Stephan Saalfeld

@herrsaalfeld
304 Followers
96 Following
560 Posts
scalable image analysis, ML, software design at HHMI Janelia
Jobhttps://www.janelia.org/lab/saalfeld-lab
GitHubhttps://github.com/axtimwalde
PGPE912 500E B791 3D81 4CDD 29A8 D84E 640A E9FA 00A2
Previouslyhttps://qoto.org/@herrsaalfeld
The digital sphinx: Can a worm brain control a fly body? https://www.biorxiv.org/content/10.64898/2026.03.20.713233v1?med=mas
The digital sphinx: Can a worm brain control a fly body?

Animal intelligence is not purely a product of abstract computation in the brain, but emerges from dynamic interactions between the nervous system and the body. New connectome datasets and musculoskeletal models now enable integrated, closed-loop simulations of the neural and biomechanical systems of the fruit fly Drosophila, an ideal model organism to investigate embodied intelligence. However, many biological parameters of the nervous system and the body, as well as how they interface, remain unknown. To fill such gaps, researchers are turning to deep reinforcement learning (DRL), a data-driven optimization framework, to create virtual animals that imitate the behavior of real animals. Here, we provide a cautionary tale about the interpretation of such models. We constructed a virtual chimera of two phylogenetically distant species: a connectome of the C. elegans nematode worm and a biomechanical model of the fly body. The worm connectome receives sensory information from the fly body, and an artificial neural network is trained with DRL to map worm motor neuron activations to the fly's leg actuators. The resulting digital sphinx produces highly realistic fly walking - yet it is biologically meaningless. This exercise teaches us nothing about either animal and exposes a core peril of connectome-body models: behavioral fidelity is achievable without biological fidelity, making such models easy to overinterpret. Done carefully, virtual animals can be powerful partners to biological experiments, but only if their components and interfaces are grounded in biology. ### Competing Interest Statement The authors have declared no competing interest. NIH, U01NS136507, R01NS14543

bioRxiv

You'll have to opt-out of GitHub using your repos for AI training here: https://github.com/settings/copilot/features

Ctrl-F for "Allow GitHub to use my data for AI model training"

The problem with AI slop is not AI but slop.

Do yourself a favor. Learn ocaml, haskell, prolog, clojure. Even the Turing tarpit [1] that is brainfuck (it is a language [2]). Thank me later.

[1] https://en.wikipedia.org/wiki/Turing_tarpit
[2] https://en.wikipedia.org/wiki/Brainfuck

Turing tarpit - Wikipedia

Max Planck spin-off draws Epic Games to Tübingen: The US-based game developer is acquiring Meshcapade and will establish a presence in the Cyber Valley tech hub.

https://www.mpg.de/26082348/max-planck-spin-off-meshcapade-draws-epic-games-to-tuebingen

#Unreal #UnrealEngine #MetaHuman #Gaming

Max Planck spin-off draws Epic Games to Tübingen

Meshcapade, the Max Planck startup based in Tübingen’s Cyber Valley, is being acquired by Epic Games – a U.S. game developer and creator of Unreal Engine, a game development technology. Alongside the acquisition, Epic Games is establishing a presence in Cyber Valley. The Meshcapade team will join Epic’s AI Research team.

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 these tools a try: https://github.com/saalfeldlab/lens-correct
The split-image tool is for lens-arrays or other setups that project somehow different views of the same sample into a single image. Native installers for Linux, Mac, Win under Releases.
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.

GitHub
This is work that we presented at last year's #Cosyne workshop on #GNN s https://sites.google.com/bu.edu/gnnworkshop-cosyne2025/home. 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. https://arxiv.org/abs/2602.13325
gnnworkshop cosyne2025

It's All Connected!

Idea: "The unbillionaires list", to promote contributors to the common.

A collaborative website that lists people who created something useful to millions but purposedly choose to put in in the common and didn’t earn money directly from it (or not as much as expected)

Besides those listed in https://ploum.net/2026-01-22-why-no-european-google.html

I would add Henri Dunant (Red Cross, he died in great poverty), Didier Pittet (who invented the hydroalcoolic gel we now use everyday).

Why there’s no European Google?

Why there’s no European Google? par Ploum - Lionel Dricot.