🙌 Programme's out for the Image Data Community Days! Check out the amazing plenary sessions & workshops during our 5-day long online event! There's something for everyone - don't miss out. Registration is FREE & open to all⤵️ www.eurobioimaging.eu/events/image...

We’re looking for a new team member! 🚀 Only 3 more weeks to apply to the fantastic Vienna BioCenter PhD program

Excited to share my first PhD project: LabConstrictor 📒🐍 Have you ever created a Jupyter notebook with all your love 🫶, only for others to be unable to install it 🥲? LabConstrictor, comes to solve this! Check out how it works in the preprint 🔗 arxiv.org/abs/2603.107... or follow this thread ⬇️

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

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. 👇🎓

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... 👇🧵

🚨 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 👍

🚨 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:

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-...

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... ⬇️

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.