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Constantin Pape

@cppape

Group leader @ Uni Goettingen applying Image Analysis and Deep Learning to large microscopy data in biology.
Also @cppape.bsky.social
Goettingen user.informatik.uni-goettingen.de/~pape41/ Joined December 2015
556 Following 1.3K Followers 1K Posts

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Constantin Pape @cppape
How can we use foundation models such as (micro)SAM to improve electron microscopy segmentation? Check out our preprint! We found substantial improvements for nucleus, mito, and neurite-segmentation using initialization and semi-supervised learning with foundation models.
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Constantin Pape @cppape
Segmenting cells in microscopy is much easier these days thanks to foundation models. Can we use these models for other tasks, e.g. cell classification? See our latest work! We find big improvements for object and pixel classification compared to classical approaches.
valuation 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
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. globias.org/activities/glo…
www.globias.org GloBIAS2026 Workshop Dortmund GloBIAS 2026 Bioimage Analysts' Workshop Registration is open! Register with this link Registration is closed: We have filled all seats available. A waiting list has been created and can be accessed...