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
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....
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....
I tried it on one of our preprints and it did a pretty good job! Looks like a helpful tool for reviewing as well.
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
October 17, 2025 at 10:36 AM
I tried it on one of our preprints and it did a pretty good job! Looks like a helpful tool for reviewing as well.
Reposted by Constantin Pape
Excited to share more widely: I am starting the Dorkenwald Lab at MIT (McGovern Institute + BCS) in January 2026. We study the organizational principles of neuronal circuits using connectomics.
And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
MIT’s McGovern Institute and Department of Brain and Cognitive Sciences welcome new faculty member Sven Dorkenwald - MIT McGovern Institute
The McGovern Institute and the Department of Brain and Cognitive Sciences are pleased to announce the appointment of Sven Dorkenwald as an assistant professor starting in January 2026. A trailblazer i...
mcgovern.mit.edu
October 15, 2025 at 4:57 PM
Excited to share more widely: I am starting the Dorkenwald Lab at MIT (McGovern Institute + BCS) in January 2026. We study the organizational principles of neuronal circuits using connectomics.
And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
Reposted by Constantin Pape
Excited to announce the first @cshlnews.bsky.social meeting on Cell Modeling in Space and Time, June 2026 💫
meetings.cshl.edu/meetings.asp...
Bringing together experiments, computation and theory to explore dynamic, multi-scale cellular organization and function!
1/3
meetings.cshl.edu/meetings.asp...
Bringing together experiments, computation and theory to explore dynamic, multi-scale cellular organization and function!
1/3
October 10, 2025 at 9:23 AM
Excited to announce the first @cshlnews.bsky.social meeting on Cell Modeling in Space and Time, June 2026 💫
meetings.cshl.edu/meetings.asp...
Bringing together experiments, computation and theory to explore dynamic, multi-scale cellular organization and function!
1/3
meetings.cshl.edu/meetings.asp...
Bringing together experiments, computation and theory to explore dynamic, multi-scale cellular organization and function!
1/3
Reposted by Constantin Pape
E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.
Read more: e11.bio/blog/prism
Read more: e11.bio/blog/prism
October 1, 2025 at 2:16 PM
E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.
Read more: e11.bio/blog/prism
Read more: e11.bio/blog/prism
I did not know Taylor Swift was moonlighting in soliciting contributions for fake journals!
September 16, 2025 at 7:29 PM
I did not know Taylor Swift was moonlighting in soliciting contributions for fake journals!
If there are any arivis experts here: can you help with opening an old ".sis" file? See
forum.image.sc/t/opening-ol...
forum.image.sc/t/opening-ol...
Opening old .sis file in arivis
Hi arivis and file formats experts, we are trying to open an old .sis file in arivis. However, the file can’t be opened because it was created in an older arivis version (<4.0) and we have arivis 4.2...
forum.image.sc
September 10, 2025 at 11:48 AM
If there are any arivis experts here: can you help with opening an old ".sis" file? See
forum.image.sc/t/opening-ol...
forum.image.sc/t/opening-ol...
Reposted by Constantin Pape
We are looking for an IT engineer with a focus on operations and research data management at the Centre for Organismal Studies at @uniheidelberg in Heidelberg, Germany
#it #sysadmin #linux #researchdata
please help to spread this opening […]
[Original post on biologists.social]
#it #sysadmin #linux #researchdata
please help to spread this opening […]
[Original post on biologists.social]
September 1, 2025 at 8:58 AM
We are looking for an IT engineer with a focus on operations and research data management at the Centre for Organismal Studies at @uniheidelberg in Heidelberg, Germany
#it #sysadmin #linux #researchdata
please help to spread this opening […]
[Original post on biologists.social]
#it #sysadmin #linux #researchdata
please help to spread this opening […]
[Original post on biologists.social]
Reposted by Constantin Pape
📢 We have an opening for a tenure track assistant professor position (W1 t.t. W2) in AI in our CS dept @uni-goettingen.de, Germany.
⏰ Application deadline: Sept 19
🗣️ Please share!
uni-goettingen.de/en/697924.html
⏰ Application deadline: Sept 19
🗣️ Please share!
uni-goettingen.de/en/697924.html
W1-TT-W2 Artificial Intelligence - Georg-August-University Göttingen
Website of the Georg-August-University Göttingen
uni-goettingen.de
August 15, 2025 at 10:46 AM
📢 We have an opening for a tenure track assistant professor position (W1 t.t. W2) in AI in our CS dept @uni-goettingen.de, Germany.
⏰ Application deadline: Sept 19
🗣️ Please share!
uni-goettingen.de/en/697924.html
⏰ Application deadline: Sept 19
🗣️ Please share!
uni-goettingen.de/en/697924.html
Join us as a colleague in Göttingen!
📢 We have an opening for a tenure track assistant professor position (W1 t.t. W2) in AI in our CS dept @uni-goettingen.de, Germany.
⏰ Application deadline: Sept 19
🗣️ Please share!
uni-goettingen.de/en/697924.html
⏰ Application deadline: Sept 19
🗣️ Please share!
uni-goettingen.de/en/697924.html
W1-TT-W2 Artificial Intelligence - Georg-August-University Göttingen
Website of the Georg-August-University Göttingen
uni-goettingen.de
August 15, 2025 at 11:34 AM
Join us as a colleague in Göttingen!
Reposted by Constantin Pape
🧪Job opening at Janelia @hhmijanelia.bsky.social Integrative Imaging platform for a bioimage analyst. Please repost.
We have an open #opportunity for a BioImage Analyst to join our team! This is an excellent role for a problem solver with an empathetic, collaborative mentality who enjoys partnering with interdisciplinary scientists. Read more and apply here: hhmi.wd1.myworkdayjobs.com/en-US/Extern...
BioImage Analyst
Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. The Howard Hughes Medical Institute’s Janelia Research Campus is a pio...
hhmi.wd1.myworkdayjobs.com
February 13, 2025 at 12:17 AM
🧪Job opening at Janelia @hhmijanelia.bsky.social Integrative Imaging platform for a bioimage analyst. Please repost.
Reposted by Constantin Pape
Hello! Very excited to share our latest preprint, which is great news for us but terrible news for any diehard fans of PSNR and SSIM as image quality metrics in microscopy... (1/5)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Image quality metrics fail to accurately represent biological information in fluorescence microscopy
Image processing methods offer the potential to improve the quality of fluorescence microscopy data, allowing for image acquisition at lower, less phototoxic illumination doses. The training and evalu...
www.biorxiv.org
August 7, 2025 at 1:00 PM
Hello! Very excited to share our latest preprint, which is great news for us but terrible news for any diehard fans of PSNR and SSIM as image quality metrics in microscopy... (1/5)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Data is the key to AI advances in biology and "Still, when it comes to data, nothing compares to the real thing." An important editorial in Nature methods with a nice little shout out to microSAM:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Calling all data - Nature Methods
As life sciences research becomes enmeshed in the age of AI, real experimental data are more valuable than ever.
www.nature.com
August 7, 2025 at 4:06 PM
Data is the key to AI advances in biology and "Still, when it comes to data, nothing compares to the real thing." An important editorial in Nature methods with a nice little shout out to microSAM:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A really nice interview with Juan. Important messages:
- "I think that universities are missing a trick in not investing more in this type of work [open source software development]"
- "Never code alone."
- "I think that universities are missing a trick in not investing more in this type of work [open source software development]"
- "Never code alone."
Congratulations Juan! We're thrilled to see Napari is a finalist this year in the ARDC-sponsored Eureka Prize for Excellence in Research Software! We're lucky to have Paula Andrea Martinez elevating the research software community. Your interview is still spot on: ardc.edu.au/article/shap...
Shaping Research Software: An Interview with Dr Juan Nunez-Iglesias | ARDC
We talk to research software engineer Dr Juan Nunez-Iglesias about his journey into the world of open source software and the amazing collaborators he met on his way.
ardc.edu.au
August 7, 2025 at 9:42 AM
A really nice interview with Juan. Important messages:
- "I think that universities are missing a trick in not investing more in this type of work [open source software development]"
- "Never code alone."
- "I think that universities are missing a trick in not investing more in this type of work [open source software development]"
- "Never code alone."
Reposted by Constantin Pape
It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇
@napari.org @jni.codes is a finalist in the @ardc.edu.au Eureka Prize for Excellence in Research Software.
Learn more: youtu.be/0g_MkTa_NwQ
#EurekaPrizes
Learn more: youtu.be/0g_MkTa_NwQ
#EurekaPrizes
August 1, 2025 at 7:29 AM
It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇
Reposted by Constantin Pape
Hightech, Hoffnung, Haushaltslogik
Die Bundesregierung hat den Haushaltsentwurf für 2026 beschlossen. Was drin ist für Bildung und Forschung, – und warum die Prioritäten der Koalition in Wirklichkeit woanders liegen.
Im Wiarda-Blog: www.jmwiarda.de/blog/2025/07...
Die Bundesregierung hat den Haushaltsentwurf für 2026 beschlossen. Was drin ist für Bildung und Forschung, – und warum die Prioritäten der Koalition in Wirklichkeit woanders liegen.
Im Wiarda-Blog: www.jmwiarda.de/blog/2025/07...
July 30, 2025 at 3:30 PM
Hightech, Hoffnung, Haushaltslogik
Die Bundesregierung hat den Haushaltsentwurf für 2026 beschlossen. Was drin ist für Bildung und Forschung, – und warum die Prioritäten der Koalition in Wirklichkeit woanders liegen.
Im Wiarda-Blog: www.jmwiarda.de/blog/2025/07...
Die Bundesregierung hat den Haushaltsentwurf für 2026 beschlossen. Was drin ist für Bildung und Forschung, – und warum die Prioritäten der Koalition in Wirklichkeit woanders liegen.
Im Wiarda-Blog: www.jmwiarda.de/blog/2025/07...
Reposted by Constantin Pape
Cell tracking is never perfect, and it's important to understand the types of errors your solution contains.
Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...
You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...
You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
July 30, 2025 at 8:15 AM
Cell tracking is never perfect, and it's important to understand the types of errors your solution contains.
Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...
You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...
You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
Looking for an opportunity to work on cutting super-resolution microscopy and AI? There's still time to apply to the two positions!
Our goal is to develop methods to understand the dynamics of biomolecules, using the latest developments in super-resolution microscopy and AI-based image analysis. Apply here:
www.uni-goettingen.de/de/699491.html
www.uni-goettingen.de/de/699489.html
Feel free to reach out with further questions.
www.uni-goettingen.de/de/699491.html
www.uni-goettingen.de/de/699489.html
Feel free to reach out with further questions.
PhD Position in Artificial Intelligence (AI) for Dynamic Nanoscale Imaging (f/m/x) - Georg-August-Universität Göttingen
Webseiten der Georg-August-Universität Göttingen
www.uni-goettingen.de
July 23, 2025 at 6:36 AM
Looking for an opportunity to work on cutting super-resolution microscopy and AI? There's still time to apply to the two positions!