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).
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
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.
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
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
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
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
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.
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 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
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
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.