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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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Constantin Pape @cppape.bsky.social · 16/07/2026
We compare different foundation models (SAM and DINO variants) with classical features in ilastik and fully supervised learning. The FM features outperform classical approaches. Attentive probing yields better performance than RF, but is too slow for interactive use. See example results in the fig.
Results for object segmentation based on foundation model (FM) features with a random forest, compared with supervised learning baselines and classical features. Experiments over five different datasets covering cell classification in spatial proteomics  (CRC, HBM), high-content macroscopic imaging for animal phenotyping (Planri), nucleus classification in histopathology (PanNuke), and cell line classification in phase-contrast microscopy (LIVECell). The extra plot repots runtimes for model training and inference.
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Constantin Pape @cppape.bsky.social · 16/07/2026
We use embeddings from foundation models as features, either for a RF or different attentive probing variants. The features are averaged over masks for object classification. See the image for a method overview.
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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 · 05/07/2026
Burned 16% of my Fable usage on prompts that get immediately downgraded to Opus 4.8 😅
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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 · 18/05/2026
Sure, no more seeds on the boundaries left ...
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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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Constantin Pape @cppape.bsky.social · 18/11/2025
We comprehensively evaluate our method and then use it to analyze the morphlogy of intact mouse and gerbil cochleae, including SGN sub-types, and to validate (opto-)genetic therapies preclinically (see screenshot). CochleaNet is also applicable to lower-resolution data from commercial systems.
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Constantin Pape @cppape.bsky.social · 18/11/2025
Cochleae were cleared, stained and imaged with a high-resolution light-sheet microscope (recently published: doi.org/10.1038/s415...). After preprocessing,we segment and analyze the data with CochleaNet, using the three dedicated networks trained on newly annotated data.
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Constantin Pape @cppape.bsky.social · 18/11/2025
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....
Rendering of a full cochlea (left) with three stains (PV, VGlut3, CTBP2) shown in three different colors (red, blue, cyan). The whole cochlea is a spiral shaped structure, with spiral ganglion neurons (SGNs) in the inner helix, labeled by PV and inner hair cells (IHCs) in the outer helix, labeled by Vglur3. The figure also shows zoom ins. The right hand side shows segmentation results for SGNs, IHCs (represented by colored masks) and synapse detections (represented by colored dots).
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Constantin Pape @cppape.bsky.social · 11/11/2025
Hope my counter meme convinces you ;)
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Constantin Pape @cppape.bsky.social · 17/10/2025
The segmentation functionality and other analysis modes, for example for vesicle pool assignments and distance measurements as shown in the screenshot, are available in a napari plugin. Check out github.com/computationa... for details.
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Constantin Pape @cppape.bsky.social · 17/10/2025
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....
SynapseNet is a deep learning based software tool that automates the segmentation of vesicles, mitochondria, synaptic compartments, and the active zone. This is visualized in three panels. On the left, a section of an electron tomogram with a synaptic compartment densely filled with vesicles, which appear as round structures with dark boundary and light body in the image, is shwon. The top right panel shows the segmentation result of vesicles, visualized by masks with an individual color per vesicle and outlines for the segmented compartment (red) and active zone (blue). The bottom right panels shows a 3D rendering of the segmentation with vesicles shown as yellow spheres.
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Constantin Pape @cppape.bsky.social · 16/09/2025
I did not know Taylor Swift was moonlighting in soliciting contributions for fake journals!
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Constantin Pape @cppape.bsky.social · 16/06/2025
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.
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Constantin Pape @cppape.bsky.social · 18/05/2025
This is how well ChatGPT (o3) knows biology ;)
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Constantin Pape @cppape.bsky.social · 28/03/2025
3. The model selection now supports two additional models (Histopathology, Medical Imaging) and uses human readable names, see the screenshot below. For more on these models check out: computational-cell-analytics.github.io/micro-sam/mi...
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Constantin Pape @cppape.bsky.social · 28/03/2025
2. We added preliminary support for automatic tracking via trackastra, developed by @maweigert.bsky.social. See the video for an example result and check out computational-cell-analytics.github.io/micro-sam/mi... for details.
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Constantin Pape @cppape.bsky.social · 21/02/2025
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.
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Constantin Pape @cppape.bsky.social · 21/02/2025
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/...
Synaptic vesicles segmented with SynapseNet.
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Constantin Pape @cppape.bsky.social · 12/02/2025
Our models form the basis of micro_sam, our napari plugin for interactive and automatic segmentation. It can segment data in 2D, 3D and across time. You can find all the details at github.com/computationa...
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Constantin Pape @cppape.bsky.social · 12/02/2025
To achieve these improvements, we finetune SAM on a large LM dataset (ca. 50k images, 1.2M annotated cells) and on a large EM dataset (ca. 5k images, 90k annotated nuclei and mitos). We also add a new decoder for instance segmentation, which provides efficient automatic segmentation.
Architecture of the segment anything model with additional segmentation decoder.
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Constantin Pape @cppape.bsky.social · 12/02/2025
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...
Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.
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Constantin Pape @cppape.bsky.social · 11/02/2025
PathoSAM improves SAM forinteractive segmentation of nuclei and adds automatic and semantic segmentation. According to our experiments, it is SOTA for instance segmentation (see ) and performs well for semantic segmentation.
Nucleus instance segmentation result averaged over several histopathology datasets for PathoSAM and several other methods.
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Constantin Pape @cppape.bsky.social · 11/02/2025
Announcing PathoSAM, our foundation model for nucleus segmentation in histopathology. PathoSAM supports interactive and automatic nucleus segmentation (instance and semantic). See segmentation on a WSI from openslide, check out arxiv.org/abs/2502.00408 or read on for details.
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Constantin Pape @cppape.bsky.social · 04/02/2025
Our latest preprint PEFT-SAM is on arxiv! We study parameter efficient finetuning to adapt SAM to biomedical images and introduce a new workflow for adaptation based on only two labeled images. See our workflow and improvements in the image, check out arxiv.org/abs/2502.00418 or read on for more.
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Constantin Pape @cppape.bsky.social · 22/01/2025
Our work, MedicoSAM, is now on arXiv! We study finetuning SAM for medical images. MedicoSAM improves over SAM and models derived from it, especially for interactive segmentation, see examples in the figure. Preprint at arxiv.org/abs/2501.11734. Read on for a summary. @anwaiarchit.bsky.social
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Constantin Pape @cppape.bsky.social · 06/12/2024
First, to answer the question, according to SynapseNet the electron tomogram of the mossy fibre synapse contains 9,061 vesicles, see the reconstruction of all vesicles rendered in orange. It can also identify active zones (blue), mitochondria (red, cyan) and other synaptic structures.
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Constantin Pape @cppape.bsky.social · 06/12/2024
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.
Electron micrograph of a mossy fiber synapse with many synaptic vesicles.
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