Microscopy Technologies

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

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.

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 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.