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

For those who missed it: Elon Musk, the Royal Society, and me deevybee.blogspot.com/2024/11/why-...

This week, we're hosting the #OME_NGFF_Hackathon 2024 at the BioVisionCenter at the University of Zurich. We're bringing together 40 motivated researchers and specialist for #OMEZarr workflows, #OMEZarr Python tools & #OMEZarr Java tools. (1/3)