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
🚨 Alarm!!! 🚨
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?
20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026
✍️ Jan 15 2026 ✍️
🔁 pls!!
www.janelia.org/you-janelia/...
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?
20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026
✍️ Jan 15 2026 ✍️
🔁 pls!!
www.janelia.org/you-janelia/...
Deep Learning for Microscopy Image Analysis
Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
www.janelia.org
December 28, 2025 at 7:06 PM
🚨 Alarm!!! 🚨
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?
20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026
✍️ Jan 15 2026 ✍️
🔁 pls!!
www.janelia.org/you-janelia/...
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?
20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026
✍️ Jan 15 2026 ✍️
🔁 pls!!
www.janelia.org/you-janelia/...
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...