Constantin Pape
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cppape.bsky.social
Constantin Pape
@cppape.bsky.social
1.6K followers 370 following 110 posts
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/
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cppape.bsky.social
Constantin Pape @cppape.bsky.social · Oct 17
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.
Reposted by Constantin Pape
aakhte.bsky.social
🎉 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...
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
Reposted by Constantin Pape
huiskenlab.bsky.social
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
November 14, 2025 at 4:41 PM
Reposted by Constantin Pape
sdamrich.bsky.social
🎓 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
November 13, 2025 at 9:41 AM
Reposted by Constantin Pape
iarganda.bsky.social
📣 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...
📢 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
cppape.bsky.social
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
Reposted by Constantin Pape
compbiophys.bsky.social
🧐 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
Reposted by Constantin Pape
moalquraishi.bsky.social
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
Reposted by Constantin Pape
pawelburkhardt.bsky.social
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
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
Reposted by Constantin Pape
afoix.bsky.social
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
Reposted by Constantin Pape
napari.org
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...
October 21, 2025 at 2:32 PM
Reposted by Constantin Pape
sdorkenw.bsky.social
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...
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
cppape.bsky.social
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.
October 17, 2025 at 11:09 AM
cppape.bsky.social
I tried it on one of our preprints and it did a pretty good job! Looks like a helpful tool for reviewing as well.
odedrechavi.bsky.social Oded Rechavi @odedrechavi.bsky.social · Oct 15
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
Reposted by Constantin Pape
sdorkenw.bsky.social
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
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
Reposted by Constantin Pape
assafzaritsky.bsky.social
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
October 10, 2025 at 9:23 AM
Reposted by Constantin Pape
andrewcpayne.bsky.social
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
October 1, 2025 at 2:16 PM
cppape.bsky.social
I did not know Taylor Swift was moonlighting in soliciting contributions for fake journals!
September 16, 2025 at 7:29 PM
cppape.bsky.social
If there are any arivis experts here: can you help with opening an old ".sis" file? See
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
Reposted by Constantin Pape
jekely.biologists.social.ap.brid.gy
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]
Heidelberg castle by night with reflections of light in the Neckar river
September 1, 2025 at 8:58 AM
Reposted by Constantin Pape
aecker.bsky.social
📢 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
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
cppape.bsky.social
Join us as a colleague in Göttingen!
aecker.bsky.social Alexander Ecker @aecker.bsky.social · Aug 15
📢 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
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
Reposted by Constantin Pape
scopeshifu.bsky.social
🧪Job opening at Janelia @hhmijanelia.bsky.social Integrative Imaging platform for a bioimage analyst. Please repost.
i2janelia.bsky.social Integrative Imaging @ Janelia @i2janelia.bsky.social · Feb 12
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
Reposted by Constantin Pape
superresolusian.bsky.social
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...
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
cppape.bsky.social
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...
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
cppape.bsky.social
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."
ardc.edu.au Australian Research Data Commons (ARDC) @ardc.edu.au · Aug 7
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