🐍 Learn Python for Image Analysis — for free!
UK life scientists: join EuroBioImaging's hands-on beginner course at The Crick in London (23–25 June), running simultaneously with sites in CZ, PT and SWE!
⏰ Register by 15 April — places are limited!
✈️ Travel funding may be available
shorturl.at/v3Vsk

"But the nightmare result is that non-programmer LLM users will receive something that seems to work, and only reveals its shortcomings much later on"

Happy to share that the study is now published in Advanced Science 🙌🥳 :
advanced.onlinelibrary.wiley.com/doi/10.1002/...

I want to thank my co-authors and my amazing PI @lauraschaedel.bsky.social for all the help, lovely discussions and encouragement😀

#VeilleESR #ESR
Premières notifications officielles du soutien de base pour le CNRS: -25 % à INSU, -10% côté INEE, -25% pour INSB. Ce prélèvement s’ajoute aux 10 % que le CNRS a prélevé sur les Ressources Propres Banalisés de toutes les UMR en janvier 2026.

Thanks to all contributors @levayerr.bsky.social @leovalon.bsky.social @tomcumming.bsky.social @amichaut.bsky.social @lxenard.bsky.social @msphan.bsky.social @nicolasdray.bsky.social @ctrue.bsky.social @FrancoisSchweisguth @jeromegros.bsky.social @zenlabpasteur.bsky.social @jytinevez.bsky.social

To use EpiCure, see our online documentation for its installation: image-analysis-hub.github.io/Epicure/Inst...
with all the steps to create a virtual environement and install it. There's also an option to install without using a terminal, see: image-analysis-hub.github.io/Epicure/Inst...

For users convenience, EpiCure can import/export segmentation and track to various format, but you can also do the whole analysis pipeline, from the raw movie to data quantification within the plugin. For more details, see our preprint: www.biorxiv.org/content/10.6...

So to ease manual correction, we developed EpiCure to detect errors and assist their correction: we identified the most common segmentation errors and propose keyboard or mouse shortcuts to painlessly repair it.

Is it really necessary to go through painful manual correction? It depends on the analysis. We compared quantifications before and after corrections to highlight its impact. When long-term tracking is necessary or when studying rare cell type, the difference is drastic.

At @devstempasteur.bsky.social we study epithelia from various models. Despite awesome tools to segment and track the movies we identify one common bottleneck: the manual correction of the results. For a movie with 10,000 cells, only 5% segmentation errors => 8500 manual corrections!

I'm happy to present our new tool, EpiCure, a napari plugin to ease correction of segmentation and tracking of epithelia movies, developed in @devstempasteur.bsky.social

On oublie souvent qui est vraiment Rachida Dati. Les sourires sur les plateaux, les punchlines, mais aussi des casseroles, des procédures judiciaires, et potentiellement plus de 3,1 millions de pots de vin.

Voilà ce qu'il devrait être rappelé systématiquement quand on parle de Rachida Dati !

It's out! Happy to present ITEC, a semi supervised algorithm with an extremely low error rate that can track cells in files of any size (think Terabytes!). We used it in many organisms, including zebrafish, to study how organs form and linked it to gene expression www.biorxiv.org/content/10.6... +🧪

FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues AbstractSummary. Characterizing the distribution of biological marker expression at the single cell level in whole tissues requires diverse image analysis

Very happy to announce a short article on Fishfeats, with @gaellel.bsky.social ‬and @zenlabpasteur.bsky.social, now accepted in Bioinformatics doi.org/10.1093/bioi...

🔬 Registration is open for our pilot Introduction to napari Workshop!

napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast.

#napari #Python #ImageAnalysis #DataScience #OpenSource

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

2/ The IPEM-TOMO course:

Cryo-ET : Image Processing for Electron Microscopy/Tomography,

June 8 to 12.

Pasteur course Advanced Bioimage Analysis with Artificial Intelligence (AI) - 2026 - Research Topics The course has a specific focus on hands-on and interactive tutorials. They are meant to be convivial and foster a collaborative atmosphere between students and teachers. Each day begin with a ...

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...

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.

👇🎓

‪
🌳 Do you want to contribute to research on how humans perceive forests? Take this quick, anonymous 10-min survey 🌲

👉 www.biodiful.org#/forest

This will help us explore how people experience forest biodiversity!

Please share on 🦋 & tag @biodiful.bsky.social to reach more participants 🙏💚

🌐🌍🦤🦑🪴🍁🧪

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!

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...

👇🧵

3D assessments are necessary to determine the true, spatially resolved composition of tissues.

Standard 2D won't do.

Use CODA to switch from 2D to 3D spatial omics.

More here: www.sciencedirect.com/science/arti...

#LivingArchitectures
We put cells and cytoskeleton filaments on the architecture of the musée d'Orsay.
www.musee-orsay.fr/fr/agenda/ev...
Scientists of the #CytoMorphoLab adapted their protocols to illustrate the questions that keep them awake at night.
-> Two shows on the 24th and 25th of January.

I was invited by @focalplane.bsky.social to write a short description about it:

focalplane.biologists.com/2025/12/12/a...

📜We are thrilled to announce that the latest MorphoNet paper is officially published 🎉 ! Discover 5 varied use cases in which MorphoNet helps segment, curate, evaluate & validate complex 3D+t datasets, and much more 🧑‍💻 ! Read at @elife.bsky.social : doi.org/10.7554/eLif...

Mid-career Group Leader position in AI in genomics at Institut Pasteur, Paris - Research Institut Pasteur and the CNRS are launching a call for a mid-career group leader position in AI in genomics. We are looking for an experienced researcher (typically with > 8 years of research experien...

There a is a joint call between @pasteur.fr and @cnrsbiologie.bsky.social for a mid career group leader position in AI and genomics (or molecular biology). Don't hesistate to spread the word if you know anyone relevant.

research.pasteur.fr/en/call/mid-...

Ten years on, mixed results for the Paris Agreement

In 2015, the historic Paris Agreement, signed by 195 countries, sought to limit global warming to 2 °C. Ten years later, the results have yet to materialize, raising questions regarding the effectiveness of COP meetings, major climate gatherings whose thirtieth edition kicks off Monday in Brazil.

📣 Register to the 13th Advances in Stem Cell Biology Course #ASCBcourse at the @pasteur.fr @pasteuredu.bsky.social. Hands-on training in different models, embryonic stem cells, iPS cells and much more on #StemCells, #organoids. 🕘June22-July03, 2026
👉 shorturl.at/PyUHi

💥 LE FINAL de notre action « Fin de la COP30 : Jour de Colère » - à regarder jusqu’au bout 💙.

@scientifiquesenrebellion.fr et l'Orchestre du nouveau monde jouent le Dies Irae de Verdi après de 8h de lectures de textes scientifiques lors d'une action de 10h marquant les 10 ans de l'Accord de Paris.