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...

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)

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...

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...

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...

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...

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

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...

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

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...

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...

Our updated @napari.org video plugin includes a small widget to play videos with sound. github.com/danionella/n...

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.