Marius Pachitariu
@marius10p.bsky.social
Lab head @HHMIJanelia neuroscience, deep learning, large-scale recordings #Kilosort, #Suite2p, #Cellpose, #Rastermap, #Facemap
US scientists: Going into fall 26, how are you thinking about things? Following Fall 24 events and a tumultuous spring 25, I remember a convo with a colleague in which we agreed we just needed to wait things out until fall 25 and we'd have some clarity about the landscape (eg for funding). /1
I find myself holding seemingly contradictory views. On one hand, this is an extraordinary moment. We are watching discoveries built over decades produce treatments, and things are happening now that I couldn't imagine when I started. It is hard not to look at that and feel enormous optimism.
Nicole Rust@nicolecrust.bsky.social · last mo.US scientists: Going into fall 26, how are you thinking about things? Following Fall 24 events and a tumultuous spring 25, I remember a convo with a colleague in which we agreed we just needed to wait things out until fall 25 and we'd have some clarity about the landscape (eg for funding). /1
It has been painfully clear since Fall’24 that US science funding would tank, universities would be targeted, and any assertions about a new “gold standard” disingenuous. The question has not been “will it be that bad,” but “how bad will it be.”
Nicole Rust@nicolecrust.bsky.social · last mo.US scientists: Going into fall 26, how are you thinking about things? Following Fall 24 events and a tumultuous spring 25, I remember a convo with a colleague in which we agreed we just needed to wait things out until fall 25 and we'd have some clarity about the landscape (eg for funding). /1
Editor in Chief of Science: AI in scientific publishing: Slower, worse, and more expensive.
AI in scientific publishing: Slower, worse, and more expensive
There’s a saying in the management world, popularized by NASA administrator Daniel Goldin in the 1990s, that the goal of technological improvements is to make products faster, better, and cheaper. Alt...
doi.org
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
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.
HHMI’s Janelia Research Campus will close two of its programs dedicated to rodent work, @thetransmitter.bsky.social has learned. #neuroskyence By @callimcflurry.bsky.social www.thetransmitter.org/community/ex...
Exclusive: Janelia sunsets rodent work, launches transparent fish project
The Howard Hughes Medical Institute’s Janelia Research Campus is banking on whole-brain imaging in the Danionella fish to advance neuroscience, but some scientists forced to close their labs say that…
thetransmitter.org
for "AI" to be profitable, costs need to be aligned with token use rather than subscription, and then everyone needs to use orders of magnitude more tokens. "Agentic" workflows are for making massive token spend palatable by making the point of comparison "20 engineers" despite being the same thing.
Eryk Salvaggio@eryk.bsky.social · 3mo agoThis image from Anthropic goes out to the two guys on here who called me dumb for talking about stochastic flocks
Neuropixels + Optogenetics = Neuropixels Opto Combining high-resolution electrophysiology and optogenetics. 960 sites, 28 emitters, 2 colors. Today in @natmethods.nature.com doi.org/10.1038/s415... Thanks to @wellcometrust.bsky.social, @alleninstitute.org, @hhmijanelia.bsky.social & team.
1/ 🚨🚨Preprint alert! "Perfect" isn't always smart 🧠. Anyone can tell apart two stimuli (including our mice). But how do we extract rules that apply to new stimuli? 🧵 biorxiv.org/content/10.6... @marius10p.bsky.social @computingnature.bsky.social #neuroAI #neuroscience #AI
🚨🧠 Our paper is out! We introduce a simple computational model that generates macroscopic, long-timescale dynamics as seen in large-scale neural recordings. #neuroscience #dynamics @marius10p.bsky.social @zhong-lin.bsky.social @hhmijanelia.bsky.social Link: go.nature.com/4tRNjIu
Nature@nature.com · 4mo agoNature research paper: A critical initialization for biological neural networks go.nature.com/4tRNjIu
New preprint with @lingqiz.bsky.social: Neurodata Without Boredom: Benchmarking Agentic AI for Data Reuse arxiv.org/abs/2605.12808 1/10
🚨 Ever wanted a simple way to control the activity of thousands of neurons? We introduce an all-optical raster photostimulation method to do just that! w/ @computingnature.bsky.social @marius10p.bsky.social #FluorescenceFriday #neuroskyence www.biorxiv.org/content/10.6... 1/n
We apologize for the delay but our next profile is here! Dr. Ann Kennedy (@antihebbiann.bsky.social) combines theory & biological data to study how internal states shape social behavior by reconfiguring neural circuit dynamics. Follow the link to learn more! www.storiesofwin.org/profiles/202...
Two-photon calcium imaging at 24,000 lines/s, with the resonant axis spanning 4x what other systems can do. Inertia-free. Diffraction-limited. No tradeoffs. Che-Hang Yu developed a 4x angle multiplier for laser scanning. His paper is out today: opg.optica.org/optica/fullt... 1/n #fluorescenceFriday
👋 Neuromatch is looking for more TAs to help facilitate comp neuro + neuroAI learning this summer! You'll get to work with students from around the world and share your expertise with the global community 🧠 🌎 🤖 🌍💻 🌏 #cosyne2026 #neuroscience
Neuromatch@neuromatch.bsky.social · 6mo ago📣 We've extended the application deadline for #Neuromatch and #Climatematch Academy Students and Teaching Assistants by one week! 🚨 📅 New deadline: March 22, midnight in your local time. ➡️ Apply now: portal.neuromatchacademy.org/sign-in Tag someone who almost missed out! #TA #SummerSchool
📢📢 Announcing this year's conference on the Mathematics of Neuroscience & AI (Rome, 9-12th June). We’ve got a stellar line-up and venue, and invite everyone to join: www.neuromonster.org
Applications for July #CompNeuro, #DeepLearning, #NeuroAI & #ClimateScience are open. Learn in small collaborative pods with a dedicated TA, build real research skills, and join 13,000+ alumni worldwide. ➡️ Apply by 15 March: neuromatch.io/courses/
🔬🧠 Releasing the 1.0 version of #Suite2p and THE PAPER w/ @marius10p.bsky.social! Now with GPU acceleration. Want to use Suite2p but don’t have 100,000 neuron recordings? We show you how to get those with a standard 2p microscope #neuroscience #imaging #neuroAI www.biorxiv.org/content/10.6...
🚨 new work from the lab on how eye movements 👀 versus orofacial movements influence 🐭 visual cortex activity 🧠 #neuroscience #behavior #neuroAI
Atika Syeda@atika-syeda.bsky.social · 7mo agoExcited to share “Orofacial behaviors, not eye movements, govern neural activity in mouse visual cortex” www.biorxiv.org/content/10.6... Summary below...
Excited to share “Orofacial behaviors, not eye movements, govern neural activity in mouse visual cortex” www.biorxiv.org/content/10.6... Summary below...
A System for Live Sorting of Neuronal Spiking Activity from Large-scale Recordings https://www.biorxiv.org/content/10.64898/2025.12.29.696938v1
High performance sorting of motor unit action potentials with EMUsort https://www.biorxiv.org/content/10.64898/2026.01.06.697952v1
I have so many issues with this podcast with @earlkmiller.bsky.social . I think that this podcast nicely shows why I have trouble with such approaches. Lets go through some of the claims.
Earl K. Miller@earlkmiller.bsky.social · 10mo agoGiant Shoulders podcast: Meet the MIT Neuroscientist Proving Brainwaves are the Secret to Consciousness. youtu.be/7OFb-NG3jIw #neuroscience
Still beta-testing the app that helps people plan science, make it super clear, design their todos, and write a first version of the paper. Feeling overwhelmed by the countless aspects of doing science? Try this (for free): planyourscience.com
Scientific Paper Planner - AI-Powered Research Planning
Structure your scientific research with AI-powered guidance. From hypothesis to methodology, plan your research paper with intelligent mentoring.
planyourscience.com
Even colleagues who should know better are claiming that we are halting animal research. No, we're not. Now this NYT opinion piece appears (gift link) www.nytimes.com/2025/10/08/o... You can't just move everything to cell culture, organoids, and computers. Even this NYT piece admits that. 1/3
Is visual cortex more like chatGPT or a masked autoencoder? Come to my BCCN seminar tomorrow at 10am ET on zoom (or read the paper) to find out! #neuroscience Zoom: urldefense.com/v3/__https:/... Paper: www.biorxiv.org/content/10.1...
Qingqing Zhang@qqzhang.bsky.social · 12mo agoDoes predictive coding work in SPACE or in TIME? Most neuroscientists assume TIME, i.e. neurons predict their future sensory inputs. We show that in visual cortex predictive coding actually works across SPACE, just like the original Rao+Ballard theory #neuroscience www.biorxiv.org/cgi/content/...
New work from the lab, mismatch responses consistent with spatial but not temporal predictive coding theory.
Qingqing Zhang@qqzhang.bsky.social · 12mo agoDoes predictive coding work in SPACE or in TIME? Most neuroscientists assume TIME, i.e. neurons predict their future sensory inputs. We show that in visual cortex predictive coding actually works across SPACE, just like the original Rao+Ballard theory #neuroscience www.biorxiv.org/cgi/content/...
Does predictive coding work in SPACE or in TIME? Most neuroscientists assume TIME, i.e. neurons predict their future sensory inputs. We show that in visual cortex predictive coding actually works across SPACE, just like the original Rao+Ballard theory #neuroscience www.biorxiv.org/cgi/content/...
