Stéphane Rigaud

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!

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
👇

New preprint alert!

We developed an automated framework to optimize tracking pipelines for bacteria, along with a nice integration of tools for bacteria imaging, in the recently released TrackMate 8 (Fiji plugin).
www.biorxiv.org/content/10.6...

👇🧵

Laboratory Engineer (Senior), in Advanced Imaging, 1.5.2026-31.12.2028

🚨 Job Alert! 🚨

We have an opening at our Microscopy Core Facility in Turku 🇫🇮.
If you love imaging 🔬 and helping scientists succeed, we want you! 👇

abo.rekrytointi.com/paikat/index...

#Microscopy #ScienceJobs #CoreFacility #Imaging
@turkubioscience.bsky.social

I will be recruiting two postdocs early next year.
- One image analyst
- one biologist interested in working on lymphatics!

Reach out if you are interested 👍

Deep Learning for Microscopy Image Analysis Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,

🚨 Alarm!!! 🚨
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?

20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026

✍️ Jan 15 2026 ✍️

🔁 pls!!

www.janelia.org/you-janelia/...

Happy holidays from an amazing team.

Interested in Zebrafish brain imaging? We released a 3D printed mold that's is super helpful for us. Check it out

Customizable FDM-based zebrafish embryo mold for live imaging
www.biorxiv.org/content/10.1...

Work by Marcela and Jaakko in the lab

We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.

It ships many new features, detailed below, but that are articulated around the following:

Open-Source Developer for Deep Learning Antibiotic Discovery Platform - Research Introduction Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from I...

If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr

research.pasteur.fr/fr/job/open-...

A fluorescent embryo on black text, with the words Halfway to I2K: Virtual Tutorials on Image Analysis November 17-19, 2025 Virtual Conference for beginners to developers i2kconference.org Image Credit - "Sweet Embryo",Travis D. Carney, BINA Image Contest 2024

Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)

Still looking for our perfect doctoral candidate as part of @evomg-dn.bsky.social - come and join us to work on the evolutionary pressures that shape gene expression and disease in the uterus!

Please RT (or is it RB? not sure how our lingo has changed!)

Hi all. This is the recording of the online seminar I gave following the kind invitation of #GLOBIAS.

I share what we have learned delivering #BioimageAnalysis services in the IAH core facility of the @institutpasteur.bsky.social

research.pasteur.fr/en/team/imag...
⬇️

Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...

Job alert!

We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?

See also on the forum:
forum.image.sc/t/research-e...

with lots of pyclesperanto inside

Anyone interested in getting my job?

Do not hesitate to apply, it's a pretty good gig

Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)?
Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.

Save the date! The @pasteur.fr Pasteur course on image analysis is announced:

It will happen from the 1st of June to the 5th 2026.

This year there will be only one track: the Early Career Investigator track (beginners). 👇

We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/

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 🤘

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

🔬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 !