@jytinevez
Research engineer and core facility manager at the Institut Pasteur https://research.pasteur.fr/en/team/image-analysis-hub/ Everything #TrackMate #Mastodon-sc (the tool to track lineages in microscopy videos, not the social networks etc). Views are my own
Thanks to #Appose hackaton with @jytinevez.bsky.social, @ctrue.bsky.social, @nkiaru.bsky.social, @msphan.bsky.social, @strigaud.bsky.social, Carlos, Thomas and Julie, DeXtrusion can be **INSTALLED** and run to detect cell extrusions directly from Fiji 🤩! Appose is amazing
Yes! We have international students every year. Keep in mind that you need to be able to travel to Paris
(All these courses are built by dedicated people, and are by the way happening in Paris in June, just saying:
Organized by the great Mohamad Harastani and Eduard Baquero from the IAH and the nano imaging core!
This course is designed for PhD students, postdocs, engineers, and researchers in structural biology or cell biology with basic knowledge In SPA or cryo-ET data processing.
The deadline to apply is May 1st 2026
For more information please visit our website: www.pasteur.fr/fr/enseignem...
Participants will learn the core concepts and software tools required to analyze complex 3D data to reveal macromolecular structures directly within their native cellular environments at molecular resolution
3/ Sub-tomogram averaging in cyo-EM
6 - 10th of July 2026
This hands-on course provides in-depth training in processing large-scale cryo-electron tomography (cryo-ET) datasets using subtomogram averaging (STA) — a cutting-edge technique at the interface of structural and cell biology.
The course aims to provide all the theoretical background needed and useful tools to render the trainees autonomous in Electron Tomography.
Registration deadline: April 6, 2026.
www.pasteur.fr/en/education...
Organized by the great Anna Sartori and Anastasia Gazi, from the EM cores of Pasteur!
The course is meant for PhD students, post-doctoral fellows, engineers, and researchers who have some (Cryo-)EM experience and would like to use (Cryo-)ET in the near future. Applicants who already have tilt-series for processing will be prioritized.
Introduction to tomography, frame alignment, tomogram reconstruction, denoising, volume annotation, and particle picking for subtomogram analysis will be covered
This one-week course aims to introduce basic concepts in image analysis and practical experience in tomographic reconstructions for different needs: processing of low-dose tilt series with and without fiducials for 3D volume annotation or subtomogram averaging.
In situ studies can reveal additional important information for macromolecules and their complex environments, their adopted conformations, recruitment on specific sites and interactions with other key molecules or ultrastructure.
Electron tomography, combined with image processing is one of the most powerful methods for studying cellular details in 3D. I
2/ The IPEM-TOMO course:
Cryo-ET : Image Processing for Electron Microscopy/Tomography,
June 8 to 12.
Some impressions from last time
(We had a good time, and aim for it again.)
Organized with the great @biaunit.bsky.social , @gaellel.bsky.social and the IAH team.
This year, it focuses only on the Early Career Investigator track, which is anyone who needs to do Bioimage Analysis for their own research.
I had the chance to talk about it before (bsky.app/profile/did:...)
(No worries: the registration deadline has been extended until the 15th of March 2026)
1/ The Advanced Bioimage Analysis with Artificial Intelligence course.
This course inherits from the NEUBIAS courses, and is now in its 3rd installment, with a new name
research.pasteur.fr/en/course/ne...
Here they are, briefly introduced, in order of appearance.
Warning: for some of them the registration deadline is close
Let's get ready for a full month of training in image analysis in @pasteur.fr , this summer!
Are you interested in learning how to do bioimage analysis? For light microscopy? for cryo-EM? And for cellular cryo-EM?
Stay tuned, Pasteur offers access to THREE courses, this June.
👇🎓
🤖 How can #AI unlock the full potential of biological data?
🔬 Our @florianjug.bsky.social develops advanced AI methods to help life scientists extract deeper insights into health and disease within the MIND innovation ecosystem.
Watch the interview 👉 www.youtube.com/watch?v=ucZl...
Appose processing hackathon with @jytinevez.bsky.social, @ctrue.bsky.social, @gaellel.bsky.social, @strigaud.bsky.social, Carlos and Thomas . Simple POC with Java calling python through Appose to flip blocks. Promising!
While we sit around to find out how bad exactly it all is, a bit of cheer: the best baguette of Paris competition was won by a Sri Lankan who appears to have started as a dish washer in restaurants and eventually trained as a Boulanger.
www.paris.fr/pages/la-mei...
Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating).
A brief 🧵 (carried over from the old place)
Thanks @pasteur.fr , @pasteuredu.bsky.social , @france-bioimaging.bsky.social and @prairie-psai.bsky.social for support!
If you need bioimage analysis for your research, and want to learn to get things done with it, apply!
See you in beautiful Paris this Spring to do bioimage analysis together!
The course is organized in practical tutorials, that will be practiced on your laptop, and mainly based on academic open-source scientific software: Fiji, Icy, QuPath, Ilastik
Here is the program from last year, knowing that the one from this year will be similar
In this edition, organized with the @biaunit.bsky.social , we will focus on teaching the basics of bioimage analysis and machine learning for image analysis in Life Science.
The course is focused on beginners, with little or no experience in image analysis, but who needs it for their research
If you want to skip and register immediately, the link is this one:
www.pasteur.fr/en/education...
One week left to register to the Bioimage Analysis with AI course in Pasteur!
This June, 1 - 5.
I give a bit more details in the thread below
👇
