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Reposted by Marius Pachitariu

Carsen Stringer @computingnature.bsky.social · 15d

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 · 16d

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/...

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Marius Pachitariu @marius10p.bsky.social · 16d

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

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Marius Pachitariu @marius10p.bsky.social · 16d

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.

Marius Pachitariu @marius10p.bsky.social · 16d

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

Qingqing Zhang @qqzhang.bsky.social · 16d

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/...

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Reposted by Marius Pachitariu

Qingqing Zhang @qqzhang.bsky.social · 16d

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/...

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Marius Pachitariu @marius10p.bsky.social · Jul 16

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...

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Reposted by Marius Pachitariu

Janelia Research Campus @hhmijanelia.bsky.social · Jul 2

💻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...

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Reposted by Marius Pachitariu

Carsen Stringer @computingnature.bsky.social · Jul 2

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...

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...

www.vice.com

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Reposted by Marius Pachitariu

Janelia Research Campus @hhmijanelia.bsky.social · Jun 24

🧠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-...

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...

www.janelia.org

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Marius Pachitariu @marius10p.bsky.social · Jun 24

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

Janelia Research Campus @hhmijanelia.bsky.social · Jun 23

🚶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-...

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Reposted by Marius Pachitariu

Gabriel Stine @gabrielmstine.bsky.social · Jun 23

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

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.

tinyurl.com

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Reposted by Marius Pachitariu

Dr Nick @nmwilkinson.bsky.social · Jun 23

AI doesn't have to be shit

Marius Pachitariu @marius10p.bsky.social · May 3

🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸‍♀️. Try it now on 🤗 huggingface.co/spaces/mouse...

paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n

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Reposted by Marius Pachitariu

Janelia Research Campus @hhmijanelia.bsky.social · Jun 23

🚶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-...

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Reposted by Marius Pachitariu

Helen Matthews @helenkmatthews.bsky.social · Jun 23

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

Marius Pachitariu @marius10p.bsky.social · May 3

🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸‍♀️. Try it now on 🤗 huggingface.co/spaces/mouse...

paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n

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Reposted by Marius Pachitariu

Michał Januszewski @michalwj.bsky.social · May 22

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.

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Reposted by Marius Pachitariu

Princeton University Press @princetonupress.bsky.social · May 21

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

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Reposted by Marius Pachitariu

Markus Meister @mameister4.bsky.social · May 21

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...

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...

mitpress.mit.edu

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Marius Pachitariu @marius10p.bsky.social · May 9

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.

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Marius Pachitariu @marius10p.bsky.social · May 8

Could you share an image please?

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Reposted by Marius Pachitariu

Carlos Brody @carlosbrody.bsky.social · May 7

we're crowd-sourcing a searchable repository of tangible benefits stemming from federally-funded research. Come enjoy the great stories; or send in an idea; or volunteer to join the team.

publicusaresearchbenefits.com

please share and re-share so we get more great stories in there!

Searchable database of tangible benefits that federally-funded research gave us.

A crowd-sourced site. Health and Well-being. National Security. Prosperity.

publicusaresearchbenefits.com

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Marius Pachitariu @marius10p.bsky.social · May 4

I don't think we have good examples to look at this, but you can test it directly on the website or in the GUI and let us know.

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Marius Pachitariu @marius10p.bsky.social · May 4

Cellpose-SAM is currently available in the GUI.

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Marius Pachitariu @marius10p.bsky.social · May 4

The Cellpose-SAM backbone, yes. The SAM encoder weights were re-trained on a lot of cellular data to predict the Cellpose flows.

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Marius Pachitariu @marius10p.bsky.social · May 3

If you want to learn more, watch the talk or read the paper!

talk: www.youtube.com/watch?v=KIdY...
paper: www.biorxiv.org/content/10.1...
website: huggingface.co/spaces/mouse...
github: github.com/MouseLand/ce...

Cellpose SAM Tutorial

YouTube video by Marius Pachitariu

www.youtube.com

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Marius Pachitariu @marius10p.bsky.social · May 3

The model can be finetuned for other tasks such as panoptic segmentation with relatively little effort, comparing favorably to the best methods.

Panoptic segmentation challenge with four classes of ROIs and Cellpose-SAM performance compared to the challenge winners before and after t he challenge.

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