Microscopy Technologies

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.

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

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.

Microscopy systems available @Morphoscope

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

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

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

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

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

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

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

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

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.

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.