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... ⬇️

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/

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...

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 🤘

🔬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

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...

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..

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 -

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.

Do you want to learn #BioimageAnalysis? Do you want to strengthen your skills? We're thrilled to announce the #NEUBIAS Pasteur Course on Bioimage Analysis - May 2025! in @pasteur.fr Paris! research.pasteur.fr/en/course/ne... Details are on the page linked here, some info below 👇

Do you love and use #microscopy? There is a fantastic event taking place at the @institutpasteur.bsky.social Paris in 3 weeks, just for you :) 1/ mini symposium on imaging, AND / OR 2/ book demo slots to test the latest microscopes from partners Please share with colleagues, more below👇

After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool. www.nature.com/articles/s41...

It’s official 🎉 I am excited to share that I will start my lab this spring at the Max Planck Institute for Immunobiology and Epigenetics @mpi-ie.bsky.social in beautiful Freiburg 🤩🗻☀️ I am looking forward to new collaborations and working with the fantastic community in Freiburg & its surroundings!

The Institut Pasteur has decided to leave X (formerly Twitter) to join BlueSky! 🦋 The Institut Pasteur made this decision due to several serious issues observed on the X platform since its acquisition. Join us here to continue advocating for science. www.pasteur.fr/en/home/pres...

Our code for force inference in epithelial tissues is available online! Feel free to contact us if you're interested in using it or if you want to collaborate. Code :Ref : nature.com/articles/s4159… data.mendeley.com/datasets/78ng4…

🎓 Join us for our Spring School in Quantitative Biology: "Cell Dynamics in Developmental Systems" ✨ Featuring renowned speakers and hands-on workshops! Learn more and register: www.edu.bio.ens.psl.eu/spip.php?art...

Welcome to the official Bluesky page of the Institut Pasteur! 🔬 Explore with us the frontiers of biomedical research 🧪 Follow us to uncover groundbreaking discoveries 💡 Share knowledge for global health 🌍 Join a community passionate about progress and open science.

Our excellent colleagues in @france-bioimaging.bsky.social are back with the new yearly FBI data challenge. This year it focuses on **fusion algorithms for multi-view images in 3D** that are deep-learning based. You have an idea on how to improve fusion of multi-view, lightsheet data? Register!

If you are interested in all things stem cells and development, then this is the conference for you 🤩 We have put together an exciting and diverse list of speakers - and you can be a part of it too! 😉 Loking forward hearing from young scientists - for oral presentations register by tomorrow! 🤓 👻

2025 is now well underway and we are happy to announce that ZIDAS is coming to Basel this year ! 2025.zidas.org

#MiFoBio2025 the autumn microscopy school by @gdrimabio.bsky.social will take place from 10th to 16th October 2025. The call for workshops to share pratical knowledges is open till 31/01 ateliers-mifobio.fr We'll bring stuff as usual, stay tuned ! @cnrsingenierie.bsky.social

In many cases, you may be able to get Copilot for free, either as a teacher or open source maintainer: docs.github.com/en/copilot/m...

Finally had a bit of time to play with multi-GPU deconvolution. Using @truenorth-ia.bsky.social and @haesleinhuepf.bsky.social previous work. Here it is in action in #BigDataViewer using async and lazy processing. Look at the two poor laptop GPUs going as fast as they can:

The Wellcome Photography Prize is back📢 #WPP25 invites entries from #microscopy to medical imaging. Prizes include up to £10,000, your work shown in a public exhibition and global media coverage. 👉Find out more at wellcome.org/photoprize Enter by 14 January 2025 for free!

Looking for a job still connected to acamedia and research ? Do you like interacting with a lot of people, outreach activity, organising scientific events ? Do you have good writing and organisation skills ? We may have a job for you👇 (permanent position) emploi.pasteur.fr/offre-de-emp... 🙏RT