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About

The Image Analysis Hub is an open access, equal access core facility committed to offering support in image analysis for the Institut Pasteur campus.

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:

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.

Expertise.

The technical skills of engineers are the main resources of the IAH. They revolve around roughly 3 domains.

Our ability to contribute to our user research is of course mediated by image analysis techniques. Image processing is a part of applied mathematics, and the algorithms this field offers can address complex image quantification questions.

One of our main toolset comes from computing. Computing allows to implement the algorithms mentioned above and put them to use to address a specific scientific question. We strive not to limit ourselves to be users of bio-image analysis software, but to be able to modify them and build new tools. This involves the ability to develop software, using programming languages like Java and C++, and good software development practices.  We are the developers of several analysis tools among which TrackMate or MaMuT which supported many scientific projects. We are involved in two major software projects in imaging: Fiji and Icy. Of course, scripting languages like Python and MATLAB proved their importance for Science, and they are part of out toolbox as well.

Our ultimate goal is to address the scientific questions of our users. To this aim we must be able to understand the scientific context of the question well. For instance, some analysis tasks can be excruciatingly difficult with certain imaging modalities and made trivial with others. We must be able to advise our users also at the level of experimental design, involving if needed imaging. When relevant, we involve our partners from other facilities or experts of the domain.

Obtained labels.

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.

Logo AFNOR ISO9001

 

Equipments Booking site

IAH workstation ‘Rammstein’ • Corsair • One

This PC serves as a platform for testing the software DIVA (Institut Pasteur, Institut Curie) that allows visualization of volumetric data (and not only) by means of Virtual Reality. Also, it is equipped with […]

IAH workstation ‘Tool’ • Intel-Nvidia-MSI • PC

This PC is meant for Image Analysis; it is equipped with a strong graphic processor, which allows usage of hardware-accelerated analysis software. CPU Intel 3.60 Ghz 6 Cores/12 Threads RAM 196 Gb DD4 GPU […]

Software

Former Members

2000
2000
Name
Position
2017
2020
Emma Spanjaard
Research Engineer
2017
2020
Sébastien Herbert
Research Engineer

Courses

Microscopy – Principles and Applications of Fluorescence Microscopy

Fluorescence microscopy has revolutionized researchers’ ability to monitor cellular structures and dynamics. Over the last decades, the spectrum of applications of fluorescence microscopy has been constantly broadened by novel combinations of optics principles supported […]

2020-03-02 08:00:00 2020-03-13 19:00:00 Europe/Paris Microscopy – Principles and Applications of Fluorescence Microscopy Fluorescence microscopy has revolutionized researchers’ ability to monitor cellular structures and dynamics. Over the last decades, the spectrum of applications of fluorescence microscopy has been constantly broadened by novel combinations of optics principles supported […] 25-28 Rue du Dr Roux, 75015 Paris, France

Fundings

Partners

Publications

Download

Networks

NEUBIAS logo
NEUBIAS

Steering committee

The steering committee of the IAH includes 3 members, 2 from the Institut Pasteur, 1 external: Perrine Paul-Gilloteaux. Scientific director of the MicroPICell facility, University of Nantes. Romain Levayer. Head of the ‘Cell Death and Epithelial Homeostasis’ unit, Institut Pasteur, Paris. Philippe Bastin. Head of the ‘Trypanosome Cell Biology’ unit, Institut Pasteur, Paris.

How to access the facility?

IAH open-desks.

First and foremost, come to our open-desks! Open-desk sessions aim at addressing the questions of the campus about image analysis. During 3 hours, once every 2 weeks, the IAH and a number of people from different labs and structures will be present to deal with your images, or general questions about image analysis. We also use them as the main entry point to the facility. Whether you want to start a project, request a training or just discuss an experiment, come to our open-desks Their planning and goals can be found on the IAH open-desk page: https://research.pasteur.fr/en/news/image-analysis-opendesk/

Emails and PPMS.

You can

  • make a project request;
  • make a training request

on our PPMS instance. Our activities are billed. Contact us for more information. We can be reached at iah at pasteur dot fr. If you are unhappy with our services or want to bring a point to our attention privately, you can do so iah.feedback at pasteur dot fr. Only the facility head and the administrative assistant receive these emails and they are treated confidentially.

Team chat.

If you like instant messaging, we have a public channel on the RocketChat instance of Pasteur. We use it to:

  • announce new tools we deploy;
  • or trainings we organize;
  • post interesting conference and external training announcements;
  • post papers we find interesting and comment them;
  • answer directly quick questions you post there.

Join the IAH channel on RocketChat: https://rocketchat.pasteur.cloud/channel/iah

Access policy.

Our services require users to comply to the following policy:

1. Acknowledgements.

Users will acknowledge the IAH facility and its fundings in any publication or communication, when its services (open-desks, advices, trainings, use of workstations, projects, …) have been used for the presented work. Please also let us know when you do so. Example acknowledgement sentence: “We acknowledge the help of Image Analysis Hub of the Institut Pasteur for this work.

2. Facility usage fees.

Users agree to pay the service fees related to the facility activities. Activities are billed based on hourly rate for academic users. Contact us for pricing.

3. Responsibility.

Users remain responsible for the storage and the integrity of the original image data they provide, and for the analysis results the IAH provides to them once they are delivered.

Contact

Phone: 8218 Email: iah at pasteur dot fr Address: 25-28 Rue du Docteur Roux 75015, Paris France