Carsen Stringer

What if… spontaneous neural activity 🧠 reflects the baseline rumblings of a brainwide dynamical system initialized for learning? We find that the rumblings have macroscopic properties like those emerging from linear symmetric, critical systems 🧵 #neuroscience #neuroAI www.biorxiv.org/content/10.1...

Immune cells don't only interact with the ECM, they also interact with surrounding cells in tissue as they migrate. This video gives me so much joy because there is just so much biology here to be discovered. Sticky cells! Here, immune cells are 🔴, ectodermal cells are ⚪. Happy #FluorescenceFriday

Exciting science going on in Lorena's lab, check it out! Also #FluorescenceFriday

🎉 BEAST3D is a #NeurIPS2026 Oral! Can a moving animal's 3D shape predict what its neurons are doing, better than tracked keypoints? On average, yes. BEAST3D is a self-supervised vision transformer that reconstructs animals in 3D from unlabeled multi-camera lab video. 🧵

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...

How do 🐁deal with complex landscapes? Turns out they learn a lot very quickly. We think they do this by learning a set of repeated sparse paths, which form a type of compressed world model. Joint work with the Hermundstad lab, led by Tzuhsuan Ma and Alison Comrie: www.biorxiv.org/content/10.6...

Thank you to everyone sharing in this moment! I’m so grateful to all my trainees & collaborators… dlab.stanford.edu/group-members (pic: Peter and I together in 2017) Reading for all those asking: for technical details: dlab.stanford.edu for everyone: deisseroth.org/projections

Excited to share my lab’s latest preprint led by postdoc @yukihaba.bsky.social and grad student Ryan Schwark. We surprisingly find that spontaneous behavior in isolation predicts a naked mole-rat’s identity, its colony membership, and even rank within its colony. www.biorxiv.org/content/10.6...

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...

The game is implementation details and the depression you feel is that you actually have to grapple with biology if you want to make a unique contribution.

🚨 new work from the lab! "Hippocampal astrocytic sequences emerge during learning and memory recall" by @ryguy.io & @rsuthard.bsky.social thank you to the entire team for your camaraderie and for muscling through science together 🧠 -- we welcome all feedback! nature.com/articles/s41...

The Agrawal lab has published its first paper! "Sticking the landing: leg mechanosensory feedback coordinates the transition from flight to landing" www.biorxiv.org/content/10.6... This project was led by a technician in the lab, Tse-Wei (Wayne) Kuo. Brief 🧵on what we found

First off, these cells are gigantic. This one, for example, has >72 cm of axon! To our knowledge, it’s the longest neuron ever fully reconstructed. I leave it to the reader as an exercise to estimate the length of a human LC neuron. 5

In brain-computer interfacing, clever and adaptive decoders help brains learn complex tasks faster. These can impact the nature of solutions learned by the brain. Our new paper is one of the first attempts to study this effect. W/ @neuroamyo.bsky.social and team www.nature.com/articles/s41...

New preprint alert! 🚨 🧠 My postdoctoral work in Al Kaye’s lab has focused on understanding how animals navigate and learn from threats in their environment. To study this, I developed a virtual visual cliff height threat task, inspired by Boone et al. 2021. www.biorxiv.org/content/10.6...

If you thought "everything is everywhere" in the brain: inactivations reveal a clear distinction of labor. Sensory areas sense, colliculus promotes eligible actions (!), and prefrontal cortex integrates. The role of superior colliculus in a logistic decision www.biorxiv.org/content/10.6...

New paper from the Neurosurgery Research Team at BCM! “Neural geometry in the human hippocampus enables generalization across spatial position and gaze” led by @assiachericoni.bsky.social! 🧵 www.cell.com/neuron/abstr...

New publication from @lukesjulson.bsky.social lab and collaborators! #Neocortical long-range #inhibition promotes #cortical #synchrony and #sleep doi.org/10.1038/s415...

here are some really gorgeous results from the Nock lab on predicting suicide before it's attempted — essential data for suicide prevention

Whole-body cellular activity imaging in zebrafish, headed by Virginie Ruetten @vmsruetten.bsky.social - new paper is out: www.nature.com/articles/s41...

Our society's unfathomable cruelty to homeless people is not just morally unjustifiable, but more expensive than housing people would be. Cruelty against the homeless is an unaffordable luxury. Abandoning homeless people to avoid offending the Protestant work ethic is an unaffordable luxury.

Preprint time! What does acetylcholine do in the developing visual cortex, before the eyes even open? Read it here: "Acetylcholine mediates behavioral state-dependent modulation of spontaneous activity in the developing mouse visual cortex" www.biorxiv.org/content/10.6...

we have a backlog of work coming out over the next year on the development of innate approach/avoidance behavior. Here is part one of five. I hope this helps folks looking at the roots of visually -guided approach v. avoidance decision making.

The superposition of these two studies — both incredible — reflect a snapshot of "one big thing" systems neuroscience has yet to resolve. In mice: 1. Task-related signals are everywhere. 2. Absent large swaths of "everywhere," suprisingly sophisticated learning & behavior remains.

Our new preprint #manuskrypt is a labor of love and has a profound story behind it. @gritz122.bsky.social @argalloni.bsky.social (1/11) www.biorxiv.org/content/10.6...

Happy #FluorescenceFriday! 🏁🔥🧪 And they're off! These neural crest cells are racing past the somites on their journey to become ganglia. Beautifully captured by Yanina Alvarez 🔬#devbio

📣New paper! How does the sleeping brain help us to integrate new experiences while managing memories from the past? For his PhD work, @sabbaspoor.bsky.social recorded hippocampal ensembles in freely moving monkeys and found something unexpected. 🧵1/n www.nature.com/articles/s41... 🧪🧠📈👩‍🔬#OpenAccess

Our new preprint from @daylab.bsky.social characterizes Chst9-MSNs, a specialized NAc population with high Oprm1 expression and opioid sensitivity that is required for fentanyl reward learning. Excited to share this work! 🧠🧬 www.biorxiv.org/content/10.6...

🎉 *extremely* excited to share our human single neuron + movie dataset is out in #ScientificData! 📄 Human neuron activity during an 83-minute movie from 2,286 neurons and 29 patients 🔗https://www.nature.com/articles/s41597-026-07955-0 1st public dataset from @humansingleneuron.bsky.social!🧵

We used these reporters to image developing zebrafish peripheral nerves at high resolution over time. Here is a rendering of a myelinated sensory nerve (the posterior lateral line): myelin in green, with nfasca/NF186 marking nodes of Ranvier in magenta

New Toettchlab paper alert! Harrison Oatman just published his beautiful work combining software design for "smart" microscopy+optogenetics and some really beautiful work understanding EGFR-driven collective cell migration. www.cell.com/cell-systems...

Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...

Can a cancer become a new species of parasite? Here's my story on the discovery of a transmissible cancer lurking in Vermont catfish. Gift link: nyti.ms/4whfi6v

This afternoon's imaging lab at #IALSJanelia is all about subcellular structures, highlighted here by myosin (white) and actin (orange). These membrane ruffles were captured on our lattice light-sheet microscope by @cmhobson.bsky.social

Replay of procedural memory is independent of the hippocampus 👀👀 www.nature.com/articles/s41...

"Four months into an appeal, Ms. McDonald, a cancer survivor who weighs 69 pounds, bustles to food banks, stretches ground turkey with oatmeal, and skips meals to feed three teenage boys." www.nytimes.com/2026/07/20/u...

Microscopy beautifully reveals the dynamic nature of biology but quantifying that motion can be tricky! In the latest paper from @aicjanelia.bsky.social, out now in @jcellsci.bsky.social, we present a tool for measuring amorphous motion: OpticalFlow3D journals.biologists.com/jcs/article/... (1/7)

Took me a month to recover from this boot camp(jk) but I had a blast during my two weeks at Janelia in June💻Some highlights: an attempt at 3D segmentation, meeting scientists I’ve been following (@computingnature.bsky.social @mishaahrens.bsky.social), and the food&nature! @hhmijanelia.bsky.social

we've been doing this too but more as performance art to see what we can get the bots to do. so far the answer is "anything" github.com/dwebagents/A... i think my favorite is the PR whose only text was "butter" which got us the butter mode page: dwebagents.github.io/AgentPipe/bu...

PHASE ONE of our fight against the OMB rule is complete and YOU ALL SHOWED UP!!! HALF A MILLION COMMENTS is WILD. We absolutely exceeded our goal of 100,000! So, what happens next??? Welcome to PHASE TWO: Pressure and Preparation! 1/x

Hippocampal engrams configure prefrontal context representations to guide flexible decisions Impressive combo of methods to manipulate and record this process: www.biorxiv.org/content/10.6...

Our Impact Scholars @neuromatch.bsky.social project on 𝗵𝗼𝘄 𝗿𝗲𝘄𝗮𝗿𝗱 𝘃𝘀 𝗲𝘅𝗽𝗲𝗿𝗶𝗲𝗻𝗰𝗲 𝘀𝗵𝗮𝗽𝗲 𝗻𝗲𝘂𝗿𝗮𝗹 𝗽𝗼𝗽𝘂𝗹𝗮𝘁𝗶𝗼𝗻 𝗱𝘆𝗻𝗮𝗺𝗶𝗰𝘀 𝗶𝗻 𝗺𝗼𝘂𝘀𝗲 𝘃𝗶𝘀𝘂𝗮𝗹 𝗰𝗼𝗿𝘁𝗲𝘅 is out! 
 With 𝗝𝗼𝗵𝗻 𝗠𝗮𝗱𝗿𝗶𝗱-𝗖𝗮𝗿𝘃𝗮𝗷𝗮𝗹 @johnmadridcarvajal.bsky.social, 𝗞𝗮𝘁𝗷𝗮 𝗞𝗮𝘂𝗿𝗶𝗻𝗸𝗼𝘀𝗸𝗶, 𝗜𝘀𝗵𝗮𝘁𝗽𝗿𝗲𝗲𝘁 𝗦𝗶𝗻𝗴𝗵, 𝗥𝗼𝗵𝗶𝘁 𝗝𝗲𝘀𝘄𝗮𝗻𝘁𝗵. 🧠 👉 zenodo.org/records/2064... 🧵👇 1/8

Excited to share our new study characterizing spatial gene expression in the human NAc led by @prashanthi-ravi.bsky.social @svitlanabach.bsky.social @rphillips3.bsky.social in collaboration with @martinowk.bsky.social @stephaniehicks.bsky.social @alexisbattle.bsky.social @lcolladotor.bsky.social.

Excited to share this preprint from @ianoldenburg.bsky.social . To evoke movement with holo stim, you need the right pattern at the right time! Interestingly, the preparatory state before spont motion is not the same as the state permissive for evoked motion. Dig in! www.biorxiv.org/content/10.6...

🚨 HEADS UP: If you haven't submitted a comment on the OMB proposal yet, there's still time - but it's running out! There are only 11 days left to push back against Russell Vought's attempt to give political appointees unprecedented control over federal research funding. Take Action: zurl.co/R83IO

Excited to share our new preprint! We explore the link between the locus coeruleus (LC) and arousal for astrocytes, pyramidal cells, interneurons in the hippocampus. A fantastic collaboration with @sianduss.bsky.social @bohaceklab.bsky.social, and many others: www.biorxiv.org/content/10.6... 1/5

Nice break-down of a mechanism for attention to boost activity in neocortex (via basal forebrain projections). From @kepecslab.bsky.social and crew: www.cell.com/cell/abstrac... #neuroscience 🧪

What if part of Huntington's disease wasn't just damage, but a circuit stuck in the wrong pattern? Our new paper, out today in Nature, tests that idea.