Constantin Pape
@cppape.bsky.social
Group leader @ Uni Göttingen for Computational Cell Analytics. Working on AI for biology and medicine with a focus on microscopy image analysis with deep learning.
https://user.informatik.uni-goettingen.de/~pape41/
https://user.informatik.uni-goettingen.de/~pape41/
Pinned
Constantin Pape
@cppape.bsky.social
· Nov 18
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....
Reposted by Constantin Pape
🔬 We're hiring a Junior Group Leader for Data-Driven Digital Twins/System Models in medicine/life sciences at @uni_goettingen! Perfect opportunity for early-career researchers who want to:
- Lead their own research group
- Work at the intersection of AI, simulation, and biomedicine
- Lead their own research group
- Work at the intersection of AI, simulation, and biomedicine
December 19, 2025 at 8:02 AM
🔬 We're hiring a Junior Group Leader for Data-Driven Digital Twins/System Models in medicine/life sciences at @uni_goettingen! Perfect opportunity for early-career researchers who want to:
- Lead their own research group
- Work at the intersection of AI, simulation, and biomedicine
- Lead their own research group
- Work at the intersection of AI, simulation, and biomedicine
Reposted by Constantin Pape
🧠🪰 The adult Drosophila brain connectome now gives us a complete wiring diagram of ~140k neurons. But a wiring diagram alone isn’t understanding.
How is this massive network organized?
Our paper tackles that question by mapping community structure across the entire fly brain. 1/
How is this massive network organized?
Our paper tackles that question by mapping community structure across the entire fly brain. 1/
New lab paper - will say more about this in a little while
December 15, 2025 at 3:11 PM
🧠🪰 The adult Drosophila brain connectome now gives us a complete wiring diagram of ~140k neurons. But a wiring diagram alone isn’t understanding.
How is this massive network organized?
Our paper tackles that question by mapping community structure across the entire fly brain. 1/
How is this massive network organized?
Our paper tackles that question by mapping community structure across the entire fly brain. 1/
Reposted by Constantin Pape
📣 Paper alert: We present dense attentive probing (DeAP), a method to measure the representation quality of various vision backbones for dense prediction tasks. It uses small, parameter-efficient readouts with learnable masks to generate dense predictions from backbone features of any size.
November 28, 2025 at 1:25 PM
📣 Paper alert: We present dense attentive probing (DeAP), a method to measure the representation quality of various vision backbones for dense prediction tasks. It uses small, parameter-efficient readouts with learnable masks to generate dense predictions from backbone features of any size.
Reposted by Constantin Pape
We’ll be at @neuripsconf.bsky.social on Wednesday, 3 December, from 11 a.m. to 2 p.m. (San Diego time). Come and chat with us about why distance matrices and invariances are cool! 🎉 #InterdisciplinaryML #neurips2025 #bioimageanalysis #shapequantification
December 1, 2025 at 8:27 AM
We’ll be at @neuripsconf.bsky.social on Wednesday, 3 December, from 11 a.m. to 2 p.m. (San Diego time). Come and chat with us about why distance matrices and invariances are cool! 🎉 #InterdisciplinaryML #neurips2025 #bioimageanalysis #shapequantification
Reposted by Constantin Pape
Our new paper showcasing molecular connectomics with pan-expansion microscopy is out in @natbiotech.nature.com! www.nature.com/articles/s41...
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)
November 27, 2025 at 4:40 AM
Our new paper showcasing molecular connectomics with pan-expansion microscopy is out in @natbiotech.nature.com! www.nature.com/articles/s41...
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)
Reposted by Constantin Pape
📢 Paper alert 📢
Chirality is known to be important for the movement of microorganisms and active matter. In our new paper out today in @natphys.nature.com, we show that chirality is used by malaria parasites to control their motion patterns:
doi.org/10.1038/s415...
Here comes a 🧵 ... (1/9)
Chirality is known to be important for the movement of microorganisms and active matter. In our new paper out today in @natphys.nature.com, we show that chirality is used by malaria parasites to control their motion patterns:
doi.org/10.1038/s415...
Here comes a 🧵 ... (1/9)
November 24, 2025 at 5:50 PM
📢 Paper alert 📢
Chirality is known to be important for the movement of microorganisms and active matter. In our new paper out today in @natphys.nature.com, we show that chirality is used by malaria parasites to control their motion patterns:
doi.org/10.1038/s415...
Here comes a 🧵 ... (1/9)
Chirality is known to be important for the movement of microorganisms and active matter. In our new paper out today in @natphys.nature.com, we show that chirality is used by malaria parasites to control their motion patterns:
doi.org/10.1038/s415...
Here comes a 🧵 ... (1/9)
Reposted by Constantin Pape
🔬 Exciting PostDoc Opportunity! 🐁🧠
We - the @sinzlab.bsky.social (sinzlab.org) and @trose-neuro.bsky.social (troselab.de) Labs - are seeking an experimental postdoc to work at @unibonn.bsky.social with cutting-edge miniature 2-photon microscopy and gaze tracking in freely behaving mice.
We - the @sinzlab.bsky.social (sinzlab.org) and @trose-neuro.bsky.social (troselab.de) Labs - are seeking an experimental postdoc to work at @unibonn.bsky.social with cutting-edge miniature 2-photon microscopy and gaze tracking in freely behaving mice.
November 21, 2025 at 5:05 PM
🔬 Exciting PostDoc Opportunity! 🐁🧠
We - the @sinzlab.bsky.social (sinzlab.org) and @trose-neuro.bsky.social (troselab.de) Labs - are seeking an experimental postdoc to work at @unibonn.bsky.social with cutting-edge miniature 2-photon microscopy and gaze tracking in freely behaving mice.
We - the @sinzlab.bsky.social (sinzlab.org) and @trose-neuro.bsky.social (troselab.de) Labs - are seeking an experimental postdoc to work at @unibonn.bsky.social with cutting-edge miniature 2-photon microscopy and gaze tracking in freely behaving mice.
Reposted by Constantin Pape
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer
Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...
forum.image.sc
November 21, 2025 at 9:29 AM
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
Reposted by Constantin Pape
Studying cochlear neuroanatomy demands imaging the entire cochlea at subcellular resolution. In our recent study (tinyurl.com/isotropicLSFM), we recorded the cochlea at isotropic resolution across the whole organ, laying the groundwork for what follows…
#lightsheet
#isotropic
#cochlea
#lightsheet
#isotropic
#cochlea
November 20, 2025 at 9:20 PM
Studying cochlear neuroanatomy demands imaging the entire cochlea at subcellular resolution. In our recent study (tinyurl.com/isotropicLSFM), we recorded the cochlea at isotropic resolution across the whole organ, laying the groundwork for what follows…
#lightsheet
#isotropic
#cochlea
#lightsheet
#isotropic
#cochlea
Reposted by Constantin Pape
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....
November 20, 2025 at 9:20 PM
Reposted by Constantin Pape
🧬 10 @dfg.de-funded PhD positions at @goettingen-campus.de 🧬
❗Focus: Evolution of gene regulatory networks & Wnt signaling in emerging models (insects, snails, flatworms, cnidarians).
💻 Methods: 'Omics, Bioinformatics, CRISPR/RNAi & Imaging.
📌Start: June 2026.
#EvoDevo #Genomics #Bioinformatics
❗Focus: Evolution of gene regulatory networks & Wnt signaling in emerging models (insects, snails, flatworms, cnidarians).
💻 Methods: 'Omics, Bioinformatics, CRISPR/RNAi & Imaging.
📌Start: June 2026.
#EvoDevo #Genomics #Bioinformatics
November 18, 2025 at 2:04 PM
🧬 10 @dfg.de-funded PhD positions at @goettingen-campus.de 🧬
❗Focus: Evolution of gene regulatory networks & Wnt signaling in emerging models (insects, snails, flatworms, cnidarians).
💻 Methods: 'Omics, Bioinformatics, CRISPR/RNAi & Imaging.
📌Start: June 2026.
#EvoDevo #Genomics #Bioinformatics
❗Focus: Evolution of gene regulatory networks & Wnt signaling in emerging models (insects, snails, flatworms, cnidarians).
💻 Methods: 'Omics, Bioinformatics, CRISPR/RNAi & Imaging.
📌Start: June 2026.
#EvoDevo #Genomics #Bioinformatics
Reposted by Constantin Pape
For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing.
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
Python package managers: uv vs pixi?
When I talk to people about Python package management in 2025 I see the following tools in active use; uv, pixi, pip, conda, mamba, micromamba and poetry. There may be others, but I don’t hear much ab...
jacobtomlinson.dev
November 18, 2025 at 12:56 PM
For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing.
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
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....
November 18, 2025 at 7:59 AM
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....
Reposted by Constantin Pape
🎉 I am very glad to share that our paper on the rapid isotropic light-sheet microscope has just been published in Nature Biotechnology @natbiotech.nature.com.
🔗 Read the full article:
www.nature.com/articles/s41...
🔗 Read the full article:
www.nature.com/articles/s41...
Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue - Nature Biotechnology
A light-sheet microscope built from off-the-shelf components enables high-resolution clear tissue imaging.
www.nature.com
November 14, 2025 at 9:27 PM
🎉 I am very glad to share that our paper on the rapid isotropic light-sheet microscope has just been published in Nature Biotechnology @natbiotech.nature.com.
🔗 Read the full article:
www.nature.com/articles/s41...
🔗 Read the full article:
www.nature.com/articles/s41...
Reposted by Constantin Pape
Happy to see our paper “Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue” in @natbiotech.nature.com – with Tobias Moser’s lab from @unimedizin-goe.bsky.social and @janwenzel.bsky.social
www.nature.com/articles/s41...
#microscopy #lightsheet
www.nature.com/articles/s41...
#microscopy #lightsheet
November 14, 2025 at 4:41 PM
Happy to see our paper “Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue” in @natbiotech.nature.com – with Tobias Moser’s lab from @unimedizin-goe.bsky.social and @janwenzel.bsky.social
www.nature.com/articles/s41...
#microscopy #lightsheet
www.nature.com/articles/s41...
#microscopy #lightsheet
Reposted by Constantin Pape
🎓 We're hiring two PhD students in #MachineLearning for my new group at the Hertie Institute for AI in Brain Health, University of Tübingen!
Work on unsupervised learning, #DeepLearning, and #Neuroscience in a vibrant research environment.
👇 Details below
Work on unsupervised learning, #DeepLearning, and #Neuroscience in a vibrant research environment.
👇 Details below
November 13, 2025 at 9:41 AM
🎓 We're hiring two PhD students in #MachineLearning for my new group at the Hertie Institute for AI in Brain Health, University of Tübingen!
Work on unsupervised learning, #DeepLearning, and #Neuroscience in a vibrant research environment.
👇 Details below
Work on unsupervised learning, #DeepLearning, and #Neuroscience in a vibrant research environment.
👇 Details below
Reposted by Constantin Pape
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group
The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...
cvpd.github.io
September 30, 2025 at 11:01 AM
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
I am reviewing a paper where the authors treat their (single fluorophore = single channel) microscopy images as RGB, and then when the fluorophore changes, change the pseudo-color (blue for DAPI, red for mCherry) and add data augmentation to make the model work for both ...
November 9, 2025 at 3:12 PM
I am reviewing a paper where the authors treat their (single fluorophore = single channel) microscopy images as RGB, and then when the fluorophore changes, change the pseudo-color (blue for DAPI, red for mCherry) and add data augmentation to make the model work for both ...
Reposted by Constantin Pape
🧐 Are you a computational physicist and expert in probability theory? 👉 Contribute to our project "Theory and Algorithms for Structure Determination from Single Molecule X-Ray Scattering Images" as PhD student or Postdoc! 🔗 Check our job advert for more details www.mpinat.mpg.de/4988122/09-2...
April 1, 2025 at 1:01 PM
🧐 Are you a computational physicist and expert in probability theory? 👉 Contribute to our project "Theory and Algorithms for Structure Determination from Single Molecule X-Ray Scattering Images" as PhD student or Postdoc! 🔗 Check our job advert for more details www.mpinat.mpg.de/4988122/09-2...
Reposted by Constantin Pape
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Reposted by Constantin Pape
First neurons didn’t appear overnight. We trace their roots to ancient secretory cells - showing how lifestyle & behavior shaped the evolution of first synapses.🧠🌊 #Evolution #Neuroscience
Our latest in @natrevneuro.nature.com
Link: rdcu.be/eMX3E
@jeffcolgren.bsky.social @msarscentre.bsky.social
Our latest in @natrevneuro.nature.com
Link: rdcu.be/eMX3E
@jeffcolgren.bsky.social @msarscentre.bsky.social
The evolutionary origins of synaptic proteins and their changing roles in different organisms across evolution
Nature Reviews Neuroscience - Recent studies have shed further light on the evolutionary origins of chemical synapses, In this Review, Colgren and Burkhardt explore how ancient proteins were...
rdcu.be
October 27, 2025 at 6:48 PM
First neurons didn’t appear overnight. We trace their roots to ancient secretory cells - showing how lifestyle & behavior shaped the evolution of first synapses.🧠🌊 #Evolution #Neuroscience
Our latest in @natrevneuro.nature.com
Link: rdcu.be/eMX3E
@jeffcolgren.bsky.social @msarscentre.bsky.social
Our latest in @natrevneuro.nature.com
Link: rdcu.be/eMX3E
@jeffcolgren.bsky.social @msarscentre.bsky.social
Reposted by Constantin Pape
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🌺
October 22, 2025 at 8:23 PM
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🌺
Reposted by Constantin Pape
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:
napari.org/island-dispa...
napari.org/island-dispa...
October 21, 2025 at 2:32 PM
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:
napari.org/island-dispa...
napari.org/island-dispa...
Reposted by Constantin Pape
The Shanahan Fellowship is a unique PostDoc opportunity at the intersection of Neuroscience and Data Science. If you are considering a PostDoc in this area, I encourage you to apply!
Applications are open! And due by Dec 1st
alleninstitute.org/shanahan-fou...
Applications are open! And due by Dec 1st
alleninstitute.org/shanahan-fou...
Allen Institute - Shanahan Foundation Fellowship at the Interface of Data and Neuroscience 2025-2026
Thank you for applying for the Shanahan Foundation Fellowship at the Interface of Data and Neuroscience. Applications for the Fall 2026 cohort will close at 11:59pm PT on December 1st, 2025.
Important...
alleninstitute.submittable.com
October 18, 2025 at 1:14 AM
The Shanahan Fellowship is a unique PostDoc opportunity at the intersection of Neuroscience and Data Science. If you are considering a PostDoc in this area, I encourage you to apply!
Applications are open! And due by Dec 1st
alleninstitute.org/shanahan-fou...
Applications are open! And due by Dec 1st
alleninstitute.org/shanahan-fou...
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....
www.molbiolcell.org/doi/full/10....
October 17, 2025 at 11:09 AM
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....
www.molbiolcell.org/doi/full/10....