. 

Moreover, we have developed a unique pipe-line of analysis of large stacks of 3D EM images. This pipe-line is composed of segmentation steps followed by Ilastik approach for recognition of objects of interests coupled with a serie of home-made plugin specific for quantification. As requested by the network of French electronic microscopists, we are actively collaborating to make available our process to make this pipe-line available for others colleagues and especially the FBI users, as requested by the network of French electronic microscopists. Our work allowed us to develop international collaboration with Andrea Volterra, a world-class leader in the field of FIB-SEM in Neurobiology.

R&D team

Spatial-Cell-ID EQUIPEX R&D team

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R&D team: Spatial-Cell-ID EQUIPEX R&D team

Team Leader: Jonathan Enriquez

jonathan.enriquez@ens-lyon.fr
ENS de Lyon - Institut de Génomique Fonctionnelle de Lyon (IGFL), 32-34 Avenue Tony Garnier, 69007 Lyon, France

Transcriptomic heterogeneity of cells in organisms over time and space necessitates state-of-the-art technologies to access this variability and its dynamics in situ. Hence, the Spatial-Cell-ID facility aims to enhance the spatial resolution of MERFISH for pinpointing transcripts of specific genes (ranging from a few to thousands) in situ, achieving cellular and subcellular precision over time. To achieve this, we employ a microfluidics device enabling multiple rounds of hybridization (smFISH) synchronized with an advanced 3D STED microscope, providing precise spatial localization of RNA spots with a resolution of 50 nm. This technology is tailored for whole-mount samples across diverse organisms, spanning from mammalian cells to invertebrate systems such as Drosophila and C. elegans. Supported by EquipEx+ funding, Spatial-Cell-ID will be nationally accessible through the LyMIC core facility. Our facility complements commercial systems focused on imaging larger samples at lower 2D resolution. Our bespoke solution not only surpasses current state-of-the-art capabilities but also maintains its position at the forefront of technology, with potential future integration of genomic and spatial proteomic techniques.

Publications

Bouchet M., Urdy S., Guan W., Kabir C., Garvis S., Enriquez J. A simple smiFISH pipeline to quantify mRNA at the single-cell level in 3D. (2023). STAR Protocols. Volume 4, Issue 2, 2023, 102316.