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About

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:

  1. Offer walk-in support and trainings for questions involving image analysis.
  2. Build and deploy custom analysis tools for projects requiring special developments.
  3. Maintain an infrastructure for autonomous image analysis.
  4. Develop original and innovative software tools for image analysis, whose scope exceed user projects.

Services.

We offer 4 kind of personalized services on top of our teaching activities:

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:

On these workstations you will also find the open-source academic softwares Fiji and Icy.

Trainings.

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.

Our softwares:

  • Using Mastodon for cells and organelles tracking in large samples.
  • Simple tracking with TrackMate.

Consultative projects.

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.

Collaborative projects.

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.

Examples.

Measuring the polarization of T cells. Image M. Mastrogiovanni (Lymphocyte Cell Biology Unit, Institut Pasteur), J.-Y. Tinevez (IAH)
Identification and segmentation of stem cells in the drosophila post-embryonic brain. Image P. Speder (Brain Plasticity in Response to the Environment unit, Institut Pasteur), S. Rigaud (IAH).
Cell migration assay. Image G. Jacquemet (Cell Migration lab, Åbi Akademi University), J.-Y. Tinevez (IAH).
Colony counting on non-microscopy images. N. Gupta (Membrane Traffic and Cell Division unit), J.-Y. Tinevez (IAH).
Modeling a bacteria crossing a mitocondrium in electron microscopy images. Image Z. Uzum (Evolutionary Biology if the Microbial Cell, Institut Pasteur), D. Ershov (IAH).
Measuring the association of degradosome spots in Helicobacter pylori. Tejada-Arranz et al., 2020.
Automated doublet length measurement in super-resolution images. C. Leduc (Cell Polarity, Migration and Cancer unit), J.-Y. Tinevez (IAH)

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

Following the ISO9001 certification, the IAH obtained the IBISA label in October 2019.

Satisfaction surveys.

We run satisfaction surveys every year, targetted to our users. You can access here the survey results and analysis:

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

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

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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