Tracking coordinated cellular dynamics directly from images -- New method paper by labmates @bgraedel.bsky.social & @macdobry.bsky.social ! Python package & @napari.org plugin, all the good stuff: Paper: doi.org/10.1242/jcs.... Code: github.com/pertzlab/arc... Plugin: github.com/pertzlab/arc...

For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing. I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow. jacobtomlinson.dev/posts/2025/p...

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 🧵

Community information is here napari.org/stable/commu...

Happy Halloween from the napari team!

It was a fantastic opportunity to finally meet the people behind this software that I have been using for years and is so important for my work! A big thank you to all core developers who were so welcoming, and patiently guided participants in their attempts to contribute back to napari!

This was a very interesting talk! If you work in a core facility you’ll find plenty of good ideas about organisation and/or be reassured that certain things, like planning workload, are difficult for everyone, even the best organized.

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...

napari 0.6.5 is out! 🚀 Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: https://napari.org/dev/release/release_0_6_5.html

BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...

📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social! Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬 📅 Applications open Oct 6 (deadline: ~Oct 27) 📍 San Sebastian, Spain. 👉 cvpd.github.io/post/2025-09...

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 working with OME-Zarrs in Switzerland? We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)

Come and work with us 5-year position available for a University Researcher in Bioimaging 1.11.2025-31.12.2030 abo.rekrytointi.com/paikat/index...

Post an image from your summer that confers peace

Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...

“New paper out 🎉 We built a system to automate optogenetic cell control across scales. For the demo, we made the cells spell my name — because if you can’t use science to feed your ego, what’s the point? 😎🧫✨”

A very good idea! I’m deeply skeptical current models can find “new physics” but this would be a good test. Surprised nobody has done this yet. Probably not in the interest of most model trainers to highlight their limits and dehype them. Clarification: I do think that LLMs can be very useful tools!

You thought the publication business had reached the bottom with predatory journals, insane publication fees, data harvesting etc? No, it can dig deeper 🎉! #justpreprint

"a fascinating case study on the limits of AI in biology and the harms of current publishing incentives" rachel.fast.ai/posts/2025-0...

New release: napari-omero 0.5.0 😀@openmicroscopy.org @napari.org thanks to some big contributions from @psobolewskiphd.bsky.social , @will-j-moore.bsky.social and of course @talley.codes. Some features in spotlight 👇 First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:

To look into: a Python alternative to ZEMAX... github.com/HarrisonKram...

And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵

CellPhePy is now available 🎉🎉🎉 in the journal of #microscopy. A python version for #CellPhe. See doi.org/10.1111/jmi.... Thanks @ukri.org and @wellcometrust.bsky.social for funding @globias.bsky.social @globalbioimaging.bsky.social @eurobioimaging.bsky.social @bioimaginguk.bsky.social

🚀 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)

PREPRINT OUT ✨ "hack" your microscope to work as a 3D printer! print micrometer sized features at cm scale. a method for easy and cheap microfabrication, with a focus on biological applications. THREAD ↓ www.biorxiv.org/content/10.1...

Announcing PathoSAM, our foundation model for nucleus segmentation in histopathology. PathoSAM supports interactive and automatic nucleus segmentation (instance and semantic). See segmentation on a WSI from openslide, check out arxiv.org/abs/2502.00408 or read on for details.

I recently visited TU Dresden for two guest lectures about Prompt Engineering, RAG, Agents and Multi-Modal #LLMs. thanks to Simon Razniewski @scadsai.bsky.social for having me! My slides are available #openaccess 💻🤖🔓 zenodo.org/records/1469...

Very useful thread on how to efficiently use LLMs to write. As usual, reality is not a binary choice between “let the model write your entire paper” and “never ever use a model”.

What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n www.biorxiv.org/content/10.1...

The Image & Optics Facility @ Institute of Science and Technology Austria is expanding it’s image analysis services and has a vacant position for a service oriented *Image Analysis Specialist* with a strong interest for data infrastructure organization🔬🧑‍💻📈 - sharing is much appreciated

Has AI really learnt "the language of life"? If we compare "sequence prediction" AI with actual research on genomic mechanisms, we get a sense of what "understanding" does and doesn't mean.

Interesting discussion and an important point as I think these two aspects are often conflated: scientists are not software engineers and are not supposed to create perfect code. But it should be usable! Packaging can be daunting, so ask a researcher software engineer at your university for help!

Really a no brainer. Another thing one can do: when asked to review a paper that is not pre-printed, tell editor you only review preprinted papers and suggest authors submit a preprint first.

Forget the click-baity title. This almost 4 hour long collection of short musical fragments with fun commentary is a wonderful guide through the last 400 years of Western music. Bet you'll discover something wonderful you hadn't known about. www.youtube.com/watch?v=qEzm...

After science, time for music! In honour of Beethoven's baptism day (it's unclear when exactly he was born) a short thread in the spirit of @loveinner.bsky.social of some of my favourite recordings (and I don't pretend to any absolute truth!)

For more details, check out the preprint www.biorxiv.org/content/10.1... - or ask anything here! (+here's a bonus movie that didn't quite make the cut) 🌀

I just made a long overdue update to microfilm guiwitz.github.io/microfilm now 0.3.0! Beyond adaptations to recent Python and Matplotlib, I added support for the great cmap library cmap-docs.readthedocs.io by @talleylambert.bsky.social for easy access to the best (and most psychedelic) colormaps!1/2

🚀 We're hiring! Join the German BioImaging Team as a Software Developer! 💻 Build scalable #bioimaging solutions 🌍 Collaborate globally 🎯 Contribute to open science through #OMEZarr @openmicroscopy.org Remote, full-time. Apply by 31 Jan 2025: bit.ly/3Zrd4SR

What an interesting article. I confess I would not have given the accurate « Crickian » definition of the Central Dogma myself. « The Central Dogma says, in simple terms, that reverse translation, from protein to nucleic acid, never occurs ».

thinking of calling this "The Illusion Illusion" (more examples below)

Do you want to learn light microscopy? The registration for the Pasteur course 'Principles and Applications of Fluorescence Microscopy' in March 2025 are open!! pasteur.fr/en/pafm 10 March – 21 March 2025 plz RT! #PAFM is back after a two-year break 🤩🌈🔬🪛 👇thread

So many interesting images in #microscopymonday and #fluorescencefriday. Often I think “would be a good demo data for this algorithm or that course” but data are not available. It would be cool is if people also shared the raw data! No need for perfection, a simple upload to Zenodo is already good!

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!

It looks like this platform might finally be the one to replace the other crazy place! Lots of new followers via starter packs so: I’m a physicist, turned biologist, turned bioimage analyst/software developer. I’ll mostly write about science, image analysis and sometimes about music! No politics!