Here we go again! 🤣

Segmenting individual cells in microscopy is much easier these days thanks to foundation models. Can we use these models for other tasks, such as cell classification? We investigate in our latest work, finding big improvements for object and pixel classification compared to classical approaches.

Hi all, Felt like a good opportunity to share an update after a long time! 🥳 #MIDL2026 just got wrapped up, with another exciting conference in Taiwan! (1/7)

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.

MPI for Multidisciplinary Sciences@mpi-nat.bsky.social · 4w ago

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)

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! 🍻🏝️🚀

Johannes Soltwedel@jo-soltwedel.bsky.social · last mo.

🚨Just out: #NGFF specification 0.6 (rc0): ngff.openmicroscopy.org/specificatio... What's new, what's what? Short thread 🧵👇

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

BioImage Computing

a truly interdisciplinary workshop

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.

Anwai Archit@anwaiarchit.bsky.social · last yr.

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!🧵

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)

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression

Nature Methods - Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in...

rdcu.be

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...

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression - Nature Methods

Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in both iST and live imag...

nature.com

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

Sebastian von Haaren@haarensv.bsky.social · last yr.

A small but special moment: My illustration is on the cover of the March issue of Nature Methods! A huge hug to @anwaiarchit.bsky.social and @cppape.bsky.social — it was a pleasure to work alongside you on this! www.nature.com/nmeth/volume...

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

EMBL Events@events.embl.org · last yr.

That's a wrap for #EMBLDeepLearning 🌠 A huge thank you to everyone who attended this advanced course 🙌 We hope the hands-on element of applying deep learning-based methods to your own data and image analysis problems was useful. Until next time!

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...

Uni Göttingen@uni-goettingen.de · last yr.

Automatic cell analysis using #AI Researchers retrained existing AI-based software on over 17,000 microscopy images with over 2 million structures to develop this new model - Segment Anything for Microscopy: www.uni-goettingen.de/en/3240.html... #NatureMethods research: doi.org/10.1038/s415...