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Reposted by Benjamin Judkewitz

Institut de Psychiatrie et Neuroscience de Paris (Inserm 1266) @ipnp.bsky.social · Jun 29

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 · May 21

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 · May 21

I‘m really glad it works for you and thanks a lot for sharing! Watching this video is satisfying to me, too!

Benjamin Judkewitz @benjulab.bsky.social · May 18

Welcome, Kim!

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Benjamin Judkewitz @benjulab.bsky.social · May 12

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 · May 12

They do have cabbage scans: stacks.wellcomecollection.org/peering-thro...

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?

stacks.wellcomecollection.org

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Benjamin Judkewitz @benjulab.bsky.social · May 12

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 · May 12

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 · May 12

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 · May 6

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

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Reposted by Benjamin Judkewitz

Katie Tschida @katietschida.bsky.social · Mar 26

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...

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

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Reposted by Benjamin Judkewitz

Benjamin Judkewitz @benjulab.bsky.social · Nov 3

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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Reposted by Benjamin Judkewitz

Dinu F Albeanu @dinanthos.bsky.social · Jan 14

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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Reposted by Benjamin Judkewitz

Peter Rupprecht @ptrrupprecht.bsky.social · Jan 8

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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Reposted by Benjamin Judkewitz

Portugues Lab @portugueslab.bsky.social · Dec 20

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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Reposted by Benjamin Judkewitz

Urs Böhm @urslucasboehm.bsky.social · Dec 18

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 · Dec 18

Why not?

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Reposted by Benjamin Judkewitz

Inbal Shainer 🎗️ @ishainer.bsky.social · Dec 12

Come join us! Please repost 🙏🏼

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Benjamin Judkewitz @benjulab.bsky.social · Dec 12

Nice! Do you expect the same effect for 2D and 3D interpolations?

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Benjamin Judkewitz @benjulab.bsky.social · Dec 10

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 · Dec 4

Could you add me, please?

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Benjamin Judkewitz @benjulab.bsky.social · Nov 29

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 · Nov 29

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...

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.

www.nature.com

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Benjamin Judkewitz @benjulab.bsky.social · Nov 29

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 · Nov 29

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....
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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

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