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Constantin Pape

@cppape.bsky.social

Group leader @ Uni Göttingen for Computational Cell Analytics and @ MPINAT for Machine Intelligence in the Life Sciences. AI for biology and medicine with a focus on microscopy. https://user.informatik.uni-goettingen.de/~pape41/

141 Posts1673 Follower399 Folgt
John Bogovic@bogovicj.bsky.social · 3w ago

It's an exciting day for #Fiji users! Now read and write @zarr.dev v3 and #OMEZarr v0.5. Don't want a million tiny files in your #zarr? Shard that sucker! Read the details here forum.image.sc/t/fiji-can-r...

Fiji can read and write Zarr3 & OME-Zarr v0.5 (new N5 release!)

Updating your Fiji-Latest installation will give you the newest versions of the N5 library, enabling OME-Zarr v0.5 / Zarr v3 support with sharding! What's new? Reading zarr 3 datasets (sharded and u...

forum.image.sc

Constantin Pape@cppape.bsky.social · 3w ago

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.

Evaluation of different methods for pixel classification (top) and object classification (bottom) on the LIVECell dataset. Dark green bars show the F1-Score, which measures the classification / segmentation quality (higher is better), light green bars show the runtimes. Five different settings are compared for each task: Ilastik features + random forest (RF), microSAM embeddings + RF, SAM2 embeddings + RF, and uSAM, SAM2 + attentive probing (DeAP and ObAP). microSAM feature perform best for RF based methods, attentive probing outperforms RF based approaches, but at a much higher runtime.
Constantin Pape@cppape.bsky.social · 3w ago

Initial thoughts on 5.6-Sol: actually makes codex useful (was not helpful for C++ with 5.5 for me at all). Still unhinged compared to Claude (large performance critical refactors without careful benchmarking when not being explicitly told -> lead to major regressions, Opus would not do this)

Constantin Pape@cppape.bsky.social · 4w ago

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)

Portrait picture of Contantin Pape wearing a blue tshirt leaning against a sign of MPI-NAT.
Josh Moore@joshmoore.bsky.social · last mo.

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 🧵👇

Constantin Pape@cppape.bsky.social · last mo.

Want to learn about the latest trends and developments in bioimage analysis? Join us for the GLOBIAS workshop in Dortmund this November! I will be hosting a session on foundation models / AI. www.globias.org/activities/g...

GloBIAS2026 Workshop Dortmund

GloBIAS 2026 Bioimage Analysts' Workshop Registration is open! Register with this link! 10-13 November, 2026 - Tuesday to Friday Leibniz-Institut für Analytische Wissenschaften – ISAS – e. V. (https...

globias.org

Constantin Pape@cppape.bsky.social · last mo.

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.

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Virginie Uhlmann@virginieuhlmann.bsky.social · 2mo ago

📢📢 We are hiring a Bioimage Analyst at the BioVisionCenter! 📢📢 Join our collaboration with the Flow Cytometry Facility and contribute back to the international efforts on open standards for bioimaging data! More information here, reach out if you have any question: jobs.uzh.ch/job-vacancie...

UZH: Bioimage Analyst

The University of Zurich is the largest university in Switzerland and one of the most prominent in Europe. For research purposes the Biovision Center and Flow Cytometry Facility offer services to supp...

jobs.uzh.ch

Jakob Troidl@jakobtroidl.bsky.social · 2mo ago

📢 We're recruiting AI Scientists at HHMI Janelia. I'm biased, but these are exceptional opportunities. You'd join as an independent scientist with access to excellent computational infrastructure, some of the best biological data in the world, and a vibrant collaborative environment.

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European Conference on Computer Vision #ECCV2026@eccv.bsky.social · 3mo ago

We are still a bit more than a day away from the deadline to submit your final #ECCV2026 recommendation. Make sure to discuss your papers with your fellow reviewers before submitting your recommendations!

European Conference on Computer Vision #ECCV2026@eccv.bsky.social · 3mo ago

The #ECCV2026 reviewer discussion period has started! Reviewers should carefully read the authors’ rebuttal, consider the other reviews, and actively participate in the discussion BEFORE finalizing their reviews.

Constantin Pape@cppape.bsky.social · 3mo ago

Claude code is so funny. Ask it to generate optimized watershed code: Yes sir! Here's the validated optimized C++ code 10x faster than skimage. Ask it to generate meaningful seeds for the example image: undersegments everything and confidently declares that this are now great parameters.

Simon F. Nørrelykke@simonfn.bsky.social · 3mo ago

The SwissBIAS Annual Meeting is taking place on June 3rd in Bern. Registration deadline: Friday, May 15th, so make sure to secure your spot now! We look forward to seeing you all there for a fantastic day of science, networking, and inspiration. @swissbias.bsky.social tinyurl.com/SwissBIAS2026

SwissBIAS annual meeting 2026

It is the time of the year to make veterans meet new members, discuss to foster feedback on existing activities and promote new initiatives.

eventbrite.com

Constantin Pape@cppape.bsky.social · 3mo ago

After reviewing a couple of agentic tools for microscopy segmentation: I think this is a bad idea. Setting up these systems is so complicated that it negates any potential productivity gains.

Peter O'Toole@yorkbioimaging.bsky.social · 3mo ago

Not just for microscopists, but relevant to all technical specialists. Making the invisible visible: A global examination of careers and recognition for Imaging Scientists in core facilities - Thompson - Journal of Microscopy - Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...

Making the invisible visible: A global examination of careers and recognition for Imaging Scientists in core facilities

Modern life-science research relies heavily on advanced imaging technologies, from microscopes that reveal the structure of cells to imaging systems used in biomedical research. These instruments are...

onlinelibrary.wiley.com