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Stephan Saalfeld

@herrsaalfeld.bsky.social

790 followers 140 following 53 posts

scalable data analysis, modeling, AI, software design at HHMI Janelia https://mastodon.social/@herrsaalfeld

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Stephan Saalfeld @herrsaalfeld.bsky.social · Nov 15

We are looking for exceptional #AIScientist|s to join our #AI@HHMI initiative at #HHMIJanelia. We want to uncover fundamental principles underlying complex biological systems that are inaccessible without new innovations that combine #AI with experimental design.

ai.hhmi.org#join-our-team

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AI@HHMI teaser saying "AI@HHMI | Accelerating Innovation in Biology". The backdrop is an artistic rendering of the compute graph of a network architecture for semantic image segmentation that I think looks really cute.

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Reposted by Stephan Saalfeld

Davi Bock @dddavi.bsky.social · 1d

I love this piece!

It shows the many ways a connectome can be put to use, AND the many complementary modalities that are needed, beyond the connectome, to answer real questions.

And it makes me feel good about having helped to generate the thing. :)

The Transmitter @thetransmitter.bsky.social · 1d

To celebrate the first anniversary of the release of FlyWire, we asked nine neuroscientists to share how they are using connectome data in their research and what they hope is in store for the future of fly connectomics.

By @franciscorr25.bsky.social

#neuroskyence

bit.ly/3Wx5nt3

How FlyWire is redefining Drosophila research, one year in

Nine Drosophila researchers share how the connectome transformed the field and what additional new tools they would like to see.

bit.ly

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Reposted by Stephan Saalfeld

Janelia Research Campus @hhmijanelia.bsky.social · 21h

🔊 Listen to Senior Group Leader Hari Shroff discuss microscopy, biology and his path through science in the latest episode of Ashoka University's The Science of It podcast: https://www.youtube.com/watch?v=dyoP5HwAFAc&list=PLaTCrA79FLSx-NV34W0Ee2Ei8FgmBDEKn&index=16

The Science of Microscopy | Innovator Hari Shroff | The Science of It Ep. 4

Microscopist Hari Shroff takes us deeper into the world of nature's tiniest beings in the latest episode of Ashoka University's #TheScienceofIt podcast. What made a computer scientist and physicist turn to building microscopes to explore the beauty of ...

www.youtube.com

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Reposted by Stephan Saalfeld

Nicolas Chiaruttini @nkiaru.bsky.social · 21h

#QuPath + Imglib2 and #BDV ❤️

Promising start!

(Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)

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Reposted by Stephan Saalfeld

Nicolas Chiaruttini @nkiaru.bsky.social · 1d

I managed to make #ABBA work with a white background and dark mode! #FijiSc #BDV. Useless for the moment, but I like it.

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Reposted by Stephan Saalfeld

Institute of Neurobiology - UPR @neurobio-upr.bsky.social · 2d

Apply now!!! 🔥

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Reposted by Stephan Saalfeld

Janelia FlyEM @janelia-flyem.bsky.social · 2d

We're very proud to be releasing the complete male fly CNS connectome!

It's the product of a huge team effort here at Janelia in partnership with the Cambridge Fly Connectomics group (@jefferis.bsky.social and colleagues), plus invaluable collaborators.

More soon...
www.janelia.org/project-team...

Male CNS Connectome

A team of researchers has unveiled the complete connectome of a male fruit fly central nervous system —a seamless map of all the neurons in the brain and nerve cord of a single male fruit fly and the ...

www.janelia.org

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Reposted by Stephan Saalfeld

Megan Ranney MD MPH @meganranney.bsky.social · 5d

“framing science as a debate to be won makes it easy to paint established scientists as opponents who must be overcome”

An interesting thesis and suggestion of a solution

www.nytimes.com/2025/10/03/o... 🎁

Opinion | How the Manosphere Hijacks Young Men’s Interest in Science

www.nytimes.com

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Reposted by Stephan Saalfeld

Peter Rupprecht @ptrrupprecht.bsky.social · Aug 11

New blog post, where I review some recent interesting papers on the role of cell organelles for neuronal calcium signaling: gcamp6f.com/2025/08/11/i...
Featuring work by @lorenabenedetti.bsky.social, O'Hare et al. and Lin et al.!

Interesting papers on the role of cell organelles in neuronal dendrites for calcium signaling

Researchers utilize calcium imaging to track neuronal activity in the brain, highlighting the role of calcium as a signaling molecule. Recent studies investigate intracellular calcium dynamics, par…

gcamp6f.com

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Stephan Saalfeld @herrsaalfeld.bsky.social · 6d

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Reposted by Stephan Saalfeld

Andrew Payne @andrewcpayne.bsky.social · 7d

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

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Reposted by Stephan Saalfeld

Stowers Institute @stowersinstitute.bsky.social · 8d

NEWS🎉 We’re excited to announce @hhmijanelia.bsky.social Investigator David Stern will join the Institute from Janelia Research Campus. His lab studies how aphids transform plants at the genetic level, uncovering secrets of #evolution & new strategies for pest control. @hhmi.org bit.ly/4np96Fb

Stowers Institute recruits renowned developmental and evolutionary…

David Stern, Ph.D., brings groundbreaking research on insect–plant interactions for next-generation pest control to the Institute.

bit.ly

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Reposted by Stephan Saalfeld

Tom Aarsen @tomaarsen.com · 7d

We're announcing a new update to MTEB: RTEB

It's a new multilingual text embedding retrieval benchmark with private (!) datasets, to ensure that we measure true generalization and avoid (accidental) overfitting.

Details in our blogpost below 🧵

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Stephan Saalfeld @herrsaalfeld.bsky.social · 8d

Say hi to @dddavi.bsky.social 🙂

Reposted by Stephan Saalfeld

Siân Culley @superresolusian.bsky.social · 9d

BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...

Bioimage Analysis Specialist | King's College London

www.kcl.ac.uk

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Reposted by Stephan Saalfeld

Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 12d

Back to work on #bigvolumebrowser, I've added the import of point clouds that change over time. The test data generation was a pleasant detour into the world of attractors (Thomas' cyclically symmetric is shown).

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Reposted by Stephan Saalfeld

Drug Monkey @drugmonkey.bsky.social · 12d

This may be the most important paper ever published about NIH funded research.

www.science.org/doi/10.1126/...

What if NIH had been 40% smaller?

Replaying history with less NIH funding shows widespread impacts on drug-linked research

www.science.org

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Stephan Saalfeld @herrsaalfeld.bsky.social · 12d

If somebody was prosecuted with malicious intent, can't they sue the prosecutor for prosecution with malicious intent? Are you planning to support such cases?

Reposted by Stephan Saalfeld

Frederick "Erick" Matsen @matsen.bsky.social · 13d

The final version of our transformer-based model of natural selection has come out in MBE. I hope some molecular evolution researchers find this interesting & useful as a way to express richer models of natural selection. doi.org/10.1093/mol... (short 🧵)

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Stephan Saalfeld @herrsaalfeld.bsky.social · 15d

Congratulations @philipschoene.bsky.social ! #LoPaTs

bsky.app

Reposted by Stephan Saalfeld

Sven Truckenbrodt @sventruckenbrodt.bsky.social · 16d

The Molecular Brain Mapping group at the MRC-LMB is hiring! 🌈🧠

I'm looking for people who are excited about revealing the many molecular layers of the "hidden connectome" with expansion microscopy, in a highly intersectional environment exploring ideas in meta-science.

mrc.tal.net/vx/mobile-0/...

Postdoctoral Scientist - Neurobiology - Dr Sven Truckenbrodt - LMB 2698 - Medical Research Council

Location: Cambridge. Vacancy: Postdoctoral Scientist - Neurobiology - Dr Sven Truckenbrodt - LMB 2698. Closing Date: 09/10/2025, 23:55

mrc.tal.net

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Reposted by Stephan Saalfeld

Virginie Uhlmann @virginieuhlmann.bsky.social · 15d

You may have heard me talk about learned shape representations for a long time, but it took @afoix.bsky.social's hard work to bring it to life 🍾 Catch her at @neuripsconf.bsky.social to find out more!!

Anna Foix @afoix.bsky.social · 15d

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)

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Reposted by Stephan Saalfeld

EMBL-EBI @ebi.embl.org · 15d

Do you study proteins?
The new PDBe entry pages make it easier to explore protein structures.

🟢 Visualise ligands & macromolecules with improved 3D viewers
🟢 Get background info from AI-based annotations
🟢 Add your own annotations to viewers without leaving the browser

@pdbeurope.bsky.social
🧬🖥️

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Reposted by Stephan Saalfeld

Aafke Gros @aafkegros.bsky.social · 19d

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

Microscopy Nodes: handling large biological volumes — Blender Conference 2025

YouTube video by Blender

youtu.be

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Stephan Saalfeld @herrsaalfeld.bsky.social · 19d

Pretty! What's the speedup?

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Max Planck Institute for the Physics of Complex Systems @mpipks.bsky.social · 19d

Passive morphogenesis of the gut: work by @zhaoshh.bsky.social @lepuslapis.bsky.social @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social and collaborators at Princeton University, @flatironinstitute.org now #published @pnas.org:

doi.org/10.1073/pnas.2505160122

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