Constantin Pape
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cppape.bsky.social
Constantin Pape
@cppape.bsky.social
1.6K followers 380 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 · 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....
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).
Reposted by Constantin Pape
jo-soltwedel.bsky.social
I'll never get tired of lazily browsing elastix-coregistered #WSI data in @napari.org using the upcoming @openmicroscopy.org ome-zarr @zarr.dev format version that allows to specify and read transformations directly from the image data itself.

Data source: rodare.hzdr.de/record/3131
February 12, 2026 at 5:11 PM
Reposted by Constantin Pape
jni.fosstodon.org.ap.brid.gy
smart microscopy postdoc position in Montpellier, France. Could definitely do worse. With @glyg

https://forum.image.sc/t/up-to-4-year-postdoc-position-in-montpellier-smart-microscopy/119201

#foss #microscopy #getfedihired
February 11, 2026 at 10:08 AM
cppape.bsky.social
Interested in applying for an ERC, Emmy Noether, or local AI research group this year? Join our info call! I will also be there ;).
sinzlab.bsky.social Fabian Sinz @sinzlab.bsky.social · 10d
Early career researcher: Are you thinking about writing an ERC , Emmy Noether Proposal, or Lower Saxony AI Group application, and are you interested to work with us at @uni-goettingen.de and @goettingen-campus.de
Information Event on Funding Programs - Georg-August-University Göttingen
Website of the Georg-August-University Göttingen
www.uni-goettingen.de
February 5, 2026 at 5:56 PM
Reposted by Constantin Pape
sinzlab.bsky.social
Early career researcher: Are you thinking about writing an ERC , Emmy Noether Proposal, or Lower Saxony AI Group application, and are you interested to work with us at @uni-goettingen.de and @goettingen-campus.de
Information Event on Funding Programs - Georg-August-University Göttingen
Website of the Georg-August-University Göttingen
www.uni-goettingen.de
February 4, 2026 at 4:33 PM
Reposted by Constantin Pape
lucamarconato.bsky.social
We are hiring a Research Software Engineer to enhance and maintain the SpatialData framework.

We will work together with colleagues at EMBL, DKFZ, GSK, and across the scverse community.

🔗 Deadline: 15/02/2026
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
Research Software Engineer - Spatial-omics
The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...
embl.wd103.myworkdayjobs.com
February 2, 2026 at 9:38 AM
Reposted by Constantin Pape
david-j-barry.bsky.social
AMAZING JOB OPPORTUNITY ALERT!!!

@calm-stp.bsky.social is hiring a Data & Systems Steward! 🧬

🔹Manage #bioimage data & #OMERO admin
🔹Automate via #Python/#Bash
🔹Support #FAIR principles
🔹Work closely with @crick-ia-team.bsky.social

⏰ Deadline: 08 Feb 2026

Apply: www.crick.ac.uk/careers-stud...
https://doi.org/10.5281/zenodo.14762435 https://bsky.app/profile/falk-illustrations.de
January 31, 2026 at 2:35 PM
Reposted by Constantin Pape
florianjug.bsky.social
🚨 Only a few days left to apply for maybe the best microscopy course there is!!! 🚨
👇👇👇👇👇👇👇👇👇👇👇
January 21, 2026 at 10:37 PM
Reposted by Constantin Pape
karel-mocaer.bsky.social
We are excited to share that we are hosting a hands-on course on "Electron Microscopy of Marine Environmental Samples" 🔬🌊
📍Naples, Italy 🗓️ 8th-11th of April 2026
If you are interested, check the program below!
Registration is open until the 12th of February. We look forward to seeing you there!
January 20, 2026 at 4:32 PM
Reposted by Constantin Pape
florianjug.bsky.social
🚨 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/...
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
Reposted by Constantin Pape
sinzlab.bsky.social
🔬 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
December 19, 2025 at 8:02 AM
Reposted by Constantin Pape
richardfbetzel.bsky.social
🧠🪰 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/
richardfbetzel.bsky.social Rick Betzel @richardfbetzel.bsky.social · Dec 14
New lab paper - will say more about this in a little while
December 15, 2025 at 3:11 PM
Reposted by Constantin Pape
timojl.bsky.social
📣 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
Reposted by Constantin Pape
afoix.bsky.social
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
Reposted by Constantin Pape
kuanawanda.bsky.social
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)
November 27, 2025 at 4:40 AM
Reposted by Constantin Pape
ulrichschwarz.bsky.social
📢 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)
November 24, 2025 at 5:50 PM
Reposted by Constantin Pape
sinzlab.bsky.social
🔬 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.
November 21, 2025 at 5:05 PM
Reposted by Constantin Pape
ekatrukha.bsky.social
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...
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
Reposted by Constantin Pape
huiskenlab.bsky.social
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
November 20, 2025 at 9:20 PM
Reposted by Constantin Pape
huiskenlab.bsky.social
This work is nicely summarised by @cppape.bsky.social:
bsky.app/profile/cppa...
cppape.bsky.social 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....
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).
November 20, 2025 at 9:20 PM
Reposted by Constantin Pape
posnienlab.bsky.social
🧬 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
November 18, 2025 at 2:04 PM
Reposted by Constantin Pape
jacobtomlinson.dev
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...
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
cppape.bsky.social
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).
November 18, 2025 at 7:59 AM
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