AI meets cutting-edge microscopy: Welcome Constantin Pape, head of our new Machine Intelligence in the Life Sciences group! 👋 🔬 His team develops AI methods to analyze high-resolution microscopy & cryo-EM data to better understand the function of proteins and protein complexes inside cells. (1/3)

Sharing a big update: I started a group at the MPINAT in Göttingen! We will develop AI for analyzing how proteins interact in the cellular environment based on cutting edge imaging. This appointment is in parallel to the university, where I will retain my current group.

Johannes joined @gerbi-gmb.de with a clear first major task: help lead the completion of #NGFF RFC-5. Today, just before heading off on a well-earned holiday and just shy of his one-year anniversary, 0.6 has a release candidate. Kudos, @jo-soltwedel.bsky.social! 🍻🏝️🚀

How can we use foundation models such as (micro)SAM to improve electron microscopy segmentation? Check out our new preprint where we found substantial improvements for nucleus, mito, and neurite-segmentation based on initialization and semi-supervised learning with foundation models.

@jo-soltwedel.bsky.social presenting about how important FAIR data management is for efficiently leveraging AI in a trustworthy manner. Small differences in underlying data annotation and metadata can effect AI-based analysis output a lot. #ELMI2026 @gerbi-gmb.de #OME-Zarr

Hello #world, meet 1,000× Expansion Microscopy. A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy. Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us. Story: www.biorxiv.org/content/10.6...

🔬 One more year! BioImage Computing has been accepted to @eccv.bsky.social 🎉 Show us your work at the intersection of computer vision, ML & biology! Check out our speaker lineup: @arratemunoz.bsky.social, @jakobtroidl.bsky.social & Juliette Griffié 👏 ⏳ Deadline: 13 July ℹ️ www.bioimagecomputing.com

At MIDL YRB, we love organizing cool online events that bring young minds in the bio(medical) imaging community together. This time, we’re excited to have @virginieuhlmann.bsky.social share her story! 🥳 Join us tomorrow, 20 May! www.midl.io/yr-storytime @midl-conference.bsky.social

Looking for a PhD position at the intersection of AI, imaging, and gene therapy? Apply for this position in my lab: tinyurl.com/2a2v6tvx Part of sfb1690.uni-goettingen.de to study hearing, vision, and more. Plus, you can create pretty pictures as the one below :).

Preprint alert! CochleaNet, our framework for analyzing light-sheet data of the cochlea. It consists of three networks to segment spiral ganglion neurons, inner hair cells, and to detect synapses. See rendering of a full cochlea in the image, find the preprint at doi.org/10.1101/2025....

Don’t miss Elena’s (from @ilastik-team.bsky.social lab) brilliant work @ #ICCV2025 with @anwaiarchit.bsky.social & @cppape.bsky.social poster 292 @ 11:15AM 🔬They tackle segmentation of massive 3D microscopy images & show how BatchRenorm removes tiling artifacts boosting transferability and clarity🌺

Are you studying synapses in electron microscopy? Tired of annotating vesicles? We have the tool for you! SynapseNet implements automatic segmentation and analysis of vesicles and other synaptic structures and has now been published: www.molbiolcell.org/doi/full/10....

Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues. The paper: arxiv.org/abs/2503.19545 1/🧵

Data is the key to AI advances in biology and "Still, when it comes to data, nothing compares to the real thing." An important editorial in Nature methods with a nice little shout out to microSAM: www.nature.com/articles/s41...

Anwai represented the lab at MIDL very well! Read his thread for details on our two latest papers on foundation models for microscopy, histopathology and medical imaging.

We presented our latest work on "PathoSAM" and "Late PEFT" last week at #MIDL2025 (Salt Lake City)! The community is growing and MIDL is becoming the venue-to-go for high quality research discussion!🧵

Are you looking for an exciting position at the intersection of super-resolution microscopy and AI? Then check out the PhD and PostDoc position we offer for a joint project with the Group of Stephan Hell at MPI Göttingen. Please share with anyone interested, read on for links and details.

We released version 1.6 of micro_sam: - Improvements for automatic tracking. - A new experimental mode for object classification. - **New versions of the LM and EM models** The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.

Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com! Since the pre-print, we have added many features, notably native 3D detection! @maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social Paper: rdcu.be/epIB7 (1/N)

A nice advance for imaging-based spatially resolved transcriptomics from the Weigert and La Manno labs. Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. www.nature.com/articles/s41...

Announcing the new release v1.4.0 of microSAM. The main changes are: 1. Simplified installation on windows. 2. Preliminary support for automatic tracking. 3. Improved interface for model selection. Read on for a quick summary of the changes.

@anwaiarchit.bsky.social & @cppape.bsky.social demonstrating the power of micro-sam, the napari plugin for the microscopy segment anything model, in their awesome workshop at the #TiM2025 conference in Münsingen. 🔬🦠💻

Our March issue is now live! 🥳 nature.com/nmeth/volume... The cover represents the process of cell and organelle segmentation by Segment Anything for Microscopy. Paper here: nature.com/articles/s41... Cover by Sebastian von Haaren.

Another feather for Segment Anything for Microscopy. We made it to the cover for @naturemethods.bsky.social! And all thanks to our amazing @haarensv.bsky.social for this! <3

Automatische Zellanalyse mit #KI: Forschende trainierten eine bestehende, KI-basierte Software neu. Das Modell „Segment Anything for Microscopy“ kann Bilder von Geweben, Zellen und anderen Strukturen genau segmentieren: s.gwdg.de/HqkMz2; s.gwdg.de/iTejKW Forschungsteam mit bsky.app/profile/cppa...

It was soooo much fun to brainstorm solutions with everyone, together!❤️ #EMBLDeepLearning

Thank you @unigoettingen.bsky.social for the feature!😍 μsam got some super cool feature updates last week. Don't wait for the next release, go check us out now! github.com/computationa...

Because we have seen these improvements and due to popular demand, cc @ritastrack.bsky.social @jianxuchen.bsky.social, we have decided to start a call for community data submission to further improve our models: computational-cell-analytics.github.io/micro-sam/mi... . Looking forward to any feedback

Our next micro_sam release is here! We have a new model for light microscopy, that massively improves for automatic segmentation! See the qualitative and quantitative comparison in the images, v2 is our previous version, v3 is the new one.

Help improve MicroSAM!

Look at all of those #OMEZarrs! 🤩

I actually tested these two and also SamCell (recently on Biorxiv). Here's the quick and dirty results - might still be finetuned, and I might have not always picked the best settings.

Our first deposition of synaptic vesicles segmentations is now in the Cryo ET Portal! We segmented vesicles in over 50 tomograms to enable analysis of membrane proteins and more. cryoetdataportal.czscience.com/depositions/...

🎤 Another speaker joins #TiM2025! We’re thrilled to announce @ritastrack.bsky.social as a new speaker, delivering an exciting talk on Wednesday. Huge thanks to her for joining us! Stay tuned for more updates on our TiM page: bit.ly/3BPN9fB

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...

Cannot really emphasize how amazing this tool is! For me, it checks many important boxes: - feels intuitive - powerful - customizable - flexible Many congratulations to @anwaiarchit.bsky.social , @cppape.bsky.social and the whole team! Looking forward to play with it and push its limits! 😁💻

It is an honor to read these words from you, Rita. Read the beautiful summary by @ritastrack.bsky.social on μsam and CellPose3 in the 🧵!

A lot happening for microscopy segmentation. Thanks for highlighting our paper and CellPose 3, Rita!

Segment Anything for Microscopy (μSAM) is based on Segment Anything, the vision transformer model for image segmentation, and offers generalist models for light and electron microscopy segmentation tasks. www.nature.com/articles/s41...

One of our most used tools these days in the facility. Really fantastic work!

μsam is live in Nature Methods!🥳 Huge thanks to @cppape.bsky.social for being the absolute best PI, guiding me through every step in this journey, @ritastrack.bsky.social for amazing handling of our paper & all reviewers for helping us strengthen μsam. Go check our tool and paper right away!😉🧵

PathoSAM is our attempt to bridge the gap of a unified foundation model for interactive & automatic nuclei segmentation in histopathology. Not only that, we show how it can be extended for a different segmentation task! Here's a trailer to so much more what PathoSAM offers!🥳🧵

A question I get asked often: 1) How many images should I annotate for finetuning VFMs & 2) how much resources VFMs need for custom finetuning? Here's our attempt to answer them: Our novel efficient workflow enables you to harness the strengths of SAM with a few labeled images🧵

MedicoSAM is here! 🥳 Our vision foundation model shows promising results for interactive segmentation, for both 2d & 3d medical images, across several tasks and imaging modalities! Don't take my word for this, check us out & try to "segment anything" on medical images! 😉🧵

There was quite some interest in SynapseNet, our tool for synapse analysis in electron micrographs, since we announced it. If you want to use it yourself you can now find a video tutorial that shows how to use its napari plugin. youtu.be/7n8Oq1uAByE

Want to know how many vesicles there are in a mossy fibre synapse, without counting thousands of vesicles by hand in electron micrographs? Our new tool SynapseNet has you covered and is now available as a preprint www.biorxiv.org/content/10.1... . Read on for a short overview of our paper.

You can join @anwaiarchit.bsky.social and me for a workshop on #micro-sam at #TiM2025 !

The long-awaited #TiM2025 workshop list is here!🌟 From basic #microscopy to advanced techniques like lightsheet, FLIM, CLEM & more! Full list on our event page: bit.ly/3BPN9fB Stay tuned for workshop registration opening next year for registered participants! ⏳

The MIDL Young Researcher Board is happy to announce the next online event within its annual cycle: MIDL Winter Workshop 2025 (midl.io/winter-works...). Two workshops, specifically designed for young researchers at the time of the (academic) year where you need it the most!🧵

Our Virtual I2K Workshop for #micro_sam is on YouTube now! 🥳