The Image Analysis Hub is an open access, equal access core facility committed to offering bioimage analysis services to the scientific community.
We are a facility coordinated within the C2RT of the Institut Pasteur and are fully dedicated to service in Image Analysis. The IAH was created at the end of 2017 and is composed today of 3 research engineers that are dedicated 100% to the facility, and one administrative assistant.
What we do.
We are one of the few independent core fully facilities dedicated to and specialized in service in bioimage analysis.
The scope of our offering includes all imaging modalities, whether coming from optical microscopy, electron microscopy, NMR, small animal imaging, … Images can come from imaging core facilities or not.
We work by collaborating scientifically with our users, trying to achieve a significant added-value to their Research. This happens typically via two types of contribution:
- Quantification projects. A user would delegate an analysis task to us, a sub-part of their research project. Our goal then is produce scientific results from their images, up to the production of a figure for a publication, with the redaction of the associated Materials andMethods section.
- Custom development of analysis tools. We strive not to limit ourselves to be users of bioimage analysis software, but to be able to modify them and build new tools. We are the developers of several analysis tools among which TrackMate or MaMuT which supported several scientific projects. We are involved in two major software projects in imaging: Fiji and Icy.
In details , our missions follow four axes:
- Offer walk-in support and trainings for questions involving image analysis.
- Build and deploy custom analysis tools for projects requiring special developments.
- Maintain an infrastructure for autonomous image analysis.
- Develop original and innovative software tools for image analysis, whose scope exceed user projects.
Access to commercial softwares and workstations.
We have several workstations in our ‘aquarium’ room (Francois Jacob building, main hall, room 26-01-17), that we share with our colleagues from other facilities. On these workstations (see the equipment section below) we offer access and maintain the following softwares:
- Imaris (complete package) on workstation Tool.
- Huygens on workstation Perceneige.
- Arivis vision 4D on workstation Rammstein.
You can also access some of these softwares on virtual machines accessible remotely. This proved invaluable during the pandemic-induced lockdowns. The virtual machines are powerful enough to grant you decent computing power wherever you are.
We can train you on the commercial softwares listed above, plus the ones we created. Note that there are no training requirements to access our workstations: you can book the workstations and use the softwares there without a training. We offer personalized one-to-one trainings, that will introduce you to the core usage of the softwares. The trainings we offer are: Commercial softwares:
- Using Imaris for the visualization of 3D images. Object detection and segmentation..
- Deconvolution with Huygens,
- Large image visualization and analysis with Arivis vision 4D.
If you have a quick question on bioimage analysis, or want to discuss experimental design involving image quantitation, come and meet us during our open-desks (see in the Past news section for details and schedule). Open-desks happen every 2 Thursdays, in the morning. You can come without appointment and we will meet and try to answer your question immediately, first come first serve.
If your question involve a longer effort or some development work, we will create a collaborative project with you. During such a IAH project, an engineer will collaborate with you and create a tool, adapt a pipeline or perform an analysis to answer your question. This involves scientific work from us beyond a purely technical contribution. There is no selection committee for IAH project submissions. If a project is deemed feasible, the proposal is accepted and treated in order of submission. Feasibility assessment includes cost and time considerations, as well as image quality vs desired robustness of results. A research project can be linked to several IAH projects, possibly with different engineers. IAH projects are tailored to address a single specific bioimage analysis question. To submit a IAH project, come to one of our open-desks.
The IAH operates within a Quality Management System following the ISO-9001:2015 norm, and we achieved certification by the AFNOR in 2019, within the C2RT ISO-9001 certification. Following the ISO9001 certification, the IAH obtained the IBISA label in October 2019.
We run satisfaction surveys every year, targetted to our users. You can access here the survey results and analysis: