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

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...

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...

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 🧪

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

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.

Connectome datasets alone are generally not sufficient to predict neural activity. However, pairing connectivity information with neural recordings can produce accurate predictions of activity in unrecorded neurons www.nature.com/articles/s41...

How can we organize current theoretical approaches for developmental biology - from information to dynamical systems & GRNs - into a common framework? We propose to think along Marr's 3 levels: computational problem, algorithm, implementation Check out our review: arxiv.org/abs/2510.24536

Conrad Hal Waddington was born OTD in 1905. His “epigenetic landscape” is a diagrammatic representation of the constraints influencing embryonic development. On his 50th birthday, his colleagues gave him a pinball machine on the model of the epigenetic landscape. 🧪 🦫🦋 🌱🐋 #HistSTM #philsci #evobio

We have written two reviews providing a practical guide and fundamentals of cell migration: (1) How to select an optimal cell migration assay, (2) How to analyze cell migration data. We also added a perspective on AI methods of analysis. Coming out soon in Nature Methods.

New issue of Nature - with NINE studies on #brain #development from the BRAIN Initiative Cell Atlas Network (BICAN) 🧠🧪🔬 An amazing set of resources for all scientists working on the brain! 🧠 Immersive feature: www.nature.com/immersive/d4... 🧠 Perspective: www.nature.com/articles/s41...

Do flies feel pain? Spooky new preprint from our lab on the cells and circuits that mediate nociceptive behaviors in adult Drosophila, led by graduate student (and newly minted PhD!) @jonesjes.bsky.social. 🪰⚡👻🎃 www.biorxiv.org/content/10.1...

The songbird basal ganglia connectome https://www.biorxiv.org/content/10.1101/2025.10.25.684569v1

🧠🌟🐭 Excited to share some of my postdoc work on the evolution of dexterity! We compared deer mice evolved in forest vs prairie habitats. We found that forest mice have: (1) more corticospinal neurons (CSNs) (2) better hand dexterity (3) more dexterous climbing, which is linked to CSN number🧵

doi.org/10.1126/scie... This seems rad: overexpressing FruM in a set of proboscis-motorneuron-projecting neurons makes melanogaster males add food-sharing to their courtship repertoire. It is fascinating to see evolutionary shifts in behavior be tied so concretely to shifts in brain development!

Don’t forget the umlaut! Did you know the wild-type strain ‘Tu’ came from a pet shop in the German town of Reutlingen, a nearby city of Tübingen? This area was one of the sites of “The Big Screen” co-led by Christiane Nüsslein-Volhard in the 1990s. #ZebrafishFunFacts @maxplanckcampus.bsky.social 🧪

great thread on the idea that a bunch of phenotype variability is not just nature vs nuture, but nature vs nature vs... randomness

Very grateful for the opportunity to present at Bernstein 2025 + an amazing conference overall 😊 @bernsteinneuro.bsky.social For anyone interested in the data here is the link to Zenodo: zenodo.org/records/1709... And the (almost final version of) the paper: elifesciences.org/reviewed-pre...

Look at her go! #invertebrates 🌿

Exciting news for #drosophila #connectomics and #neuroscience enthusiasts: the Drosophila male central nervous system connectome is now live for exploration. Find out more at the landing page hosted by our Janelia FlyEM collaborators www.janelia.org/project-team....

Un-frigging-believable. I have waited for something like this for so long!

Latest imaging data from our completely re-designed ExA-SPIM system. Expansion-assisted imaging (3X expansion, 0.3 NA) enables brain-wide imaging with high-contrast and <400 nm effective resolution.

🧵1/14 Preprint thread! Can we predict a cell’s fate based on its dynamics? 🔮 Our new study unveils a framework for watching development unfold in real-time, revealing how a cell's shape and movement encode info about its future fate. 🔬📄 Preprint: tinyurl.com/4shf8v4x

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)

Preprint - Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo. www.biorxiv.org/content/10.1...

So how did it work out? Well, some things went well and others not so well. We published a paper with our results and reflections on the process. If you're interested in spiking neural networks, sound localisation, or anarchist science, check it out: www.eneuro.org/content/12/7...

I rarely dive into circuit-mapping papers, but this blockbuster from @ribeirocarlitos.bsky.social lab is a doozy! Check it out. www.biorxiv.org/content/10.1...

Public access to the first fly connectome that spans the whole CNS - BANC!: codex.flywire.ai?dataset=banc Different from prior connectomes - it is brain + cord (think spinal cord) We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...

Introducing five concepts from dynamical systems to decode developmental regulatory mechanisms, have a read! @perez-carrasco.bsky.social‬ @roederlab.bsky.social @mpipz.bsky.social This effort started in a morphogenesis meeting @kitp-ucsb.bsky.social‬ in 2023. journals.biologists.com/dev/article/...

"people use it very differently".. this applies to so many concepts in neuroscience! We (@irinapochinok.bsky.social and Simon Musall) put together a #BernsteinConference Workshop on exactly this and @juangallego.bsky.social will be one of our speakers! @bernsteinneuro.bsky.social shorturl.at/4kV00

Beautiful and inspiring work from Gero Miesenböck and colleagues www.nature.com/articles/s41...

Cell tracking is never perfect, and it's important to understand the types of errors your solution contains. Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d... You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.

Check out our new review/perspective (w/ @juangallego.bsky.social & Devika Narain) on neural manifolds in the brain! It was a lot of fun to think through these ideas over the past couple of years, and I'm excited it's finally out in the world! 🔗: www.nature.com/articles/s41... 📄: rdcu.be/ex8hW

When neurons change, but behavior doesn’t: Excitability changes driving representational drift New preprint of work with Christian Machens: www.biorxiv.org/content/10.1...

If you've ever wanted to know what the actin filaments on the scales in a developing moth wing look like in 3D, here you go! Kyle DeMarr from @mullinslab.bsky.social acquired these beautiful data on the single objective light sheet at the UCSF Center for Advanced Light Microscopy. #snouty

1 To predict the behaviour of a primate, would you rather base your guess on a closely related species or one with a similar brain shape? We looked at brains & behaviours of 70 species, you’ll be surprised! 🧵Thread on our new preprint with @r3rt0.bsky.social , doi.org/10.1101/2025...

1/ Mapping synaptic connectivity between individual neurons is extremely laborious. We developed BRISC, a new method that makes it possible to map inputs onto 100s of neurons in the same animal in a matter of weeks! Led by Alex Becalick and @antblot.bsky.social. 🧵 www.biorxiv.org/content/10.1...

No new genes needed to fly - just rewire what you have! 🦇🧬 Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social doi.org/10.1038/s415... #EvoDevo #SingleCell #BatWings

This isn't a coincidence, IMO. The fly community is generally super rigorous - because there are so many tools and techniques available, people expect you to really nail things in order to get published (and keep getting funded)

Our preprint on tracking cells in 2p calcium imaging during development is now online at @elife.bsky.social ! Its cool that the reviews are open - now its revision time 🫡🫡🫡 doi.org/10.7554/eLif...