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

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!

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

Welcome, Kim!

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.

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?

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

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.

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).

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...

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...

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...

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...

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

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!

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...

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.

job offer for a postdoctoral position working on zebrafish spinal cord imaging

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

Why not?

Come join us! Please repost 🙏🏼

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

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.

Could you add me, please?

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...

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.

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...

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

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.

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....
🧵

by the one and only @urslucasboehm.bsky.social, who just joined bluesky

Could you add me, please?

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

Thank you for this list! Could you add me too, please?

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