Marius Pachitariu

"I saw what open, rigorous, and collaborative science could look like. I saw people I wanted to become, and a path I hadn't known was there." - Kirollus Abdallah, Eygpt

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

Planyourscience.com now applauds the good changes you make - and pushes back on the less good one.

@sebastianseung.bsky.social Did you follow through on your plan to visit Epstein island?

Hey @eboyden3.bsky.social care to explain?

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.

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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

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...

Yes! More generally for affective and/or very salient outcomes, everything could be different. We only measured visual cortex in benign "daily life" scenarios.

Another way to think of it is novel items/situations versus novel temporal order of familiar items. However, it could be different in non-sensory brain areas, or in other species, or in other modalities.

New work from the lab, mismatch responses consistent with spatial but not temporal predictive coding theory.

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/...

TetO‐jGCaMP8s is a drop in replacement for the @crisniell.bsky.social mice with all the nice properties of 8s. High, dense expression, and doesn't have the aberrant activity. Was used here: www.nature.com/articles/s41...

💻A new class of simplified ‘minimodels’ developed by Fengtong Du, Miguel Angel Núñez-Ochoa, @marius10p.bsky.social & @computingnature.bsky.social can predict the visual responses of individual neurons in the primary visual cortex, helping shed light on how we see.👀
➡️ www.janelia.org/news/new-com...

Doing This Might Actually Make You Smarter You’re scrolling through TikTok with the sound off. Waiting in line for a coffee. Watching a guy try to parallel park for the third time...

Doing this might make you smarter ... (www.vice.com/en/article/d...) News coverage of our study on unsupervised learning in mice by @zhong-lin.bsky.social + @marius10p.bsky.social

#neuroscience #AI
www.nature.com/articles/s41...

Zoning out could be beneficial—and may actually help us learn faster Actions that may seem unproductive – like aimlessly wandering around a city or exploring a new mall – could play an important role in how our brains learn, according research from HHMI’s Janelia...

🧠Zoning out could be beneficial—and may actually help us learn faster.

🥼New research led by @zhong-lin.bsky.social @marius10p.bsky.social @computingnature.bsky.social

🔗 www.janelia.org/news/zoning-...

Your brain learns for you even when you're not actively learning. Maybe. (in mice).

Large-scale high-density brain-wide neural recording in nonhuman primates - Nature Neuroscience Neuropixels 1.0 NHP is a 45-mm, high-density silicon probe capable of recording large numbers of neurons with single-neuron resolution from most areas in a macaque’s brain.

Our paper on NHP neuropixels is finally out in Nat Neuro! These probes have already been transformative and will usher in a new era of primate neuroscience. I am extremely proud to have played a very small role in this project. I can't wait to see what our community discovers. tinyurl.com/54u3hrj8

AI doesn't have to be shit

🚶Aimlessly wandering around a city or exploring the new mall may seem unproductive, but new research led by @zh0ng0.bsky.social @marius10p.bsky.social @computingnature.bsky.social suggests it could play an important role in how our brains learn.‬‬ 🧠
🔗 www.janelia.org/news/zoning-...

Everyone in the lab is raving about Cellpose-SAM. Segmenting the previously unsegmentable across a range of different cell types and markers.

Wouldn't it be great if we could not only image large connectomic volumes but also completely reconstruct them? And if a whole mouse brain project didn't cost billions?

With the PATHFINDER preprint (www.biorxiv.org/content/10.1...), we preview a future where it doesn't have to.

A neuroscientist's bold proposal for tackling one of the greatest challenges of our time--brain and mental illnesses

A neuroscientist’s bold proposal for tackling one of the greatest challenges of our time—brain and mental illnesses.

Nicole C. Rust's Elusive Cures publishes June 10. Learn more and preorder yours: press.princeton.edu/books/hardco... (5 August UK pub) @nicolecrust.bsky.social

Mathematics in Biology Biology has turned into a quantitative science. The core problems in the life sciences today involve complex systems that require mathematical expression, ye...

If you're planning a course with mathematical methods content, or use such methods in your own work, please take a look at "Mathematics in Biology", by Meister, Lee, and Portugues, published at MIT Press. 1/2 @portugueslab.bsky.social mitpress.mit.edu/978026204940...

Ok, yes, this one will be tough no matter what. It might work a little better if there was more context, for example if the FOV was larger.