Stephan Saalfeld

We opened 4 PhD positions at @humantechnopole.bsky.social together with Polimi (see 👇).

My lab offers a PhD project on "Computational Morphogenesis": use state-of-the-art machine learning methods together with realistic simulations to build digital twins of developing tissue.

Apply by March 26.

Looking forward to heading off to Cosyne next week, and excited to be part of a two day workshop about connectomics, with day one being about species comparison and day two about using data for constraining models. alleninstitute.github.io/connectomics...

Ping.

A central somatotopic map of the fly leg supports spatially targeted grooming https://www.biorxiv.org/content/10.64898/2026.02.27.708590v1

Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context.
Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social

Yep, it lags a little. But still quite impressive considering that each "pixel" is a 150 MPixel multires image. Overall the total number of 'adressable' pixels in this 2D image are 225x225x150 Mpix = 7.6 Tera pixels. #ImageJ #Fiji #BigDataViewer

After 5 years of developing, a new preprint from the lab - introducing our workflow for comparative insect connectomics, aimed at democratizing connectomics. @erc.europa.eu @lundvision.bsky.social @biologylu.bsky.social Read it here: www.biorxiv.org/content/10.6...

Evolved Virtual Creatures by Karl Sims, 1994 Demo of simulated block creatures performing various evolved behaviors.

Christian Donlan of @theguardian.com unfortunately missed that #AnLife is exactly Karl Sim's evolved creatures www.karlsims.com/evolved-virt..., beautiful work from 1994, and not a recent AI wonder. Cute though! www.theguardian.com/games/2026/f...

People sitting on stairs discussing a project. Text highlighting the next EMBO Lab Leadership for Scientists in the Americas live online course running on17-20 March 2026 still has places available.

Scientists in the #Americas: spots still open for the @embo.org Lab #Leadership online course. Spread over 4 days, March 17-20, 9am-3:30pm NY time. Built for life science researchers. #EMBOLabLead Register before places fill up: www.embolableadership.org/course/embol...

Long Lake, Little Lakes Valley, Inyo National Forest, CA, photos from 2007, 2016, 2023 showing the same dead tree.

Some people are just mean though... And some places are just nice. That tree trunk ain't goin' anywhere 😀

We are excited to be recruiting a new tenure track group leader in the Structural Studies Division at MRC LMB! It is an amazing place to start your own lab.
@mrclmb.bsky.social

Please get in touch if you have any questions.
www.nature.com/naturecareer...

Accelerating Innovation in Biology HHMI’s $500 million over the next 10 years will support AI-driven projects and embed AI systems throughout the scientific process in labs across HHMI.

Join us in building foundational datasets and models for microscopy with @jakobtroidl.bsky.social and many others

AI Engineer Pre-Training: lnkd.in/eyEEV5nm
AI Engineer Post-Training: lnkd.in/eShVQ3y9
Data Engineer Data: lnkd.in/eCvm58xH
Data Engineer Pipelines: lnkd.in/ec6qGJkX

ai.hhmi.org

YouTube video by Johanna M. Dela Cruz Interactive 3D Visualization of Multiple Volumes & Shapes in FIJI (BigVolumeBrowser)

In the #BigVolumeBrowser news, there is a new awesome video tutorial about it made by certified magician Johanna M. Dela Cruz.
Check it out: www.youtube.com/watch?v=c0fr... (1/2)

As in: Interesting start, then flat and boring forever?

The spring call for the ELBE Postdoctoral Fellows Program is open now: www.csbdresden.de/join-us/as-a.... Join the @csbdresden.bsky.social for a fully funded fellowship. @mpi-cbg.de @mpipks.bsky.social

GitHub - saalfeldlab/lens-correct: Correcting lens-distortion in confocal stacks Correcting lens-distortion in confocal stacks. Contribute to saalfeldlab/lens-correct development by creating an account on GitHub.

If your imaging system has poorly characterized constant distortions leading to chromatic aberration, shoddy stitching, or false measurements (the answer is likely yes), you may want to give this tool a try. Native installers for Linux, Mac, Win under Releases github.com/saalfeldlab/...

YouTube video by Cephla Self-driving microscopes

How self-driving cars motivated us to build a universal diagnostics platform for malaria/Tb. The arc of technology is unpredictable at best.

m.youtube.com/watch?v=gbeg...

Altair-LSFM – new high-resolution, open-source, sample-scanning approach to light-sheet fluorescence microscopy for sub-cellular imaging

📹 @john-haug.bsky.social et al @kevin-dean.bsky.social lab
UT Southwestern Medical Center in @elife.bsky.social

➡️ bpod.org.uk/archive/2026... with
John Ankers

Graph neural networks uncover structure and functions underlying the activity of simulated neural assemblies Graph neural networks trained to predict observable dynamics can be used to decompose the temporal activity of complex heterogeneous systems into simple, interpretable representations. Here we apply t...

This is work that we presented at last year's #Cosyne workshop on #GNN s sites.google.com/bu.edu/gnnwo.... Better late than never. You can reproduce everything with the associated notebooks. I think it's a good start to learn how to use GNNs to infer something about NNs. arxiv.org/abs/2602.13325

Two funded PhD positions investigating the evolution of sarcomeres @ibdm.bsky.social in @biancah0406.bsky.social and our lab, together with @cnidevo.bsky.social - Interested to explore how similar or different Jellyfish sarcomeres are to Drosophila or human ones?
www.ibdm.univ-amu.fr/ibdm_job/2-a...

Long in the making, but happy to present the Chlamydomonas chlororibosome!
Cryo-ET🔬reveals a large new domain on the small subunit, built from multiple extensions in conserved ribosomal proteins.
bioRxiv 📖: shorturl.at/q44tG
This suggests greater chlororibosome diversity than expected!
1/n 🧵

🚨 new work from the lab on how eye movements 👀 versus orofacial movements influence 🐭 visual cortex activity 🧠 #neuroscience #behavior #neuroAI

There was so much to unpack with this data, we teamed up with the marvellous @margotriggi.bsky.social to help explain what we think is going on. (Please also check out our model of central apparatus assembly here: www.biorxiv.org/content/10.6...)

This is finally out in J Neuroscience! A micropatterned presynapse-on-glass approach to resolve the nanoscale architecture and function of presynapses
www.jneurosci.org/content/earl...

Really excited to share our new paper in @nature.com! We uncovered how a physical instability of the cytoplasm coupled with the cell cycle drives cytoplasmic partitioning in early embryos #zebrafish #drosophila. Read more in this🧵 www.nature.com/articles/s41... 🤩
@poldresden.bsky.social @mpi-cbg.de

PhD position in my lab!

Check out this new approach to colocalization analysis from @owfpuls.bsky.social along with members of the AIC and Advanced Bioimaging Unit teams, now out in @jcellsci.bsky.social!

journals.biologists.com/jcs/article/...

Poster of the EM course in Naples with marine samples. The Electron Microscopy Hands-On Course: sample preparation and imaging of marine environmental samples arises from a very strong and active collaboration between the Stazione Zoologica Anton Dohrn and the EMBL in Heidelberg. The aim of the course is to provide a theoretical and practical training on electron microscopy starting from the basics to the preparation of samples with high pressure freezing and image acquisition using TEM and SEM.

If you are interested in electron microscopy, registration is still open for the

"Electron Microscopy Hands-On Course: sample preparation and imaging of marine environmental samples"

at Stazione Zoologica in Naples.

WIth great teachers from Naples […]

[Original post on biologists.social]

Yes 🙂

1/n: A new collaborative preprint from the lab to start the year: "A multi-ring shifter network computes head direction in zebrafish" together with Siyuan Mei, Martin Stemmler and Andreas Herz from the LMU, Munich.