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
PhD position in my lab in #AI #RNA, in co-supervision with superstar @florianjug.bsky.social
www.polimi.it/dottorato/fu...
www.polimi.it/dottorato/fu...
November 24, 2025 at 11:05 AM
PhD position in my lab in #AI #RNA, in co-supervision with superstar @florianjug.bsky.social
www.polimi.it/dottorato/fu...
www.polimi.it/dottorato/fu...
Reposted by Stephan Saalfeld
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
Reposted by Stephan Saalfeld
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...
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
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...
forum.image.sc/t/bigvolumeb...
Reposted by Stephan Saalfeld
Wow, huge work, congratulations to all!
November 20, 2025 at 12:40 PM
Wow, huge work, congratulations to all!
Reposted by Stephan Saalfeld
1. New preprint resolving a conundrum in systems neuroscience with an AI scientist, and humans Reilly Tilbury, Dabin Kwon, @haydari.bsky.social, @jacobmratliff.bsky.social, @bio-emergent.bsky.social, @carandinilab.net, @kevinjmiller.bsky.social, @neurokim.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Characterizing neuronal population geometry with AI equation discovery
The visual cortex contains millions of neurons, whose combined activity forms a population code representing visual stimuli. There is, however, a discrepancy between our understanding of this code at ...
www.biorxiv.org
November 14, 2025 at 6:07 PM
1. New preprint resolving a conundrum in systems neuroscience with an AI scientist, and humans Reilly Tilbury, Dabin Kwon, @haydari.bsky.social, @jacobmratliff.bsky.social, @bio-emergent.bsky.social, @carandinilab.net, @kevinjmiller.bsky.social, @neurokim.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Stephan Saalfeld
We are looking for a scientific computing associate interested in data-driven equation discovery here at @hhmijanelia.bsky.social. This is an alternative to a postdoc that you can use to move into academic or software jobs. Please spread the word!
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
Scientific Computing Associate - Data-Driven Equation Discovery
Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. The Howard Hughes Medical Institute’s Janelia Research Campus is a pio...
hhmi.wd1.myworkdayjobs.com
November 7, 2025 at 9:08 PM
We are looking for a scientific computing associate interested in data-driven equation discovery here at @hhmijanelia.bsky.social. This is an alternative to a postdoc that you can use to move into academic or software jobs. Please spread the word!
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
Reposted by Stephan Saalfeld
Curious about or committed to collective behavior? Please register and submit your abstract ASAP! We are hoping to have a big crowd in Heidelberg in February.
Have you submitted your abstract for #EESCollectivity? No? It's about time! This new event will discuss how collective behaviours arise from fundamental principles across biological systems, from cells to animal groups. 🦠🐾
👉 Join us and submit your abstract by 18 Nov: s.embl.org/ees26-01-bl
👉 Join us and submit your abstract by 18 Nov: s.embl.org/ees26-01-bl
November 7, 2025 at 9:55 AM
Curious about or committed to collective behavior? Please register and submit your abstract ASAP! We are hoping to have a big crowd in Heidelberg in February.
Reposted by Stephan Saalfeld
The songbird basal ganglia connectome https://www.biorxiv.org/content/10.1101/2025.10.25.684569v1
October 27, 2025 at 8:15 AM
The songbird basal ganglia connectome https://www.biorxiv.org/content/10.1101/2025.10.25.684569v1
Reposted by Stephan Saalfeld
A new, nerdy paper. We figured out (some) of the rules underlying cell-permeability of probes and designed ligands that light up, grab, and move proteins around. Awesome @hhmijanelia.bsky.social x @uwmadison.bsky.social x @stjuderesearch.bsky.social collaboration! www.pnas.org/doi/10.1073/...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
October 27, 2025 at 9:43 PM
A new, nerdy paper. We figured out (some) of the rules underlying cell-permeability of probes and designed ligands that light up, grab, and move proteins around. Awesome @hhmijanelia.bsky.social x @uwmadison.bsky.social x @stjuderesearch.bsky.social collaboration! www.pnas.org/doi/10.1073/...
Reposted by Stephan Saalfeld
The new @mpi-cbg.de research group leader Daniela Egas Santander is looking for a Postdoctoral Researcher (m/f/d) in Applied Topology for Biology. Apply until November 16th here: careers.mpi-cbg.de/jobs/6002777...
October 24, 2025 at 8:28 AM
The new @mpi-cbg.de research group leader Daniela Egas Santander is looking for a Postdoctoral Researcher (m/f/d) in Applied Topology for Biology. Apply until November 16th here: careers.mpi-cbg.de/jobs/6002777...
Reposted by Stephan Saalfeld
Join the team at Janelia to use #theory, computation, and modeling to tackle bold questions in #biology. Collaborate across scientific disciplines to drive discovery.
Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram
#computationalbiology #sciencecareers
Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram
#computationalbiology #sciencecareers
October 23, 2025 at 5:00 PM
Join the team at Janelia to use #theory, computation, and modeling to tackle bold questions in #biology. Collaborate across scientific disciplines to drive discovery.
Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram
#computationalbiology #sciencecareers
Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram
#computationalbiology #sciencecareers
Reposted by Stephan Saalfeld
Hello dear diary, today I've added some minor features, like highlighting boxes and canvas selecting objects + manual transform mode. Small update, mucho trabajo, but it should be helpful for user experience #bigvolumebrowser
October 17, 2025 at 3:35 PM
Hello dear diary, today I've added some minor features, like highlighting boxes and canvas selecting objects + manual transform mode. Small update, mucho trabajo, but it should be helpful for user experience #bigvolumebrowser
Reposted by Stephan Saalfeld
The Shanahan Fellowship is a unique PostDoc opportunity at the intersection of Neuroscience and Data Science. If you are considering a PostDoc in this area, I encourage you to apply!
Applications are open! And due by Dec 1st
alleninstitute.org/shanahan-fou...
Applications are open! And due by Dec 1st
alleninstitute.org/shanahan-fou...
Allen Institute - Shanahan Foundation Fellowship at the Interface of Data and Neuroscience 2025-2026
Thank you for applying for the Shanahan Foundation Fellowship at the Interface of Data and Neuroscience. Applications for the Fall 2026 cohort will close at 11:59pm PT on December 1st, 2025.
Important...
alleninstitute.submittable.com
October 18, 2025 at 1:14 AM
The Shanahan Fellowship is a unique PostDoc opportunity at the intersection of Neuroscience and Data Science. If you are considering a PostDoc in this area, I encourage you to apply!
Applications are open! And due by Dec 1st
alleninstitute.org/shanahan-fou...
Applications are open! And due by Dec 1st
alleninstitute.org/shanahan-fou...
Reposted by Stephan Saalfeld
Very excited to be co-organizing this meeting. Hope to see you there!
Have you submitted your abstract for #EESCollectivity? No? It's about time! This new event will discuss how collective behaviours arise from fundamental principles across biological systems, from cells to animal groups. 🦠🐾
👉 Join us and submit your abstract by 18 Nov: s.embl.org/ees26-01-bl
👉 Join us and submit your abstract by 18 Nov: s.embl.org/ees26-01-bl
October 17, 2025 at 11:38 AM
Very excited to be co-organizing this meeting. Hope to see you there!
Reposted by Stephan Saalfeld
Excited to share our new #biorxivpreprint:
“Sexual dimorphism in the complete connectome of the Drosophila male central nervous system” www.biorxiv.org/content/10.1...
We describe the #connectomics reconstruction and analysis of an entire adult #maleCNS #drosophila central nervous system. 1/10
“Sexual dimorphism in the complete connectome of the Drosophila male central nervous system” www.biorxiv.org/content/10.1...
We describe the #connectomics reconstruction and analysis of an entire adult #maleCNS #drosophila central nervous system. 1/10
October 15, 2025 at 4:17 PM
Excited to share our new #biorxivpreprint:
“Sexual dimorphism in the complete connectome of the Drosophila male central nervous system” www.biorxiv.org/content/10.1...
We describe the #connectomics reconstruction and analysis of an entire adult #maleCNS #drosophila central nervous system. 1/10
“Sexual dimorphism in the complete connectome of the Drosophila male central nervous system” www.biorxiv.org/content/10.1...
We describe the #connectomics reconstruction and analysis of an entire adult #maleCNS #drosophila central nervous system. 1/10
Reposted by Stephan Saalfeld
The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 11, 2025 at 1:30 PM
The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Stephan Saalfeld
Cell Physics community is missing Jochen Guck deeply.. He was a very kind and generous person, one of the most creative minds, and always ready to help everyone in the field.. He inspired many of us.. He will always be missed..
October 7, 2025 at 7:02 AM
Cell Physics community is missing Jochen Guck deeply.. He was a very kind and generous person, one of the most creative minds, and always ready to help everyone in the field.. He inspired many of us.. He will always be missed..
Reposted by Stephan Saalfeld
Great Job - Great Colleagues - Great Science👍
Help us pick the next generation of @hhmi.org Investigators, Freeman Hrabowski Scholars, Hanna Gray Fellows, Gilliam Fellows
Relocation to DC is required, perfect for academic PIs looking for their next chapter
hhmi.wd1.myworkdayjobs.com/External/job...
Help us pick the next generation of @hhmi.org Investigators, Freeman Hrabowski Scholars, Hanna Gray Fellows, Gilliam Fellows
Relocation to DC is required, perfect for academic PIs looking for their next chapter
hhmi.wd1.myworkdayjobs.com/External/job...
Senior Director - Scientific Officer
Primary Work Address: 4000 Jones Bridge Road, Chevy Chase, MD, 20815 Current HHMI Employees, click here to apply via your Workday account. The Howard Hughes Medical Institute (HHMI) advances the disco...
hhmi.wd1.myworkdayjobs.com
October 9, 2025 at 9:48 PM
Great Job - Great Colleagues - Great Science👍
Help us pick the next generation of @hhmi.org Investigators, Freeman Hrabowski Scholars, Hanna Gray Fellows, Gilliam Fellows
Relocation to DC is required, perfect for academic PIs looking for their next chapter
hhmi.wd1.myworkdayjobs.com/External/job...
Help us pick the next generation of @hhmi.org Investigators, Freeman Hrabowski Scholars, Hanna Gray Fellows, Gilliam Fellows
Relocation to DC is required, perfect for academic PIs looking for their next chapter
hhmi.wd1.myworkdayjobs.com/External/job...
Reposted by Stephan Saalfeld
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. :)
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. :)
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
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
October 7, 2025 at 3:53 PM
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. :)
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. :)
Reposted by Stephan Saalfeld
🔊 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
October 7, 2025 at 8:00 PM
🔊 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
Reposted by Stephan Saalfeld
#QuPath + Imglib2 and #BDV ❤️
Promising start!
(Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)
Promising start!
(Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)
October 7, 2025 at 8:34 PM
#QuPath + Imglib2 and #BDV ❤️
Promising start!
(Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)
Promising start!
(Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)
Reposted by Stephan Saalfeld
Apply now!!! 🔥
October 6, 2025 at 4:44 PM
Apply now!!! 🔥
Reposted by Stephan Saalfeld
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...
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
October 5, 2025 at 6:02 PM
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...
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...