Microscopy Technologies

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.

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.

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.

 PICsL has been founded in 2002 in the context of a partnership between CIML and IBDM. This technological facility has for main objective to give access to forefront technologies in cellular imaging to 45 research groups (500 scientists). The facility is located in the two institutes on the same campus and offers a variety of state-of-the art imaging systems (multiphoton, confocal imaging, electron microscopy). In addition, during the past years, specific R&D projects have been launched in research teams of the institutes, which now benefit to an increasing number of scientists. First built as collaborative projects between teams (e.g. H. Rigneault/D. Marguet, PF Lenne/T Lecuit), they have proven to be of general interest for a large community at local, national and international levels. Bringing these new technologies to a shared infrastructure in Marseilles has significantly enlarged the service offered to users.

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

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

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.

MARS is a research facility born from a collaboration between R&D groups at the CBS, and the PIBS, MRI and IPAM facilities. The main objective of MARS is to offer the scientific community access to a selection of advanced microscopy technologies, generally not commercially available. To achieve this aim, we implement in MARS state-of-the-art optical microscopy methods developed by R&D teams of the FBI node (Nollmann, Margeat, Milhiet, Mollard). MARS offers access, training, and support to several custom-made optical setups.

Three R&D teams are part of the MARS facility to port their methodological developments. The group of Emmanuel Margeat develops single molecule FRET and fluctuation microscopies to investigate the structure, dynamics, and interactions of macromolecular complexes, with a specific focus on membrane receptors and transcription regulation. The team of Marcelo Nollmann (see Group website) specializes in the development and implementation of super-resolution and advanced microscopy methods to investigate DNA organization and remodeling. Specifically, the team has developed two-color ultra-stable PALM/STORM microscope (currently available at MARS), a 3D-PALM setup based on adaptive optics, and multi-focal plane microscopy. The group is currently working as well in the combination of these methods with structured illumination microscopies. Together with the group of Pierre-Emmanuel Milhiet, the team has recently developed a combo PALM/STORM/Atomic Force Microscopy.

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/ ).

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.

PIBBS-Optics facility gathers state-of-the-art, custom built setups for various advanced microscopy techniques, such as Single Molecule Localization Microscopy, Multi-Focal Microscopy, smFRET, PIE-FCCS, 2-photons FCS, single particle tracking…

Located in the CBS (Centre de Biochimie Structurale, Montpellier), it offers access to advanced microscopies to the scientific community through local, national and international collaborations.

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

More details are available on our website:

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

APEX is a platform characterized by a double expertise in veterinary anatomic pathologic and fluorescence bio-imaging. APEX is set up on veterinary pathologists certified by the European board committee in combination with engineers dedicated to bio-imaging. To face to scientific problems of imaging, APEX suggests new developments in high- technology microscopy such as spectral imaging confocal microscopy, Total Internal Reflection Fluorescence (TIRF), photoactivation localization microscopy (PALM), Airyscan and stochastic optical reconstruction microscopy (STORM) or multiphoton microscopy. With experts in complementary fields as facilitators, APEX originally proposes an integrated offer in veterinary histopathology as well as in tissue and cell phenotyping in a large spectrum of animal species.

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 500 Ac in our catalog) as well as multiplex staining, a technique that can highlight up to 6 different proteins per slide, fluorescence or chromogenic. 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.

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.

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.