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Benjamin Judkewitz

@benjulab.bsky.social
2.7K followers 387 following 29 posts

brainwide circuits, acoustic communication, danionella, microscopy jlab.berlin

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Reposted by Benjamin Judkewitz
Matt Lovett-Barron @mlovettbarron.bsky.social · 23/09/2026
Our lab's latest paper on the neurobiology of collective behavior is now published www.nature.com/articles/s41... This is the work of a great team in the lab - led by Jo-Hsien Yu, with Geoff Meyerhof, Jimjohn Milan, and Julia Napoli @nature.com @danionella.bsky.social
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Danionella @danionella.bsky.social · 05/07/2026
I thought I was a quirky little underdog fish with cool tricks, widening the model-organism spectrum. Suddenly, headlines: "Billion Dollar Fish Takes Over" Holy Mackerel! I guess there weren't any smaller fish to fry. Anyway, I'm still the same, still making the case for model diversity.
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Emilie Macé @mace-lab.bsky.social · 16/03/2026
1/8. New preprint! Using fUSi in head-fixed mice🐭, we found that arousal events trigger a brain-wide wave of activity 🌊🧠. Surprisingly, this pattern was preserved during opto manipulations of the locus coeruleus, pointing to a minor role for noradrenergic tone. www.biorxiv.org/content/10.6...
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Benjamin Judkewitz @benjulab.bsky.social · 16/03/2026
Do you know if stout infantfish brain size has been quantified – or is this an assumption based on the smaller body? (obviously a reasonable assumption)
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Benjamin Judkewitz @benjulab.bsky.social · 16/03/2026
How do fish localize sound without interaural cues? @johve.bsky.social et al. found a behavioral algorithm for directional hearing that predicts behavior from a pressure/motion phase comparison and accounts for how this relationship varies with distance. www.cell.com/current-biol...
cell.com
An algorithm underlying directional hearing in fish
Veith et al. show how a fish—Danionella cerebrum—can reliably startle away from sound. It uses the relative phase between particle motion and pressure to infer the direction of sound. This sensorimoto...
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Reposted by Benjamin Judkewitz
Alex Schier @schierlab.bsky.social · 12/03/2026
Very happy to see this out. 👏 @yinanwan.bsky.social Bogdan Bintu and team. Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...
science.org
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...
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Benjamin Judkewitz @benjulab.bsky.social · 12/03/2026
Online viewer: atlas.danionella.org/cerebrum Atlas data repository: gin.g-node.org/danionella/d... Code: gin.g-node.org/danionella/K... @danionella.bsky.social
atlas.danionella.org
Danionella c. Brain Atlas
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Benjamin Judkewitz @benjulab.bsky.social · 12/03/2026
Tiny, transparent, and now charted! Our brain atlas of adult Danionella cerebrum includes >200 annotated regions, 29 whole-brain in situs, and male/female reference volumes – openly available, versioned and extendable. Work by @nkadobyansky.bsky.social and team. www.biorxiv.org/content/10.6...
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Reposted by Benjamin Judkewitz
Bahl Lab @bahllab.bsky.social · 05/03/2026
New paper out: www.nature.com/articles/s41... 🥳 Congratulations to our PhD student Katja for her inspiring work just published in Nature Communications on how the larval zebrafish brain processes multiple visual features. Check out a short summary of the work here: tinyurl.com/yzv4ct9k
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Benjamin Judkewitz @benjulab.bsky.social · 05/03/2026
First whole-brain recording of social sound processing in a vertebrate. Surprises start in the hindbrain; thalamus gates conspecific calls; male and female brains diverge downstream. Work by @joerghenninger.bsky.social, @mh123.bsky.social sky.social and team. www.biorxiv.org/content/10.6...
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Hao Yin @haoyin.bsky.social · 10/02/2026
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...
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Benjamin Judkewitz @benjulab.bsky.social · 29/01/2026
Our updated @napari.org video plugin includes a small widget to play videos with sound. github.com/danionella/n...
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Institut de Psychiatrie et Neuroscience de Paris (Inserm 1266) @ipnp.bsky.social · 29/06/2025
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
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Reposted by Benjamin Judkewitz
Owen Randlett @owenrandlett.bsky.social · 21/05/2025
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!
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Benjamin Judkewitz @benjulab.bsky.social · 21/05/2025
I‘m really glad it works for you and thanks a lot for sharing! Watching this video is satisfying to me, too!
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Benjamin Judkewitz @benjulab.bsky.social · 18/05/2025
Welcome, Kim!
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Benjamin Judkewitz @benjulab.bsky.social · 12/05/2025
Haven't tried but it might work. Is the part at the same resolution as the whole? Same-to-same or same-to-similar sample? Consider posting photos & details here: github.com/danionella/w... Warpfield determines transformations between 3D volumes only, and can apply them to 3D volumes and coordinates.
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Benjamin Judkewitz @benjulab.bsky.social · 12/05/2025
They do have cabbage scans: stacks.wellcomecollection.org/peering-thro...
stacks.wellcomecollection.org
Peering through MRI scans of fruit and veg, part 1
What do you see when you pass fruit and vegetables through an MRI scanner? And how many animated GIFs can you make?
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Benjamin Judkewitz @benjulab.bsky.social · 12/05/2025
Who wouldn't want to do that? Unfortunately I don't think this would be a good tool for it. You probably need many discontinuities and flips to go from car to artichoke. Although not (yet) strictly enforced, this library tends to generate smooth fields and local displacements.
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Benjamin Judkewitz @benjulab.bsky.social · 12/05/2025
Since alt-text doesn't seem to render for videos, here are the video credits: Registration of artichoke 3D MRI using warpfield. Data by Alexandr Khrapichev, Oxford (source: Wellcome Collection, CC BY).
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Benjamin Judkewitz @benjulab.bsky.social · 12/05/2025
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...
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Benjamin Judkewitz @benjulab.bsky.social · 06/05/2025
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.com
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
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Katie Tschida @katietschida.bsky.social · 26/03/2025
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...
biorxiv.org
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...
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Benjamin Judkewitz @benjulab.bsky.social · 03/11/2024
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
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Dinu F Albeanu @dinanthos.bsky.social · 14/01/2025
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!
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Peter Rupprecht @ptrrupprecht.bsky.social · 08/01/2025
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...
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Portugues Lab @portugueslab.bsky.social · 20/12/2024
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.
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Urs Böhm @urslucasboehm.bsky.social · 18/12/2024
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
job offer for a postdoctoral position working on zebrafish spinal cord imaging
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Benjamin Judkewitz @benjulab.bsky.social · 18/12/2024
Why not?
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Reposted by Benjamin Judkewitz
Inbal Shainer @ishainer.bsky.social · 12/12/2024
Come join us! Please repost 🙏🏼
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Benjamin Judkewitz @benjulab.bsky.social · 12/12/2024
Nice! Do you expect the same effect for 2D and 3D interpolations?
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Benjamin Judkewitz @benjulab.bsky.social · 10/12/2024
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.
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Benjamin Judkewitz @benjulab.bsky.social · 04/12/2024
Could you add me, please?
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Benjamin Judkewitz @benjulab.bsky.social · 29/11/2024
Next stop: brain. We are interested in brain-wide circuits underlying acoustic communication (from hearing to sound production), which we currently study with the volumetric whole-brain microscope developed by @mh123.bsky.social and Jörg Henninger. www.nature.com/articles/s41...
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Benjamin Judkewitz @benjulab.bsky.social · 29/11/2024
How do they know who is talking? Sound localization by fish was long considered physically impossible, and yet it was shown behaviorally. With underwater sound illusions and laser vibrometry, Johannes Veith and @tomchaigne.bsky.social identified an underlying mechanism www.nature.com/articles/s41...
nature.com
The mechanism for directional hearing in fish - Nature
A study demonstrates that the fish Danionella cerebrum is able to discriminate the direction of sound by comparing the relative phase of pressure and particle motion.
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Benjamin Judkewitz @benjulab.bsky.social · 29/11/2024
Danionella clicks can reach 140 dB! How can a tiny fish under 12 mm produce such unusually loud sounds? Verity Cook found a unique sound production apparatus that shoots a specialized cartilage against the swim bladder, accelerating at over 20000 m/s^2: www.pnas.org/doi/10.1073/... Video with sound
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Benjamin Judkewitz @benjulab.bsky.social · 29/11/2024
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.... 🧵
doi.org
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.
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Benjamin Judkewitz @benjulab.bsky.social · 13/11/2024
by the one and only @urslucasboehm.bsky.social, who just joined bluesky
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Benjamin Judkewitz @benjulab.bsky.social · 13/11/2024
Could you add me, please?
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Mike Ando @dmikeando.bsky.social · 19/09/2024
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
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Benjamin Judkewitz @benjulab.bsky.social · 13/11/2024
Thank you for this list! Could you add me too, please?
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Laura Grima @lauragrima.bsky.social · 10/11/2024
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
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Benjamin Judkewitz @benjulab.bsky.social · 11/11/2024
Aren't mice bony fishes with fur? (could you add me too, please?)
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Benjamin Judkewitz @benjulab.bsky.social · 10/11/2024
Me too! Thanks for putting it together.
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Danionella @danionella.bsky.social · 07/11/2024
Switched waters to Bluesky. Still singing, still transparent, and back to having the smallest vertebrate brain around.
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Fredrik Jutfelt 🐠 @jutfelt.bsky.social · 07/11/2024
I think science twitter is finally moving here. Welcome everybody! 🧪
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Benjamin Judkewitz @benjulab.bsky.social · 07/11/2024
Now published as www.nature.com/articles/s41...
nature.com
Fast and light-efficient remote focusing for volumetric voltage imaging - Nature Communications
The authors develop a high-speed remote focusing method for volumetric voltage imaging enabling imaging at 500 volumes/s. This is combined with light sheet microscopy to record data from >100 ...
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Benjamin Judkewitz @benjulab.bsky.social · 03/11/2024
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
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