Stephan Saalfeld
@herrsaalfeld.bsky.social
scalable data analysis, modeling, AI, software design at HHMI Janelia
https://mastodon.social/@herrsaalfeld
https://mastodon.social/@herrsaalfeld
Pinned
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
1/4
ai.hhmi.org#join-our-team
1/4
Reposted by Stephan Saalfeld
🚨 new work from the lab on how eye movements 👀 versus orofacial movements influence 🐭 visual cortex activity 🧠 #neuroscience #behavior #neuroAI
Excited to share “Orofacial behaviors, not eye movements, govern neural activity in mouse visual cortex”
www.biorxiv.org/content/10.6...
Summary below...
www.biorxiv.org/content/10.6...
Summary below...
February 9, 2026 at 5:39 PM
🚨 new work from the lab on how eye movements 👀 versus orofacial movements influence 🐭 visual cortex activity 🧠 #neuroscience #behavior #neuroAI
Reposted by Stephan Saalfeld
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...)
February 6, 2026 at 11:20 AM
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...)
Reposted by Stephan Saalfeld
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...
www.jneurosci.org/content/earl...
January 30, 2026 at 9:49 AM
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...
www.jneurosci.org/content/earl...
Reposted by Stephan Saalfeld
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
@poldresden.bsky.social @mpi-cbg.de
January 28, 2026 at 4:10 PM
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
@poldresden.bsky.social @mpi-cbg.de
Reposted by Stephan Saalfeld
PhD position in my lab!
January 28, 2026 at 5:25 PM
PhD position in my lab!
Reposted by Stephan Saalfeld
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/...
journals.biologists.com/jcs/article/...
🧪 We are excited to share this novel open access paper on Phasor Mixing Coefficient to analyze colocalization, developed by folks @i2janelia.bsky.social and @aicjanelia.bsky.social. This is also the first technical paper jointly published with our sister imaging center @malacridalab.bsky.social!
January 28, 2026 at 5:53 PM
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/...
journals.biologists.com/jcs/article/...
Reposted by Stephan Saalfeld
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]
"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]
January 13, 2026 at 7:08 AM
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]
"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]
Reposted by Stephan Saalfeld
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.
January 2, 2026 at 5:52 PM
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.
Reposted by Stephan Saalfeld
Are you a bachelor or master student anywhere in the world, and would like to come to us to work full-time on a supervised research project? Applications for the 2026 MPIA Summer Internship are open now!
Summer internships
www.mpia.de
December 17, 2025 at 9:13 PM
Are you a bachelor or master student anywhere in the world, and would like to come to us to work full-time on a supervised research project? Applications for the 2026 MPIA Summer Internship are open now!
Reposted by Stephan Saalfeld
Final version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
December 19, 2025 at 4:45 PM
Final version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.
Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
Reposted by Stephan Saalfeld
New preprint showing how the membrane-associated periodic skeleton (MPS) restricts endocytosis in neurons: www.biorxiv.org/content/10.6...
It nicely confirms our work from last year (science.org/doi/10.1126/science.ado2032) and extends it to other compartments in more mature neurons
It nicely confirms our work from last year (science.org/doi/10.1126/science.ado2032) and extends it to other compartments in more mature neurons
Membrane-associated periodic skeleton regulates major forms of endocytosis in neurons through a signaling-driven positive feedback loop
Endocytosis enables neurons to internalize molecules, maintaining homeostasis and responsiveness. The neuronal membrane-associated periodic skeleton (MPS), an actin-spectrin-based cytoskeletal lattice...
www.biorxiv.org
December 17, 2025 at 11:48 AM
New preprint showing how the membrane-associated periodic skeleton (MPS) restricts endocytosis in neurons: www.biorxiv.org/content/10.6...
It nicely confirms our work from last year (science.org/doi/10.1126/science.ado2032) and extends it to other compartments in more mature neurons
It nicely confirms our work from last year (science.org/doi/10.1126/science.ado2032) and extends it to other compartments in more mature neurons
Reposted by Stephan Saalfeld
Apply by Feb. 3 to become a Janelia Group Leader!
Group Leaders drive breakthroughs & experimental approaches in imaging, molecular engineering, protein chemistry, mass spectrometry, & methods that don't yet exist. Learn more: janelia.org/groupleader 🧪
Group Leaders drive breakthroughs & experimental approaches in imaging, molecular engineering, protein chemistry, mass spectrometry, & methods that don't yet exist. Learn more: janelia.org/groupleader 🧪
December 15, 2025 at 3:10 PM
Apply by Feb. 3 to become a Janelia Group Leader!
Group Leaders drive breakthroughs & experimental approaches in imaging, molecular engineering, protein chemistry, mass spectrometry, & methods that don't yet exist. Learn more: janelia.org/groupleader 🧪
Group Leaders drive breakthroughs & experimental approaches in imaging, molecular engineering, protein chemistry, mass spectrometry, & methods that don't yet exist. Learn more: janelia.org/groupleader 🧪
Reposted by Stephan Saalfeld
An awesome figure illustrating key aspects of hippocampal encoding and replay during continuous behavior ; from great work by Brian Lustig and co www.biorxiv.org/content/10.6...
December 14, 2025 at 2:35 AM
An awesome figure illustrating key aspects of hippocampal encoding and replay during continuous behavior ; from great work by Brian Lustig and co www.biorxiv.org/content/10.6...
Reposted by Stephan Saalfeld
Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets https://www.biorxiv.org/content/10.64898/2025.12.10.693416v1
December 13, 2025 at 6:46 AM
Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets https://www.biorxiv.org/content/10.64898/2025.12.10.693416v1
Reposted by Stephan Saalfeld
I am currently reading Innumeracy.
We were warned about the dangers of a society incapable of doing basic math 37 years ago.
How I wish elected officials, anti-vaxxers and conspiracy theorists would read that book😞.
We were warned about the dangers of a society incapable of doing basic math 37 years ago.
How I wish elected officials, anti-vaxxers and conspiracy theorists would read that book😞.
December 12, 2025 at 6:33 PM
I am currently reading Innumeracy.
We were warned about the dangers of a society incapable of doing basic math 37 years ago.
How I wish elected officials, anti-vaxxers and conspiracy theorists would read that book😞.
We were warned about the dangers of a society incapable of doing basic math 37 years ago.
How I wish elected officials, anti-vaxxers and conspiracy theorists would read that book😞.
Reposted by Stephan Saalfeld
New release of #BigVolumeBrowser. Many things were added: UI improvement (thanks to @kwolbachia.bsky.social feedback), pyramidization for BioFormats dataset, bug fixes.
Now there is an isosurface rendering mode (1/4)
Now there is an isosurface rendering mode (1/4)
December 12, 2025 at 10:10 AM
New release of #BigVolumeBrowser. Many things were added: UI improvement (thanks to @kwolbachia.bsky.social feedback), pyramidization for BioFormats dataset, bug fixes.
Now there is an isosurface rendering mode (1/4)
Now there is an isosurface rendering mode (1/4)
Devcontainers are great. But related, does anybody know of a good mechanism to bleep the secrets that ClaudeCode or OpenCode spill when they decide to ignore deny rules? Like a rule that replaceAll()s everything on the client before it goes out?
December 12, 2025 at 4:03 AM
Devcontainers are great. But related, does anybody know of a good mechanism to bleep the secrets that ClaudeCode or OpenCode spill when they decide to ignore deny rules? Like a rule that replaceAll()s everything on the client before it goes out?
Reposted by Stephan Saalfeld
I had heard this was coming, but it’s still an amazing indication of how far we’ve come in the last decade or so!
Our Method of the Year 2025 is...drumroll please...EM-based connectomics!!
Our Editorial introduces our choice and highlights six Comments and other related content in this special issue. Please join us in celebrating EM-based connectomics! 🎉🧠🔬
www.nature.com/articles/s41...
Our Editorial introduces our choice and highlights six Comments and other related content in this special issue. Please join us in celebrating EM-based connectomics! 🎉🧠🔬
www.nature.com/articles/s41...
Method of the Year 2025: electron microscopy-based connectomics - Nature Methods
A large network of interconnected neurons serves as the basis of brain function and of behavior. Methodological advances have enabled the reconstruction of large-scale and even whole-brain connectomes...
www.nature.com
December 8, 2025 at 5:47 PM
I had heard this was coming, but it’s still an amazing indication of how far we’ve come in the last decade or so!
Reposted by Stephan Saalfeld
Have you ever wondered what you would find if you could keep your eyes on a bee for more than a few meters? Us, too!
preprint (with videos!) + thread 🧵
Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking
www.biorxiv.org/content/10.6...
1/9
preprint (with videos!) + thread 🧵
Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking
www.biorxiv.org/content/10.6...
1/9
December 6, 2025 at 2:01 PM
Have you ever wondered what you would find if you could keep your eyes on a bee for more than a few meters? Us, too!
preprint (with videos!) + thread 🧵
Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking
www.biorxiv.org/content/10.6...
1/9
preprint (with videos!) + thread 🧵
Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking
www.biorxiv.org/content/10.6...
1/9
Reposted by Stephan Saalfeld
(1/2): Using cryo-electron tomography and an instrument like this one, HHMI Investigator Michael Rosen & team (not pictured) have captured the most detailed images to date of the molecules inside chromatin condensates. hhmi.news/4iFBIrV
December 5, 2025 at 5:43 PM
(1/2): Using cryo-electron tomography and an instrument like this one, HHMI Investigator Michael Rosen & team (not pictured) have captured the most detailed images to date of the molecules inside chromatin condensates. hhmi.news/4iFBIrV
Reposted by Stephan Saalfeld
Very excited to show off our latest data. Videos hot off the microscope! Come see what crazy things cells of al types are up to tomorrow!
Cells can hunt prey, solve mazes, and learn from past experience. Does this mean they can think, at some level? Find out more at our upcoming session on "Cell Behavior and Cognition" at the ASCB/EMBO #cellbio2025 meeting, Saturday 1-3 pm rm 115.
December 5, 2025 at 8:45 PM
Very excited to show off our latest data. Videos hot off the microscope! Come see what crazy things cells of al types are up to tomorrow!
Reposted by Stephan Saalfeld
I am very much in favor, we just put out a recent preprint thinking about learning to navigate from the perspective of generative models of trajectories www.biorxiv.org/content/10.1...
Composing trajectories for rapid inference of navigational goals
Animals efficiently learn to navigate their environment. In the laboratory, naive mice explore their environment via highly structured trajectories and can learn to localize new spatial targets in as ...
www.biorxiv.org
December 4, 2025 at 1:27 PM
I am very much in favor, we just put out a recent preprint thinking about learning to navigate from the perspective of generative models of trajectories www.biorxiv.org/content/10.1...
Reposted by Stephan Saalfeld
The era of coding agents is here. How do we approach this as scientists?
Wednesday Dec 10th at 9am PT I'll livestream an interactive demo of what I have learned (matsen.group/agentic.html) about how to leverage agentic coding to do rigorous science.
www.youtube.com/watch?v=Rbhs...
Wednesday Dec 10th at 9am PT I'll livestream an interactive demo of what I have learned (matsen.group/agentic.html) about how to leverage agentic coding to do rigorous science.
www.youtube.com/watch?v=Rbhs...
Agentic Coding for Scientists (Dec 2025 edition)
YouTube video by Erick Matsen
www.youtube.com
December 2, 2025 at 6:57 PM
The era of coding agents is here. How do we approach this as scientists?
Wednesday Dec 10th at 9am PT I'll livestream an interactive demo of what I have learned (matsen.group/agentic.html) about how to leverage agentic coding to do rigorous science.
www.youtube.com/watch?v=Rbhs...
Wednesday Dec 10th at 9am PT I'll livestream an interactive demo of what I have learned (matsen.group/agentic.html) about how to leverage agentic coding to do rigorous science.
www.youtube.com/watch?v=Rbhs...
Reposted by Stephan Saalfeld
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
forum.image.sc/t/toward-bet...
Toward better 2D - 3D registration in BigWarp
BigWarp has so far focused on 2D-2D or 3D-3D registration, and not on 2D-3D registration. After a conversation with @Christian_Tischer , we thought some simple UI changes could make the support for 2...
forum.image.sc
November 29, 2025 at 6:03 PM
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
forum.image.sc/t/toward-bet...
Reposted by Stephan Saalfeld
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)
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
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)
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)