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Constantin Pape

@cppape.bsky.social
1.7K followers 400 following 144 posts

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. user.informatik.uni-goettingen.de/~…

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Reposted by Constantin Pape
Davi Bock @dddavi.bsky.social · 24/09/2026
Now I can say: last week we received Notice of Award from NSF on a Midscale Research Infrastructure Design proposal for a National Connectomics and Ultrastructure Volume Observatory (NCUVO) www.uvm.edu/uvmnews/news...
uvm.edu
UVM Launches $19 Million National Observatory to Unlock…
| The University of Vermont
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Constantin Pape @cppape.bsky.social · 28/08/2026
I feel like giving up on reviewing for most biomedical imaging focused CS journals. Over the last year almost all papers I got where basically AI generated (probably the underlying experiments are real, but the descriptions seemed to be filtered through several AI rewrites)
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John Bogovic @bogovicj.bsky.social · 17/07/2026
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...
forum.image.sc
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...
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Constantin Pape @cppape.bsky.social · 16/07/2026
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.
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Constantin Pape @cppape.bsky.social · 12/07/2026
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)
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Anwai Archit @anwaiarchit.bsky.social · 12/07/2026
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)
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Constantin Pape @cppape.bsky.social · 09/07/2026
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.
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Constantin Pape @cppape.bsky.social · 05/07/2026
Burned 16% of my Fable usage on prompts that get immediately downgraded to Opus 4.8 😅
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Johannes Soltwedel @jo-soltwedel.bsky.social · 03/07/2026
🚨Just out: #NGFF specification 0.6 (rc0): ngff.openmicroscopy.org/specificatio... What's new, what's what? Short thread 🧵👇
ngff.openmicroscopy.org
Version 0.6rc0 — NGFF documentation
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Josh Moore @joshmoore.bsky.social · 03/07/2026
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! 🍻🏝️🚀
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Constantin Pape @cppape.bsky.social · 30/06/2026
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...
globias.org
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...
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Constantin Pape @cppape.bsky.social · 23/06/2026
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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Constantin Pape @cppape.bsky.social · 13/06/2026
Working on library spec stuff with Opus: this model feels so dumb now. I want Fable back! 😢
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Constantin Pape @cppape.bsky.social · 12/06/2026
Fable 5: amazing model. Safeguards: completely broken and make it unusable for many applications (bio-related and deep learning research, even unrelated to "frontier AI").
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Wei-Chung Allen Lee @darbly.bsky.social · 09/06/2026
Now published - the #BANC! A full central nervous system (CNS) connectome of a limbed animal at single-synapse resolution, enabling us to follow sensory-motor arcs and understand how the CNS controls the body. rdcu.be/fncjS. #neuroscience. Video by @quorumetrix.bsky.social 1/18
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CCP-volumeEM @ccp-volumeem.bsky.social · 02/06/2026
Now available on our YouTube channel: Chris Barnes’ CCP-volumeEM Show & Tell webinar, “OME-Zarr: A Next Generation File Format for FAIR Bioimaging Data”. Catch up here: youtu.be/HsqH6RAcJps?...
youtu.be
OME-Zarr: A next generation file format for FAIR bioimaging data with Chris Barnes
YouTube video by CCP-volumeEM
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Reposted by Constantin Pape
Ali Shaib @alishaib.bsky.social · 01/06/2026
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...
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Virginie Uhlmann @virginieuhlmann.bsky.social · 01/06/2026
📢📢 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...
jobs.uzh.ch
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...
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Martin Weigert @maweigert.bsky.social · 30/05/2026
Join us again for the Bioimage Computing workshop at ECCV 2026! Paper deadline July 13th 🔥
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Jakob Troidl @jakobtroidl.bsky.social · 27/05/2026
📢 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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Anna Foix @afoix.bsky.social · 26/05/2026
🔬 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
bioimagecomputing.com
BioImage Computing
a truly interdisciplinary workshop
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European Conference on Computer Vision #ECCV2026 @eccv.bsky.social · 20/05/2026
The deadline for submitting #ECCV2026 final reviews is TODAY! Please act responsibly and finalize your discussions and reviews.
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Anwai Archit @anwaiarchit.bsky.social · 19/05/2026
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
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European Conference on Computer Vision #ECCV2026 @eccv.bsky.social · 19/05/2026
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!
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Constantin Pape @cppape.bsky.social · 18/05/2026
Nice to see my name on that list :)
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Constantin Pape @cppape.bsky.social · 18/05/2026
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.
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Simon F. Nørrelykke @simonfn.bsky.social · 06/05/2026
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
eventbrite.com
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.
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Constantin Pape @cppape.bsky.social · 03/05/2026
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.
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Peter O'Toole @yorkbioimaging.bsky.social · 24/04/2026
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/...
onlinelibrary.wiley.com
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...
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Utz Ermel @uermel.bsky.social · 20/04/2026
Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines. 🧵👇 doi.org/10.1002/pro.70578
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Stefan Terjung @stefanterjung.bsky.social · 14/04/2026
We are looking for an experienced light microscopy specialist, motivated to support our users in the Advanced Light Microscopy Facility at EMBL Heidelberg. embl.wd103.myworkdayjobs.com/en-US/EMBL/j... -closing date 11 May 2026 @eurobioimaging.bsky.social @globalbioimaging.bsky.social
embl.wd103.myworkdayjobs.com
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Florian Jug @florianjug.bsky.social · 30/03/2026
🚨Job Alert -- again!🚨 You are into disease risk prediction based on images or other data modalities? This is for you! 🫵 careers.humantechnopole.it/job/Postdoc-... Part of our Scientific AI Flagship @humantechnopole.bsky.social and part of our mission to benefit society via biomedical #AI solutions.
careers.humantechnopole.it
Postdoc on Multimodal AI for Disease Risk Prediction
Postdoc on Multimodal AI for Disease Risk Prediction
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Image Cooperative @image.coop · 16/03/2026
Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...
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napari @napari.org · 11/03/2026
🔬 Registration is open for our pilot Introduction to napari Workshop! napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast. #napari #Python #ImageAnalysis #DataScience #OpenSource
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Constantin Pape @cppape.bsky.social · 05/03/2026
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 :).
A cochlea imaged in light-sheet microscopy (right) with staining for spiral ganglion neurons (red) and inner hair cells (blue). You will develop AI-based methods to analyze these structures, for example via segmentation of the individual cells (right) that will support gene therapy development for hearing loss and a better overall understanding of the anatomy of hearing.
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Lucien Hinderling @lhinderling.bsky.social · 03/03/2026
PAPER OUT ✨ How can we make smart microscopy more interoperable? What are the technical and cultural challenges? 30+ people from academia and industry propose a roadmap: doi.org/10.1515/mim-... Also a review of applications and repo of implementations. Join the discussion! smartmicroscopy.github.io
Screenshot of the abstract:
Smart microscopy is transforming life sciences by automating experimental imaging workflows and enabling real-time adaptation based on feedback from images and other data streams. This shift increases throughput, improves reproducibility, and expands the functional capabilities of microscopes. However, the current landscape is highly fragmented. Academic researchers often develop custom solutions for specific scientific needs, while industry offerings are typically proprietary and tied to specific hardware. This diversity, while fostering innovation, also creates major challenges in interoperability, reproducibility, and standardization, which slows progress and adaption. This article presents a collaborative effort between academic and industry leaders to survey the current state of smart microscopy, highlight representative implementations, and identify common technical and organizational barriers. We propose a framework for greater interoperability based on shared standards, modular software design, and community-driven development. Our goal is to support collaboration across the field and lay the groundwork for a more connected, reusable, and accessible smart microscopy ecosystem. We conclude with a call to action for researchers, hardware developers, and institutions to join in building an open, interoperable foundation that will unlock the full potential of smart microscopy in life science research.Screenshot of Figure 5: Interoperable smart microscopy ecosystem. Concept of a modular architecture for smart microscopy, where standardized experiment descriptions (e.g. useq-schema) and open data formats (e.g. OME-Zarr) allow integration of diverse microscopes, analysis tools, and user interfaces. Core components such as segmentation [76], [77], tracking [79], [80], and experiment logic are decoupled from specific hardware, enabling reuse across platforms. The system supports multiple input modalities (code, GUI, or natural language) and can be extended with additional devices like fluidics or environmental control modules. This structure enables flexible, feedback-driven acquisition strategies and cross-platform reproducibility.Screenshot of figure 4: Strategies for hardware abstraction that allow smart microscopy workflows to run across different microscope systems, illustrated with example implementations collected on the SMWG website. (A) Software communication layers: Image analysis and experiment logic are implemented in a platform-independent manner, while platform-specific adaptors control acquisition through proprietary microscope software via macros, APIs, or other interfaces. Custom GUIs allow users to configure analysis, while the vendor-provided software manages hardware and acquisition settings. By developing additional adaptors, these workflows can be extended to support microscope systems from other vendors. Example implementation: AutoMicTools , Supplementary Information S3. (B) Device-level standardization (e.g. μManager-based workflows) bypasses proprietary GUIs and provides a unified API for direct device control across manufacturers. This API abstracts vendor-specific differences, enabling consistent control of a growing collection of supported hardware. Example implementation: UU_smart_microscopy , Supplementary Information S2. (C) Event-based standardization decouples experimental design from hardware by describing acquisition events (e.g. acquire frame at x, y, t with channel c) in a structured format (e.g. useq-schema). Control software interprets these definitions and translates them into device-specific commands, enabling the use of vendor-specific features and optimizations during execution. Example implementation: rtm-pymmcore, Supplementary Information S1.
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Rob Patro @robp.bsky.social · 04/03/2026
Dear @anthropic.com please consider extending your Claude Max subscriptions to open science software devs! Our repos may not have as many stars as those of some of our OSS peers, but we develop critical infrastructure in focused areas, and might even benefit more from what Claude Max offers!
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Constantin Pape @cppape.bsky.social · 02/03/2026
Very nice work!
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Stephan Saalfeld @herrsaalfeld.bsky.social · 26/02/2026
Join us in building foundational datasets and models for microscopy with @jakobtroidl.bsky.social and many others AI Engineer Pre-Training: lnkd.in/eyEEV5nm AI Engineer Post-Training: lnkd.in/eShVQ3y9 Data Engineer Data: lnkd.in/eCvm58xH Data Engineer Pipelines: lnkd.in/ec6qGJkX ai.hhmi.org
ai.hhmi.org
Accelerating Innovation in Biology
HHMI’s $500 million over the next 10 years will support AI-driven projects and embed AI systems throughout the scientific process in labs across HHMI.
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Jean-Yves Tinevez @jytinevez.bsky.social · 24/02/2026
One week left to register to the Bioimage Analysis with AI course in Pasteur! This June, 1 - 5. I give a bit more details in the thread below 👇
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Nicolas Chiaruttini @nkiaru.bsky.social · 21/02/2026
Very informative: ome.github.io/ome-ngff-too...
ome.github.io
ome-ngff-tools
Document available viewers and other tools for the OME-NGFF image format
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Janelia Conferences @janeliaconf.bsky.social · 18/02/2026
📢 Applications are open! This meeting brings together scientists using data-driven #AI to analyze + model neural circuits and uncover how the brain performs complex computations. 🧠 Apply by May 28 ➡️ janelia.news/NAI26 @computingnature.bsky.social @sinzlab.bsky.social @srinituraga.bsky.social
janelia.news
Data-Driven AI for Neuroscience
Organizers Carsen Stringer, HHMI/Janelia Research Campus Srini Turaga, HHMI/Janelia Research Campus Atika Syeda, HHMI/Janelia Research Campus Fabian Sinz, University of Göttingen Alice Wang,
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Fabian Sinz @sinzlab.bsky.social · 18/02/2026
The Campus Institute Data Science (CIDAS) at university Göttingen has an open all for CIDAS fellows: www.uni-goettingen.de/de/694026.html You can apply for up to 85k€ to kick-start your own independent career at @uni-goettingen.de .
uni-goettingen.de
CIDAS Fellowship - Georg-August-Universität Göttingen
Webseiten der Georg-August-Universität Göttingen
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Talley Lambert @talley.codes · 16/02/2026
Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package: - fully bootstrapped Java setup (just pip install) - lazy, repeatably-indexable Array object - fully spec-compliant OME-Zarr group obj. - xarray/dask exports github.com/imaging-form... v0.0.rc1 on PyPI
github.com
GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API
Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile
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Johannes Soltwedel @jo-soltwedel.bsky.social · 12/02/2026
I'll never get tired of lazily browsing elastix-coregistered #WSI data in @napari.org using the upcoming @openmicroscopy.org ome-zarr @zarr.dev format version that allows to specify and read transformations directly from the image data itself. Data source: rodare.hzdr.de/record/3131
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Juan Nunez-Iglesias @jni.fosstodon.org.ap.brid.gy · 11/02/2026
smart microscopy postdoc position in Montpellier, France. Could definitely do worse. With @glyg forum.image.sc/t/up-to-4-year-postd… #FOSS #Microscopy #GetFediHired
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Constantin Pape @cppape.bsky.social · 05/02/2026
Interested in applying for an ERC, Emmy Noether, or local AI research group this year? Join our info call! I will also be there ;).
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Fabian Sinz @sinzlab.bsky.social · 04/02/2026
Early career researcher: Are you thinking about writing an ERC , Emmy Noether Proposal, or Lower Saxony AI Group application, and are you interested to work with us at @uni-goettingen.de and @goettingen-campus.de
uni-goettingen.de
Information Event on Funding Programs - Georg-August-University Göttingen
Website of the Georg-August-University Göttingen
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Luca Marconato @lucamarconato.bsky.social · 02/02/2026
We are hiring a Research Software Engineer to enhance and maintain the SpatialData framework. We will work together with colleagues at EMBL, DKFZ, GSK, and across the scverse community. 🔗 Deadline: 15/02/2026 embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
embl.wd103.myworkdayjobs.com
Research Software Engineer - Spatial-omics
The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...
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Dave Barry @david-j-barry.bsky.social · 31/01/2026
AMAZING JOB OPPORTUNITY ALERT!!! @calm-stp.bsky.social is hiring a Data & Systems Steward! 🧬 🔹Manage #bioimage data & #OMERO admin 🔹Automate via #Python/#Bash 🔹Support #FAIR principles 🔹Work closely with @crick-ia-team.bsky.social ⏰ Deadline: 08 Feb 2026 Apply: www.crick.ac.uk/careers-stud...
https://doi.org/10.5281/zenodo.14762435
https://bsky.app/profile/falk-illustrations.de
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