Danionella cerebrum is only 1 cm long but has 600K+ cells, and #HHMIInvestigator Peter Reddien and team have mapped them all. Their website, DigiFish, allows exploration of this cell atlas — the most detailed of an adult vertebrate — enabling regeneration & disease research: bit.ly/4BE1Qgd

#Circuit #mechanisms for disentangled #representations and generalization in the #hippocampus doi.org/10.1038/s415...

Circuit mechanisms for disentangled representations and generalization in the hippocampus - Nature Neuroscience

The hippocampus encodes different aspects of experience as disentangled variables, enabling flexible recombination and generalization to new situations. This code is supported by the geometry of popul...

doi.org

Quantitative Biology in Fin-de-siècle Vienna link.springer.com/article/10.1...

Super excited to see this work by @kutaydeniz.bsky.social now published in Science! doi.org/10.1126/science.aeg1125

Whole-body single-cell atlas of an adult vertebrate, Danionella cerebrum

A complete cell type transcriptome atlas of a vertebrate could promote understanding of animal cell type composition, organization, and evolution. The miniaturized, transparent, and regenerative teleo...

doi.org

New paper from PhD student @sarahpugly.bsky.social, co-advised by @bingbrunton.bsky.social. Neuroscientists have long sought to understand how the nervous system generates the walking rhythm. Sarah walked into our office one day with an unexpected solution... www.nature.com/articles/s41...

Connectome simulations identify a central pattern generator for fly walking - Nature

Computational simulations of a neural network based on fly connectomes identify a three-neuron circuit that is organized to produce leg motor rhythms for walking.

nature.com

Checkout our new preprint 🔬! An eye-opening analysis detailing the adoption of bioimage-analysis tools in microscopy, curated with Bruno Saraiva and @henriqueslab.bsky.social – a thread 🧵: preprint: doi.org/10.64898/2026.10.21.760457 github: github.com/HenriquesLab/mapping-bioimage-software

There's a paper going around saying that AI is now better at peer review than humans. I won't link to it because I assume that like all these AI papers it's just some sort of marketing. My only comment is that we don't have to critique this paper because we already know human PR isn't very good.

What does it mean to say the organism is a SYSTEM? Can we make this concept precise and useful? Paul Weiss showed us how a century ago! In my new paper I recover his neglected systems view & use it to undermine four entrenched theses in biology: reductionism, genocentrism, determinism, & mechanicism

The Organism as a System: Insights from Paul Weiss - Acta Biotheoretica

Despite the remarkable successes of molecular biology over the past three quarters of a century, there is growing recognition that organisms must be understood as integrated systems if we are to fully...

link.springer.com

Neurons in models are often all the same—some researchers are trying to change that. #neuroskyence By @natmesanash.bsky.social www.thetransmitter.org/systems-neur...

Finding neuroheterogeneity’s sweet spot

Once thought to be purely detrimental to memory storage, neuronal diversity—at the right dose—is a new boon to theoretical neuroscience.

thetransmitter.org

New review from the Zhang Lab in @natmethods.nature.com led by @ammgest.bsky.social ! Explore recent advances in fluorescent proteins and biosensors, including improved photostability, high-throughput screening, quantitative imaging, and multiplexing.🔬 Check it out now!👇 doi.org/10.1038/s415...

Recent developments of fluorescent proteins and biosensors driven by cross-disciplinary insights - Nature Methods

This Review summarizes recent developments in fluorescent protein technology, including the engineering of fluorescent biosensors.

doi.org

Combining HiExM with single-organelle segmentation & machine learning reveals cellular patterns beyond the average. #BoyerLab @dina-kabbara.bsky.social: "What stands out to me most is how often a bulk average concealed meaningful differences..." #preLight⬇️ prelights.biologists.com/highlights/h...

HiExM Enables Scalable Mapping of Organelle Morphology and Spatial Heterogeneity - preLights

HiExM meets AI, revealing cellular patterns beyond the average.

prelights.biologists.com

🎉 Our paper is out today in @science.org! How does the intestine maintain the right balance of cell types? We find that signalling rhythms matter! So proud of our three shared first authors, Sonja Weterings, @hiromuneeto.bsky.social & @jddeleede.bsky.social! 🔗 www.science.org/doi/10.1126/...

The lullaby within you! :) www.nature.com/articles/s41...

A half-center oscillator regulates sleep pressure - Nature Neuroscience

Hasenhuetl et al. show that neurons innervating the dorsal fan-shaped body of Drosophila form a half-center oscillator, a circuit motif typically found in central pattern generators for locomotion. He...

nature.com

Very excited about this preprint! We present a new method to flexibly align your 2P imaging plane with curved biological structures. Great work of PhD student Shinjini Ghosh, with Fritjof Helmchen, @nvladimus.bsky.social, and many others! www.biorxiv.org/content/10.6...

Our paper is out in Nature, congrats to Qiyu, An et al! By stimulating ~20 motor cortex neurons carefully selected based on their activity, we could induce learned population activity and, sometimes, the movement itself, depending on the brain's state. www.nature.com/articles/s41...

Targeted stimulation of motor cortex ensembles drives learned movements - Nature

Optogenetic stimulation of motor-cortex neuron ensembles shows that precisely timed activity in the primary motor cortex can generate learned neural patterns and movements, demonstrating an active rol...

nature.com

Every cell has an organelle signature — a “fingerprint” created from the shape, size, & arrangement of its internal structures. Scientists at our Janelia Research Campus can now read these signatures across 1000s of cells, revealing how tissues adapt to diet & disease bit.ly/4j6DmoH 📹 Feliciano Lab@

Hey bsky! I’d like to share some cool work I recently coauthored that integrates entomology, paleontology, and German cultural history. 🔶🐜⚡️ We discovered a fossil ant in the amber collection of Johann Wolfgang von Goethe! Read on for a delightful story of #museomics and #collectomics. >> 1/

In the mid 1900s, not everyone even believed that genes played a significant role in development. C.H. Waddington’s iconic epigenetic landscapes helped to change that. New data both confirms and complicates his ideas. www.quantamagazine.org/how-does-lif...

How Does Life Unfold? A Landscape Metaphor Comes Into Its Own. | Quanta Magazine

C.H. Waddington’s powerful image of embryonic stem cells specializing on a rolling landscape has captivated biologists since the 1950s. Experimental data is finally confirming, and complicating, his v...

quantamagazine.org

I can't imagine neuroscience without optogenetics ⚡️🔬🧑‍🔬 (an example from my work at Cossart lab, stimulating developing pyramidal neurons in vivo using the channelrhodopsin ChRmine developed by the Deisseroth lab) @deisseroth.bsky.social @nobelprize.org

Are you a biologist working with microscopy images? A computer scientist wanting to work with microscopy data? Their boss??? None of these, but curious how AI has transformed microscopy image analysis? 🔬🤖 This one's for you: 📄 doi.org/10.1146/annu... More in the thread! 🧵

From Pixels to Discovery: Microscopy Image Analysis in the Age of Artificial Intelligence

Modern microscopy generates data volumes that far exceed human analytical capacity. Over the past decade, artificial intelligence (AI) has transformed microscopy image analysis into an engine for quan...

doi.org

Preprint is out! Our BakingTray software turns a 2-photon microscope into a serial-section tomography system for automated whole-organ imaging. ~€35k to convert an existing scope. 11 systems worldwide, >7,000 samples at SWC alone #neuroskyence #microscopy www.biorxiv.org/content/10.6...

CLOK: Truly beautiful new #zebrafish tool for birthdating neurons from the Koyama and Del Bene labs doi.org/10.1038/s415...

CLOK: a chemigenetic multicolor labeling system to visualize neuronal birthdate and circuit integration - Nature Neuroscience

Faini et al. develop CLOK, a method that labels neurons across a spectrum of colors according to when they were born, allowing successive generations of brain cells to be tracked as they take shape in...

doi.org

I am going to be buried with all my data, like the Pharaohs of old

Catherine Hulshof@hulshof.bsky.social · last mo.

You can't take your data with you when you die. Careers don't last very long...30 years goes by in a blink of an eye. Will you be remembered through your data? Or will your data die with you? We have a number of datasets getting dusty. Work w/ plant traits?...contact me...happy to collaborate.

With fieldwork, I didn't get to advertise our (not so now) new paper on the quantitative genetics of growth in the 🦎 in @journal-evo.bsky.social: dx.doi.org/10.1093/evol... It's an exciting paper paper in which we disentangle what it means to treat the whole growth curve as a function-valued trait!

Quantitative genetics of lifetime growth curves in a lizard

Abstract. Body size is an iconic trait in quantitative genetics. For species with indeterminate growth however, growth curve, a function-valued trait, is t

dx.doi.org

Can mathematics explain how biological patterns are formed? Alan Turing thought so. Join me, @benswedlund.bsky.social , as we explore his reaction-diffusion theory and how it transformed our understanding of pattern formation and self-organisation.

epithelial mechanics fan club@epimechfc.bsky.social · last mo.

In his seminal 1952 theoretical paper, Alan Turing proposed that partial differential equations, representing molecules (“morphogens”) that react with one another and diffuse through space, can encode spontaneous periodic pattern formation. doi.org/10.1098/rstb...

Precise structural and functional organization of the olfactory bulb neuropil early in development, revealed by volume EM, dense reconstruction and 2P calcium imaging in zebrafish. Great work by Ruth and others in collaboration with @michalwj.bsky.social www.biorxiv.org/content/10.6...

Fine ultrastructural organization of glomerular neuropil in the developing zebrafish olfactory bulb

Across animal phyla, odor information is represented in the first olfactory processing center by combinatorial activation of discrete glomeruli. To examine how this organization of olfactory processin...

biorxiv.org

Thomas Hunt Morgan was born OTD in 1866. If you're ever feeling that your work is uending and unedifying, remember that he once said this: "Two years work wasted, I have been breeding those flies for all that time and I've got nothing out of it." 🌱🐋🧪 #HistSTM

How does the developing nervous system produce so many kinds of neurons? Two studies in flies reveal transcription-factor codes linked to neurons’ lineage and birth order. By Alissa de Chassey www.thetransmitter.org/development/...

Fly neurons carry molecular signatures of their origins

The transcription factors a <em>Drosophila</em> neuron expresses offer clues to its lineage and birth order—and ultimately how neural circuits emerge.

thetransmitter.org

What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar

We are very excited to use this method to study analytically how the interaction between neural activity and plasticity rules sculpts the dynamic landscape of a network in time-- for example to steer a developing circuit towards different architectures. Check it out! arxiv.org/abs/2609.22597

Deviations from global coupling in adaptive oscillator networks: a mean-field theory for the variance of coupling weights

A wide range of physical and biological systems are adaptive networks, in which the dynamics of the nodes and of the edges connecting them co-evolve. Mean-field reductions of such systems typically tr...

arxiv.org