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).
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
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 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
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 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 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.