Benjamin Judkewitz
@benjulab.bsky.social
brainwide circuits, animal communication, danionella, microscopy
https://jlab.berlin
https://jlab.berlin
Pinned
We’re seeking a postdoc/student excited about animal communication, brain-wide circuits, microscopy, singing fish (Danionella), wacky ideas and who likes to: get things done, experiment, analyze, ask, learn, help and cooperate. jlab.berlin
Reposted by Benjamin Judkewitz
Whole-body Single-cell Spatial transcriptomic atlas of adult Danionella ~1 cm long
scRNAseq
MERFISH (500-gene)
HCR
Endothelial cell podxl+ (Fig S8)
Vascular vs Visceral mural cell (Fig S10)
Peter Reddien lab bioRxiv 2026
www.biorxiv.org/content/10.6...
scRNAseq
MERFISH (500-gene)
HCR
Endothelial cell podxl+ (Fig S8)
Vascular vs Visceral mural cell (Fig S10)
Peter Reddien lab bioRxiv 2026
www.biorxiv.org/content/10.6...
February 10, 2026 at 12:57 PM
Whole-body Single-cell Spatial transcriptomic atlas of adult Danionella ~1 cm long
scRNAseq
MERFISH (500-gene)
HCR
Endothelial cell podxl+ (Fig S8)
Vascular vs Visceral mural cell (Fig S10)
Peter Reddien lab bioRxiv 2026
www.biorxiv.org/content/10.6...
scRNAseq
MERFISH (500-gene)
HCR
Endothelial cell podxl+ (Fig S8)
Vascular vs Visceral mural cell (Fig S10)
Peter Reddien lab bioRxiv 2026
www.biorxiv.org/content/10.6...
Our updated @napari.org video plugin includes a small widget to play videos with sound. github.com/danionella/n...
January 29, 2026 at 10:08 AM
Our updated @napari.org video plugin includes a small widget to play videos with sound. github.com/danionella/n...
Reposted by Benjamin Judkewitz
Congratulations to Urs Lucas Bohm, junior leader a @ipnp.bsky.social, for his latest achievement: he is recipient of the ATIP-Avenir award for his work on spinal cord network contribution to motor behaviors, using voltage imaging techniques in zebrafish! Keep going, Urs! @inserm.fr #motordisease
June 29, 2025 at 8:59 AM
Congratulations to Urs Lucas Bohm, junior leader a @ipnp.bsky.social, for his latest achievement: he is recipient of the ATIP-Avenir award for his work on spinal cord network contribution to motor behaviors, using voltage imaging techniques in zebrafish! Keep going, Urs! @inserm.fr #motordisease
Reposted by Benjamin Judkewitz
This is great -- thanks for your efforts and the documentation. We've got it up and running for tERK stains. Some kinks for us work out but running registrations in a few seconds is so very satisfying!
May 21, 2025 at 2:30 PM
This is great -- thanks for your efforts and the documentation. We've got it up and running for tERK stains. Some kinks for us work out but running registrations in a few seconds is so very satisfying!
Introducing warpfield, an open source Python library for GPU-accelerated non-rigid 3D registration. Warps and aligns gigavoxel volumes within seconds (not hours). For 3D microscopy, region-to-region and cell-to-cell matching.
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...
May 12, 2025 at 5:25 AM
Introducing warpfield, an open source Python library for GPU-accelerated non-rigid 3D registration. Warps and aligns gigavoxel volumes within seconds (not hours). For 3D microscopy, region-to-region and cell-to-cell matching.
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...
We are releasing a GPU-accelerated oblique interpolation library for oblique plane microscopy (OPM) volume reconstruction. It avoids aliasing and interpolation artifacts caused by rectilinear interpolation approaches. github.com/danionella/o...
GitHub - danionella/opm_unshear: GPU-accelerated oblique interpolation for volume unshearing / deskewing in oblique plane microscopy (OPM)
GPU-accelerated oblique interpolation for volume unshearing / deskewing in oblique plane microscopy (OPM) - danionella/opm_unshear
github.com
May 6, 2025 at 6:15 AM
We are releasing a GPU-accelerated oblique interpolation library for oblique plane microscopy (OPM) volume reconstruction. It avoids aliasing and interpolation artifacts caused by rectilinear interpolation approaches. github.com/danionella/o...
Reposted by Benjamin Judkewitz
Another study to share, led by my grad student Nicole Pranic! Before diving in, I'll add that Nicole (who is clever, tenacious, and interested in neural changes that underlie developmental changes in social behaviors) is looking for a post-doc position! Please RT!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Vocal ontogeny in Mus musculus
Infants of many species produce distress calls when in need of parental care. As they mature and gain independence from caregivers, juveniles stop producing infant calls and begin producing adult-like...
www.biorxiv.org
March 26, 2025 at 7:03 PM
Another study to share, led by my grad student Nicole Pranic! Before diving in, I'll add that Nicole (who is clever, tenacious, and interested in neural changes that underlie developmental changes in social behaviors) is looking for a post-doc position! Please RT!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Benjamin Judkewitz
We’re seeking a postdoc/student excited about animal communication, brain-wide circuits, microscopy, singing fish (Danionella), wacky ideas and who likes to: get things done, experiment, analyze, ask, learn, help and cooperate. jlab.berlin
November 3, 2024 at 12:22 PM
We’re seeking a postdoc/student excited about animal communication, brain-wide circuits, microscopy, singing fish (Danionella), wacky ideas and who likes to: get things done, experiment, analyze, ask, learn, help and cooperate. jlab.berlin
Reposted by Benjamin Judkewitz
Interested in understanding how things work? In particular the tools you use to study the brain? Join us at TENSS 2025 where we brainstorm ideas, build and debug microscopes, electrophysiology and behavior rigs amidst the picturesque Transylvanian hills! tenss.ro
Apply by: February 16th!
Apply by: February 16th!
January 14, 2025 at 4:58 AM
Interested in understanding how things work? In particular the tools you use to study the brain? Join us at TENSS 2025 where we brainstorm ideas, build and debug microscopes, electrophysiology and behavior rigs amidst the picturesque Transylvanian hills! tenss.ro
Apply by: February 16th!
Apply by: February 16th!
Reposted by Benjamin Judkewitz
If you want to understand the brain, should you work as a neuroscientist in the lab? Or teach the subject for students? Or simply read textbooks and papers while having a normal job? In this blog post, I share some thoughts on this topic. gcamp6f.com/2025/01/08/a...
January 8, 2025 at 11:25 PM
If you want to understand the brain, should you work as a neuroscientist in the lab? Or teach the subject for students? Or simply read textbooks and papers while having a normal job? In this blog post, I share some thoughts on this topic. gcamp6f.com/2025/01/08/a...
Reposted by Benjamin Judkewitz
1/3 How does visual input affect the heading direction (HD) network?
In our latest lab preprint, Ryosuke presents "visual landmarks" to larval zebrafish and shows that the HD network tethers to the visual environment. The experiments are again inspired by the beautiful recent work in Drosophila.
In our latest lab preprint, Ryosuke presents "visual landmarks" to larval zebrafish and shows that the HD network tethers to the visual environment. The experiments are again inspired by the beautiful recent work in Drosophila.
December 20, 2024 at 8:34 AM
1/3 How does visual input affect the heading direction (HD) network?
In our latest lab preprint, Ryosuke presents "visual landmarks" to larval zebrafish and shows that the HD network tethers to the visual environment. The experiments are again inspired by the beautiful recent work in Drosophila.
In our latest lab preprint, Ryosuke presents "visual landmarks" to larval zebrafish and shows that the HD network tethers to the visual environment. The experiments are again inspired by the beautiful recent work in Drosophila.
Reposted by Benjamin Judkewitz
job offer! I am looking for a postdoc to join the nascent team. Come work with us to build microscopes and study spinal cord circuits. #ZebrafishCareers
December 18, 2024 at 5:31 PM
job offer! I am looking for a postdoc to join the nascent team. Come work with us to build microscopes and study spinal cord circuits. #ZebrafishCareers
Reposted by Benjamin Judkewitz
Come join us! Please repost 🙏🏼
December 12, 2024 at 2:32 PM
Come join us! Please repost 🙏🏼
High-speed 3D random access two-photon imaging at ≥ 300 kHz – with SPARCLS: opg.optica.org/optica/fullt...
By the outstanding @carolineberlage.bsky.social and team, including @urslucasboehm.bsky.social, @andrewplested.bsky.social et al.
By the outstanding @carolineberlage.bsky.social and team, including @urslucasboehm.bsky.social, @andrewplested.bsky.social et al.
December 10, 2024 at 8:17 PM
High-speed 3D random access two-photon imaging at ≥ 300 kHz – with SPARCLS: opg.optica.org/optica/fullt...
By the outstanding @carolineberlage.bsky.social and team, including @urslucasboehm.bsky.social, @andrewplested.bsky.social et al.
By the outstanding @carolineberlage.bsky.social and team, including @urslucasboehm.bsky.social, @andrewplested.bsky.social et al.
Reintroducing the lab by featuring some recent papers on acoustic communication in the tiny glassfish Danionella cerebrum (@danionella.bsky.social).
Antonia Groneberg carefully characterized the ontogeny of their singing in JEB: doi.org/10.1242/jeb....
🧵
Antonia Groneberg carefully characterized the ontogeny of their singing in JEB: doi.org/10.1242/jeb....
🧵
Development of sound production in Danionella cerebrum
Highlighted Article:Danionella cerebrum is one of the smallest vertebrates known to perform acoustic communication: juvenile fish develop their sexually dimorphic ability for sound production.
doi.org
November 29, 2024 at 8:49 PM
Reintroducing the lab by featuring some recent papers on acoustic communication in the tiny glassfish Danionella cerebrum (@danionella.bsky.social).
Antonia Groneberg carefully characterized the ontogeny of their singing in JEB: doi.org/10.1242/jeb....
🧵
Antonia Groneberg carefully characterized the ontogeny of their singing in JEB: doi.org/10.1242/jeb....
🧵
by the one and only @urslucasboehm.bsky.social, who just joined bluesky
Now published as www.nature.com/articles/s41...
November 13, 2024 at 2:08 PM
by the one and only @urslucasboehm.bsky.social, who just joined bluesky
Reposted by Benjamin Judkewitz
It's woefully incomplete, but I've made the start of a starter pack for folks interested in microscopy. Suggestions for who else to include (including yourself!) are very welcome.
go.bsky.app/SaYfAX3
go.bsky.app/SaYfAX3
September 19, 2024 at 4:35 PM
It's woefully incomplete, but I've made the start of a starter pack for folks interested in microscopy. Suggestions for who else to include (including yourself!) are very welcome.
go.bsky.app/SaYfAX3
go.bsky.app/SaYfAX3
Reposted by Benjamin Judkewitz
Just put together the beginnings of a systems & behavior neuro starter pack (focus on rodent work) - obviously a lot of people missing, and most included are in my own little bubble, so if you want to be added do reply here! go.bsky.app/Hxpe53o
November 10, 2024 at 11:58 PM
Just put together the beginnings of a systems & behavior neuro starter pack (focus on rodent work) - obviously a lot of people missing, and most included are in my own little bubble, so if you want to be added do reply here! go.bsky.app/Hxpe53o
Reposted by Benjamin Judkewitz
Switched waters to Bluesky. Still singing, still transparent, and back to having the smallest vertebrate brain around.
November 7, 2024 at 4:58 PM
Switched waters to Bluesky. Still singing, still transparent, and back to having the smallest vertebrate brain around.
Reposted by Benjamin Judkewitz
I think science twitter is finally moving here. Welcome everybody! 🧪
November 7, 2024 at 2:44 PM
I think science twitter is finally moving here. Welcome everybody! 🧪
Now published as www.nature.com/articles/s41...
November 7, 2024 at 4:25 PM
Now published as www.nature.com/articles/s41...
We’re seeking a postdoc/student excited about animal communication, brain-wide circuits, microscopy, singing fish (Danionella), wacky ideas and who likes to: get things done, experiment, analyze, ask, learn, help and cooperate. jlab.berlin
November 3, 2024 at 12:22 PM
We’re seeking a postdoc/student excited about animal communication, brain-wide circuits, microscopy, singing fish (Danionella), wacky ideas and who likes to: get things done, experiment, analyze, ask, learn, help and cooperate. jlab.berlin