🧵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.

Does publishing serve science or is science serving publishing? Damian Pattinson and I (@elife.bsky.social) argue scientific publishing has evolved into a system that, rather than facilitate scholarly communication, distorts and dictates it. onlinelibrary.wiley.com/doi/10.1002/... #OpenScience

Are you interested in visual systems? How are they similar or different across species? Read the review by Ryosuke @ryosuketanaka.bsky.social and Ruben published today in @natrevneuro.nature.com. It is available here: rdcu.be/enlpC

Excited to share my PhD paper! In it, we use targeted 2-photon optogenetic stimulation to determine how V1 activity is read-out in a detection task. We found that network influence, not visual coding properties, predicted the impact of ensembles on behavior - contradicting our expectations (1/5).

✨Once thought to play a supporting function in the brain, new research led by @alexbchen.bsky.social & @mishaahrens.bsky.social shows non-neuronal astroglial cells perform a leading role in regulating the activity of neurons and their connections. 🧠 🔗 www.janelia.org/news/on-the-...

There's a fair-sized literature on this (which we all sadly ignore readily). Here's a recent paper:

🚨Very excited to share a new paper from our lab in Neuron (@cp-neuron.bsky.social) on the influence of the estrous cycle on structural and functional plasticity in the hippocampus: www.sciencedirect.com/science/arti... Thread below 🧠🧪🧵:

Why does the forebrain expand dramatically while other neural regions grow less? Our new publication reveals progenitor metabolism critically shapes region-specific brain growth. Thread below. authors.elsevier.com/a/1k-udL7PXu...

📣 Now out in Nature Communications as part of the MICrONS package: Our study on excitatory morphological cell types in mouse visual cortex led by Marissa Weis. We describe a set of principles that capture the morphological diversity excitatory neurons. A thread: (1/12) www.nature.com/articles/s41...

@commsbio.bsky.social How our brains deal with uncertainty ? Ladret et al identify 2 populations of V1 neurons that are either vulnerable or resilient to variance of oriented inputs. @univ-amu.fr @umontreal-en.bsky.social @umontreal.ca @cnrs.fr laurentperrinet.github.io/publication/... #diversity

[#Infuse] Découvrez en vidéo le projet SAPA - Système Auditif du Proteux Anguinus, dont l'objectif est de mettre en évidence les facultés auditives de la salamandre des grottes en réalisant plusieurs campagnes de mesures à la Station d’Écologie Théorique et Expérimentale (SETE).

1966: Chess is the drosophila of AI 2012:"The decision to adopt drosophila as the organism of choice for genetics research had far-reaching implications...the decision to focus on chess as the measure of both human & computer intelligence had important & unintended consequences" tinyurl.com/dorsoAI

Fun with worms on @WIRED www.wired.com/story/openwo... We've been thinking about how #celegans can revolutionize science again, together with @kordinglab.bsky.social @eboyden3.bsky.social @wormsense.bsky.social and many other (also find our preprint on #arXiv)

Modern science wouldn’t exist without the online research repository known as arXiv. Three decades in, its creator still can’t let it go.

✨ Announcing a new glutamate indicator - iGluSnFR4! ✨ Launched as a pair, iGLuSnFR4s and iGluSnFR4f have high-sensitivity and fast activation/deactivation for recording synapses. More on the indicators and what they are already revealing: www.biorxiv.org/content/10.1... 🧠📈

So on March 9, a French scientist, on a visa to attend a conference in Houston, was denied entry to the US and subsequently expelled because his phone had messages decrying scientific policies put forward by the Trump administration: www.lemonde.fr/internationa...

This video is making the rounds in German #academia. The comments under the video show pretty well, that those cases of horrible treatment of junior researchers, specifically of non-German (speaking) colleagues, is not only limited to those cases and the Max-Planck society.

How does a neuron get its activity? 👀 Check out our latest preprint, where we tracked the activity of the same neurons throughout early postnatal development: www.biorxiv.org/content/10.1... see 🧵 (1/?)

Long-term in vivo imaging of single neurons in the developing mouse brain from early postnatal days on. A game-changer in figuring out developmental trajectories. From the Cossart lab. doi.org/10.1101/2025...