About

The Image Analysis Hub is an open access, equal access core facility committed to offering support in image analysis. Our webpage is: https://research.pasteur.fr/en/team/image-analysis-hub/

What we do.

As part of the C2RT, we strive to ensure the continuity between image acquisition and image analysis. To this end we rely on our expertise in imaging and collaborate with other facilities such as the UTechS-PBI and UTechS-UBI when pertinent. All requests involving images are considered.

Our services follow four axes:

1. Offer walk-in support and trainings for questions involving image analysis.

This activity aims at offering to users quick answers to scientific questions involving well-established pipelines, for which a commercial or published tool exists and can be used conveniently. Users can address their question to the facility during open-desk sessions or directly via one-to-one requests. Depending on the effort involved, the solution is derived and proposed onsite, or individual  trainings are scheduled. For general topics, the Hub organises regular courses and workshops, possibly involving external teachers or providers.

For instance, see below for the announcement of our open-desk, organised regularly every two week.

2. Build and deploy custom analysis tools for projects requiring special developments.

Research endeavours to address original questions, for which analysis tools might be lacking or incomplete. The Image Analysis Hub aims at creating or implementing novel tools based on existing algorithms to address these questions, using skills in image analysis and software development. More than just developing the analysis tool, this activity often involves deriving a suitable analysis methodology, for which the facility expertise in microscopy and biophysics is key. Engineers work in close collaboration with users within the framework of a scientific project over medium or long durations. For projects whose effort would extend beyond typical facility usage or involve original research work, the project may be directed to the BioImage Analysis unit after a discussion with all parts.

3. Maintain an infrastructure for autonomous image analysis. Deal with complex tool deployments.

Data volume and modern analysis techniques may call for a computing power not always present in Pasteur labs. Providing open-access workstations unlock barriers to compute-intensive tools. They also act as the central sharing points for commercial softwares, making them available to the whole campus. Finally, some specialized tools require special deployment efforts, e.g. to make such a tool able to exploit the HPC infrastructure of the Institut Pasteur.

4. Develop original and innovative software tools for image analysis, whose scope exceed user projects.

Software development and image analysis skills of the facility can be leveraged to build ambitious software tools shipping innovative technologies. These tools exceed the scope of single projects and address the unarticulated needs of the Pasteur community and their creation is part of the development activity of the facility.

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

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/ ).

Microscopy systems available @IPAM

The BIC (Bordeaux Imaging Center) offers resources in photonic and electronic imaging, mainly in life, health and plant sciences. It is a core facility identified at the national level as IBISA that gathers 12 highly skilled engineers. It has the ISO9001 label. The different components of the BIC are: PHOTONIC imaging, ELECTRONIC imaging, PLANT imaging. The Bordeaux Imaging Center offers access to the most advanced bio-imaging techniques for fixed and live cell imaging such as video-microscopy, confocal microscopy, multiphoton microscopy, transmission electron microscopy and scanning electron microscopy. The BIC provides a unique set of high-end equipment for super- resolution microscopy such as STED confocal microscopy, FRAP video-microscopy, lifetime imaging FLIM for the measurement of molecular interactions. We also provide access to equipment for sample preparation such as ultra-microtoms, high pressure freeze (HPF) and we can host live samples.

Microscopy systems available @BIC

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.

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.