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...

Hi! How is the rate of change of behavior represented in mouse V1? If intrigued by how we approach this question with a group of NeuroMatch fellows, take a look at our micropublication zenodo.org/records/1539... Thanks a lot to Impact Scholars program & @neuromatch.bsky.social :) !

Optogenetic storage and release of protein and mRNA in live cells and animals | Nature Communications share.google/gz8nYXZ3hUVh... #spatialbiology #imagingtools #fluorescencemicroscopy

Thank you for speaking with me about my research @iamshef.bsky.social! #newPI #metabodev #MetabolismMondays Please check out Shefali’s weekly interviews with different ECRs about metabolism and development @the-node.bsky.social! What a great initiative 👏 thenode.biologists.com/author/shefa...

After 5 amazing years @pilhoferlab.bsky.social I'm starting my lab @embl.org Grenoble this November embl.org/wollweber We'll image Asgard archaea and many other strange microbes ( #archaeasky, #protistsonsky..) to understand eukaryogenesis First job ad: #teamtomo scientist!🔬❄️ tinyurl.com/2rdu2ze6

New tools! GreenPy and ApplePy are fluorescent biosensors for pyruvate with huge responses (20–40x in vitro) and a range of affinities (10s of μM to mM). These should be game changers for imaging of metabolism! Great work by Shosei Imai @sikmys.bsky.social and team 👏. www.biorxiv.org/content/10.1...

'(...) there is no established resource for group leaders to improve their lab culture with concrete action points for implementation. Here, we introduce the SAFE Labs Handbook: a collection of thirty “commitments” which can be verifiably actioned without requiring institutional support.' #Preprint

We are proud to have @maxcapelle.bsky.social's paper out on bioRxiv! He found that phototactic behavior in #zebrafish switches during #ontogeny🐟🔆 Through elegant behavioral dissections, he identifies the navigational strategies related to this transition. www.biorxiv.org/content/10.1... Thread 👇

How do brain circuits evolve? We started looking for some answers by using synapse-resolution cross-species comparative connectomics on an entire olfactory circuit 👇 bit.ly/44aVm9E

Our work, out at Cell, shows that the brain’s dopamine signals teach each individual a unique learning trajectory. Collaborative experiment-theory effort, led by Sam Liebana in the lab. The first experiment my lab started just shy of 6y ago & v excited to see it out: www.cell.com/cell/fulltex...

New preprint from lab: www.biorxiv.org/content/10.1... Sexual dimorphism arises not through wholesale transcriptional reprogramming, but via selective sex-specific survival of neurons defined by birth order and shared developmental programs.

Violations of independence/i.i.d assumptions is the single universal biggest issue.

We’ve successfully automated part of the (neuro)scientific process. Now I may be out of a job. After a lot of iterations, here’s our framework for automatic discovery, built to embrace degeneracy and the realities of underconstrained modeling.

I've been writing a textbook on computational cognitive neuroscience, which has prompted me to assess the evidence supporting various theoretical ideas. It's striking to me how some ideas have an extraordinary shelf life despite weak evidence.