Jure Majnik

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...

20 lessons in team science: Learning from the experience of the International Brain Laboratory Leveraging large-scale neuroscience datasets requires new collaborative approaches. The International Brain Laboratory (IBL) is a distributed, open-science experiment facing these challenges. To succe...

www.cell.com/neuron/abstr...

An exciting study with Roberto Garza and Armin Bahl
biorxiv.org/content/10.6...
We combine high-throughput behavioral assays in larval zebrafish with drift-diffusion modeling studying integration dynamics across development and a variety of mutants . Give it a read :D

🛠️ February’s most-read Tools and Resources paper introduces idtracker.ai to rethink multi-animal tracking: buff.ly/Ho0b3xz

Learn more about publishing your tools or resources with us: buff.ly/pivLQX0

The ratstronaut dataset is available on DANDI!

(and analyzed with @pynapple.bsky.social 😍)

🔬🧠 Releasing the 1.0 version of #Suite2p and THE PAPER w/ @marius10p.bsky.social! Now with GPU acceleration. Want to use Suite2p but don’t have 100,000 neuron recordings? We show you how to get those with a standard 2p microscope #neuroscience #imaging #neuroAI www.biorxiv.org/content/10.6...

New paper alert! 🚨

We found that the brain's compass is remarkably stable at two scales

1️⃣ the system maintains its internal organization for weeks
2️⃣ It "remembers" its orientation for weeks, even after a single visit

This may be key to how the brain aligns its other maps.

Paper: rdcu.be/e3waP

Two posts that both illustrate the variation essential to living things--one of fruit fly ovaries and the other cultured COS cells

A perfect chance juxtaposition of posts emphasizing that variation is at the center of life, and we need approaches that highlight rather than average out that variation

This is who runs this account

A computational approach to visual ecology with deep reinforcement learning Animal vision is thought to optimize various objectives from metabolic efficiency to discrimination performance, yet its ultimate objective is to facilitate the survival of the animal within its ecolo...

I helped with this project during an MSc internship: arxiv.org/abs/2402.05266, I guess that might be an idea along those lines? Of course it depends a bit what one considers as being 'rich' in terms of stim/behaviour :)

The commitments in the SAFE Labs Handbook.

A new community-driven lab handbook for reducing conflict and creating more positive and equitable work environments gets strong support from a survey of 200 researchers.
buff.ly/K7CGFLV

I am very happy (and a bit scared) to present to you what we have been working on over the last 4 years. This manuscript is exactly what I dreamt of when I started the lab and I could not be happier and prouder of the outcome!

Examples of sequences of activity seen in multiple regions of the brain

Sequences are everywhere! In every brain region. And are written in stone.

Invariant Activity Sequences Across the Mouse Brain.

Out today, by Célian Bimbard, with @kenneth-harris.bsky.social.

Based on data by Célian and by @intlbrainlab.bsky.social.

www.biorxiv.org/content/10.6...

“A process which led from the amoeba to man appeared to the philosophers to be obviously a progress - though whether the amoeba would agree with this opinion is not known"
- Bertrand Russell, 1976.

Time-lapse video of Vampyrella lateritia eating Spirogyra algae from Science Source/Oliver Skibbe. 🦠

And here is the PDF of the 4th course @college-de-france.fr. You will find the justification and presentation of geometric representation of cell decisions, a parsimonious mathematical model for signalling and cell state transitions

tinyurl.com/yc7u296j

Thanks to all the co-authors, I had great fun working on this for the last couple of years :)

And for a TLDR/summary of the paper you can check the 'blusky'-print from the bioarxiv version of the paper: bsky.app/profile/jure...

Neuronal Activity: Keeping track of moving targets A new method for tracking the activity of individual neurons day after day in the growing brain has revealed a key developmental transition in neuronal activity.

Also with a beautifully written 'insight article' by Renata Batista-Brito and Geoffrey Terral:
*Neuronal Activity: Keeping track of moving targets*
elifesciences.org/articles/109...

My first paper just got published last week!
*Longitudinal tracking of neuronal activity from the same cells in the developing brain using Track2p*
elifesciences.org/articles/107...

Intravital observation of neuronal and immune cell dynamics in the developing mammalian brain: @cellpress.bsky.social www.cell.com/cell/fulltex...

Spatial and morphological organization of mitochondria in neurons across a connectome Neuronal function depends on mitochondria, but little is known about their organization across neurons. Using an electron microscopy Drosophila connectome, we uncovered quantitative rules governing th...

A paper from my PhD lab is on Science! This is a really cool new way to utilize EM connectome datasets. Congrats to the team!
www.science.org/doi/10.1126/...

How do neural circuits generate the walking rhythm?

Using connectome simulations, @sarahpugly.bsky.social found a minimal central pattern generator (CPG) that produces oscillations in leg motor neurons. Same circuit motif for each 🪰 leg.

w @bingbrunton.bsky.social

www.biorxiv.org/content/10.1...

Method of the Year 2025: electron microscopy-based connectomics - Nature Methods A large network of interconnected neurons serves as the basis of brain function and of behavior. Methodological advances have enabled the reconstruction of large-scale and even whole-brain connectomes...

Our Method of the Year 2025 is...drumroll please...EM-based connectomics!!

Our Editorial introduces our choice and highlights six Comments and other related content in this special issue. Please join us in celebrating EM-based connectomics! 🎉🧠🔬

www.nature.com/articles/s41...

Flipbook of zebrafish embryogenesis. Taken from December 1996 issue of @dev-journal.bsky.social. Still images from movie by Rolf Karlstrom and Don Kane. Flipping credit to @amjeve.bsky.social. #ZebrafishZunday #ZebrafishFunFacts 🧪

Reconstructing Waddington’s landscape from data | PNAS The development of a zygote into a functional organism requires that this single progenitor cell gives rise to numerous distinct cell types. Attemp...

Great to see this published: Fitting dynamical landscape models to single-cell data, creating interpretable maps of cell decision making & developmental logic

Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions

www.pnas.org/doi/10.1073/...

Happy to share the first paper from my journey at @psich.bsky.social towards X-ray connectomics, now out in @natmethods.nature.com: www.nature.com/articles/s41...

Our new paper showcasing molecular connectomics with pan-expansion microscopy is out in @natbiotech.nature.com! www.nature.com/articles/s41...
This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)

Hi, I’m David Brückner @davidbrueckner.bsky.social.

I’ll take you through how cells in a tissue can use information distributed by biochemical gradients to make decisions, and how we can measure such positional information.

buff.ly/RFxVeHh

Jaxley: differentiable simulation enables large-scale training of detailed biophysical models of neural dynamics - Nature Methods Jaxley is a versatile platform for biophysical modeling in neuroscience. It allows efficiently simulating large-scale biophysical models on CPUs, GPUs and TPUs. Model parameters can be optimized with ...

Our work on training biophysical models with Jaxley is now out in @natmethods.nature.com. Led by @deismic.bsky.social, with @philipp.hertie.ai, @ppjgoncalves.bsky.social & @jakhmack.bsky.social et al.

Paper: www.nature.com/articles/s41...

Felix Zhou's u-Segment3D is out:

www.nature.com/articles/s41...

It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.

It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.