Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating). A brief 🧵 (carried over from the old place)

🚨 𝐀𝐈 𝐦𝐞𝐞𝐭𝐬 𝐓𝐁 𝐝𝐫𝐮𝐠 𝐝𝐢𝐬𝐜𝐨𝐯𝐞𝐫𝐲! Imaging 𝐶. 𝑔𝑙𝑢𝑡𝑎𝑚𝑖𝑐𝑢𝑚 (a model for 𝑀. 𝑡𝑢𝑏𝑒𝑟𝑐𝑢𝑙𝑜𝑠𝑖𝑠) + deep learning reveals known, unseen, and novel antibiotic modes of action from images alone, a leap for TB drug discovery. ✍️ @awehenkel.bsky.social & coll. 📖 shorturl.at/9QPDy #Tuberculosis #MicroSky

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 👇

Very excited to be advertising this project with the excellent cosupervision of Peter Mergaert through @i2bcparissaclay.bsky.social and @uniexecec.bsky.social. This position is open to international applicants and will involve stints in both Penryn UK and Paris France. Please share! Apply: adum.fr

Our preprint outlining a deep learning-based phenotypic screening approach for the discovery of new TB drugs is out on bioRxiv now 💊🦠 🔗 doi.org/10.64898/202... Thank you @awehenkel.bsky.social @chzimmer.bsky.social @spetrella.bsky.social @curieuseny.bsky.social and everyone else not on bsky (yet)🙏

"In repeating that colleges have 'gone soft,' pundits are, in some sense, telling universities what they want to hear. Schools would much rather wring their hands over vague cultural 'softness' than admit the obvious: that their revenue-maximizing logic is actively undermining educational quality."

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...

Two postdoc positions opened in my team @pasteur.fr in Paris on the development of machine learning methods for single-cell multi-omics spatiotemporal data. See the announcement for all details emploi.cnrs.fr/Offres/CDD/U...

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-...

We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data. 1/14 🧵

A great plugin prototype to run Fractal tasks interactively in napari: Making interoperable workflow tasks accessible directly in a viewer (8/14 🧵)

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-...

In vivo antimicrobial activity of engineered mesoporous silica nanoparticles targeting intracellular #mycobacteria (doxycycline-loaded nanoparticles, zebrafish model of Mycobacterium marinum #infection) @lkremer1.bsky.social#mycobacteria#infection#DrugDevelopment

** Now seeking postdocs ** Join our interdisciplinary and transnational team in Würzburg (Germany) or Paris (France) to drive projects in translational biology and antibiotic drug discovery. Backgrounds in computational biology, AI, physics, or microbiology are all welcome. Please spread the word.

🚨 1 week left to apply for the Pasteur-Paris University International PhD Program (PPU)! Join an international community of scientists at the Institut Pasteur 🌍 Dedicated support, mentorship & world-class labs included. 📅Deadline: Oct 20, 2025 🎓Program start: October 2026 👉 Apply: bit.ly/CallPPU

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...

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)

We're excited to announce the first of two prize winners in our #biologists100 #sustainable #travel blog competition. Read Lea’s experience of travelling via four trains from France to Liverpool. www.biologists.com/stories/my-j... Stay tuned for next week’s post from winner two. #Sustainability

Beautiful work from @danielkrentzel.bsky.social here! Correlative EM-LM made easy! Really grateful to be part of the team.

CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data. www.nature.com/articles/s41...

Awesome to see this out. Thank you for bringing us in the journey @em-stp.bsky.social and @martinjones.bsky.social. Keep rocking @danielkrentzel.bsky.social!

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). 👇

#preprint: We optimised the preparation of tissues for #X-ray phase contrast imaging. Drying tissue samples (instead of embedding them) brings more signal in #X-ray phase contrast images. The process largely preserves #ultrastructure. @safekhan.bsky.social @andreas-t-schaefer.bsky.social

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9) www.nature.com/articles/s41...

🎓 Applications for Institut Pasteur's PhD programs open Sept 1-Oct 20, 2025 for October 2026 entry. Apply to up to 4 projects across 6 programs: PPU, PPU-IMAGINE @institutimagine.bsky.social, [email protected], PPU-EID @upcite.bsky.social & more 🧬 Register now ✍️ www.pasteur.fr/en/education...

🚨Join us! We're soon opening 3 postdoctoral positions in #AIDrivenBiology. Seeking biologists (especially microbiology and infection biology), computer scientists, and microscopy developers. Ideal candidates are those eager to use or develop next-gen tech for cell biology. Get in touch (DM/email)

Do you like developing new AI vision methods for microscopy image analysis? You love theory & implementation? 1 week left to apply for a fully funded PhD position in our lab in Dresden 🇩🇪! Topics: object detection/tracking, multimodal models & more. DM/email for details! #PhD #AcademicJobs #GPUsgoBrr

The effector caspases drive cell death, but their activation can often be survived, so how do cells make this decision? Our new preprint from @levayerr.bsky.social shows that instantaneous caspase activity is important, but past activation has a key role to play! www.biorxiv.org/content/10.1...

Many cells during development are exposed to caspase activation and yet survive. Why some die and not others ? We found out that the memory of previous caspase activation bias significantly later death comitment and bias death distribution and single cell decision www.biorxiv.org/content/10.1...

Researchers paid $9 billion over 5 years for their findings to be freely accessible. This is based on a study of the global expenditure on article processing charges (APCs) paid to six publishers for open access between 2019 and 2023. arxiv.org/abs/2407.16551

I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!

Day 4, with @jytinevez.bsky.social and tracking! #neubiaspasteur2025

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

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

Our work “AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI” is finally out in @biorxivpreprint.bsky.social !!! 😍❤️ biorxiv.org/content/10.1... @scilifelab.se , @crick.ac.uk . More about it in the thread #AI4CellFate (1/n)⬇️

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...

Day 1 of #neubiaspasteur2025 Image Analysis course in the Analysts track: @danielkrentzel.bsky.social teaches the creation of @napari.org plugins. And on day #1, the students have group projects! 😲 But things are going great as you can judge

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

🚀 We just released a major Fractal update! More flexible workflows, dynamic monitoring, and a new history system for better traceability – built to handle Terabytes of high-dimensional microscopy data in #OME-Zarr. Full announcement post here: fractal-analytics-platform.github.io/news/2025-04...

VP-CLEM-Kit: An accessible pipeline for visual proteomics using super resolution volume correlative light and electron microscopy (SR-vCLEM) https://www.biorxiv.org/content/10.1101/2025.04.08.647770v1

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 -

🚨Alô #bsky and #microscopy community, we got #ReScale4DL, our new work in @aiopticalbiolab.bsky.social , out today!😍 🥳 We present the #imageresolutionparadox phenomenon for #DL-results 🤓 👇Check it out!!

AI4AMR is a collaboration between the labs of Ivo Boneca (microbiology, Institut Pasteur, Paris), Mark Brönstrup (chemistry, Helmholtz Center for Infection Research, Braunschweig) & Christophe Zimmer (computational biology, Univ. of Würzburg and Institut Pasteur).

First preprint from my PhD is now online! We show that deep learning can recognise modes of action of antibiotics directly from brightfield images of bacteria. 🦠

Deep learning recognises antibiotic modes of action from brightfield images https://www.biorxiv.org/content/10.1101/2025.03.30.645928v1

Only five days remain to register!* Here is the tentative program: *: it is likely that there won't be a deadline extension.

The registration close Tuesday next week! research.pasteur.fr/en/course/ne...

[Event] Join the NEUBIAS BioImage Analysis Course!🖥️ 2 parallel tracks: ➡️Early career investigators – Master bioimage analysis tools ➡️Analysts – Master & deploy advanced tools, HPC 📅 May 12-16 📍 Institut Pasteur, Paris 🔗 Apply by March 31👉https://bit.ly/3DxvEBV

🚀 We’re very excited to share our latest preprint on OME-Zarr! 🚀 Our report on the 2024 OME-NGFF Workflows Hackathon is a deep dive into the status of OME-Zarr and the great work that happened last November at the BioVisionCenter in Zurich. 🔗 Read the preprint: osf.io/preprints/bi... 🧵 (1/15)

🎉CrAIC Digital Pathology Journal Club 📜 Talk: "Segmenting blood vessels in H&E stained whole slide images" 🎙️Speaker: Graham Ross, The Francis Crick Institute 📅 Date: 15:00 GMT 06/02 🌐 Details: craic-dpjc.github.io 📲 Zoom: crick.zoom.us/j/6280148436... #DigitalPathology #AI #Histology #Cancer