Stéphane Rigaud

Upcoming breaking changes in TrackMate v8 Hello TrackMate developers, This post is only important if you are developing TrackMate extensions yourself, in particular TrackMate spot detectors and segmentation modules. If not you can skip it en...

Are you developing with TrackMate?

If yes let's get in touch: I plan to make API breaking changes in the future version (v8, soonish) that will break existing detector and segmentation algorithms integration.

Details on the forum: forum.image.sc/t/upcoming-b...

Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁
Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

The @globias.bsky.social #preprint 🚨 is out, outlining global needs of BioImage Analysts, presenting how GloBIAS seeks to support and professionalize this role through education, and community building! Congrats Agustin Corbat and the entire team for pulling this through!
arxiv.org/abs/2507.06407

🧑‍🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab

📜: zenodo.org/records/1575...
👨‍💻: github.com/HenriquesLab...

Are you looking for a postdoc?
I will be looking for 2-4 people after the summer to join the lab !!
Do not hesitate to reach out and disseminate !!

We have been collaborating with Daria for years and I warmly recommend working with her.

From Local to National BioImage Analysis Hub, how to share ressources, knowledge, and especially help each others 🤘

YouTube video by Institut Pasteur EDUCATION Bioimage Analysis – Retour sur le Cours Pasteur NEUBIAS

🔬Le Cours Pasteur NEUBIAS propose une formation avancée en analyse d’images biologiques intégrant théorie, pratique et IA. Lina El Hajji, post-doc à Sorbonne Université, partage son expérience. La prochaine édition aura lieu en juin 2026 sous le nom « Advanced Bioimage Analysis with AI »

Final session where we finish our pipeline using #celltrackscolab with Laura Xénard.

For day 5 of #neubiaspasteur2025 we learned to crash our GPU memory with @strigaud.bsky.social . And also to do efficient image analysis on GPU with #clesperanto

Perfect way to finish the day with ☀️ and warm evening.

Thanks to the teachers and dear colleagues @jwpylvanainen.bsky.social @mambroset.bsky.social @gaellel.bsky.social @m-albert.bsky.social Carlos Garcia-Lopez & Heloise Monnet, and the students that join us !

4th day on the go for #neubiaspasteur2025 with a @biapyx.bsky.social practical course by @jwpylvanainen.bsky.social and a #cellpose #dask and RNA2Seg (doi.org/10.1101/2025...) course with @gaellel.bsky.social and Alice Blondel

Thank you very much to @florianjug.bsky.social and The Column for such an amazing talk! It’s always great to hear from you! #neubiaspasteur2025

3rd day of the #NEUBIASpasteur2025 with a introduction lecture to OMICS by Florian Muller, followed by a full day of #qupath by Thierry Pecot and #ome-zarr / #dask by @m-albert.bsky.social

Thank you #neubiaspasteur2025 for the great energy!
My slides on AI-based bioimage analysis pipelines (and SAMJ!) are now up on Zenodo.
I hope you took away something new! 💡

🔗 zenodo.org/records/1539...

Indeed, the participants formed groups and implemented @napari.org plugins from scratch for tasks like pixel classification or cell tracking.

At the end, the groups did a live demo of their plugin 💻

I was super impressed! 🥳

#NEUBIASPasteur2025

📚 Course materials: github.com/Image-Analys...

Repo will be fully updated at the end of the course ;)

Second day with Ilastik (@ilastik-team.bsky.social) covered by @MinhSonPhan, with @strigaud.bsky.social and @jytinevez.bsky.social as helpers. How to easily train a pixel classifier to segment focal adhesions..

First day covered #fiji by @mambroset.bsky.social and a mini-@napari.fosstodon.org.ap.brid.gy challenge to develop widgets for image processing by @danielkrentzel.bsky.social

Kick-starting the #neubiaspasteur2025 #BioImageAnalysis courses at @pasteur.fr and @pasteuredu.bsky.social

Just arrived to Institute Pasteur in Paris for Neubias Image analysis course. Todays opening talk about the future of bioimage analysis by @florianjug.bsky.social - very cool week ahead! #neubiaspasteur2025

Applications closing on May 6th 2025 for the “Train the Trainers in Bioimage Analysis” workshop, taking place on June 13th 2025 in London!

Reach out should you have any questions 👩‍💻🔬🧫

franciscrickinstitute.github.io/Train_the_tr...

GloBIAS #BioimageAnalysis #Conference 2025 – we have opened the registration for our 2025 in-person event. Please check the webpage www.globias.org/activities/b... for more information and the link to the registration form.

Tomorrow (midnight) is the last day to apply!
I am biased but I swear it will be a great course.

For instance we were just fine tuning the last 2 days of the ECI track with Laura and @jwpylvanainen.bsky.social -

GitHub - CAREamics/careamics: A deep-learning library for denoising images using Noise2Void and friends (CARE, PN2V, HDN etc.), with a focus on user-experience and documentation.) A deep-learning library for denoising images using Noise2Void and friends (CARE, PN2V, HDN etc.), with a focus on user-experience and documentation.) - CAREamics/careamics

Great to see that many noise2void inspired denoising algorithms have been ported to @pytorch.org! Kudos to @florianjug.bsky.social and many others ...
github.com/CAREamics/ca...

Team is teaching machine learning at the @pslqlife.bsky.social course on cellular dynamics. Lecture from
@gaellel.bsky.social, practical from Minh-Son with @strigaud.bsky.social and me as helpers

Preprint (update) alert!

F-BIAS: Towards a distributed national core facility for Bioimage Analysis. (arxiv.org/abs/2409.15009)

0/ In this paper we discuss our experience in federating ourselves and delivering bioimage analysis services to the scientific community in France.

👇 a short thread

Last days to register!

Only five days remain to register!*

Here is the tentative program:

*: it is likely that there won't be a deadline extension.

Registration deadline extended to the 31st of March.