Marius Pachitariu
@marius10p.bsky.social
Lab head @HHMIJanelia
neuroscience, deep learning, large-scale recordings
#Kilosort, #Suite2p, #Cellpose, #Rastermap, #Facemap
neuroscience, deep learning, large-scale recordings
#Kilosort, #Suite2p, #Cellpose, #Rastermap, #Facemap
Reposted by Marius Pachitariu
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
October 29, 2025 at 10:06 PM
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
Reposted by Marius Pachitariu
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
October 9, 2025 at 6:43 PM
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
Reposted by Marius Pachitariu
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...
Zoom: urldefense.com/v3/__https:/...
Paper: www.biorxiv.org/content/10.1...
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/...
www.biorxiv.org/cgi/content/...
September 23, 2025 at 1:23 PM
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...
Zoom: urldefense.com/v3/__https:/...
Paper: www.biorxiv.org/content/10.1...
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/...
www.biorxiv.org/cgi/content/...
September 22, 2025 at 7:23 PM
New work from the lab, mismatch responses consistent with spatial but not temporal predictive coding theory.
Reposted by Marius Pachitariu
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/...
www.biorxiv.org/cgi/content/...
September 22, 2025 at 7:09 PM
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/...
www.biorxiv.org/cgi/content/...
Reposted by Marius Pachitariu
💻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...
➡️ www.janelia.org/news/new-com...
July 2, 2025 at 8:36 PM
💻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...
➡️ www.janelia.org/news/new-com...
Reposted by Marius Pachitariu
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...
#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
July 2, 2025 at 5:18 PM
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...
#neuroscience #AI
www.nature.com/articles/s41...
Reposted by Marius Pachitariu
🧠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-...
🥼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
June 24, 2025 at 3:19 PM
🧠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-...
🥼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).
🚶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-...
🔗 www.janelia.org/news/zoning-...
June 24, 2025 at 12:15 AM
Your brain learns for you even when you're not actively learning. Maybe. (in mice).
Reposted by Marius Pachitariu
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
June 23, 2025 at 7:31 PM
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
Reposted by Marius Pachitariu
AI doesn't have to be shit
🚀🔬🦠 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
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
June 23, 2025 at 8:04 PM
AI doesn't have to be shit
Reposted by Marius Pachitariu
🚶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-...
🔗 www.janelia.org/news/zoning-...
June 23, 2025 at 7:12 PM
🚶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-...
🔗 www.janelia.org/news/zoning-...
Reposted by Marius Pachitariu
Everyone in the lab is raving about Cellpose-SAM. Segmenting the previously unsegmentable across a range of different cell types and markers.
🚀🔬🦠 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
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
June 23, 2025 at 2:32 PM
Everyone in the lab is raving about Cellpose-SAM. Segmenting the previously unsegmentable across a range of different cell types and markers.
Reposted by Marius Pachitariu
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.
With the PATHFINDER preprint (www.biorxiv.org/content/10.1...), we preview a future where it doesn't have to.
May 22, 2025 at 11:42 AM
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.
With the PATHFINDER preprint (www.biorxiv.org/content/10.1...), we preview a future where it doesn't have to.
Reposted by Marius Pachitariu
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
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
May 21, 2025 at 7:32 PM
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
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
Reposted by Marius Pachitariu
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
May 21, 2025 at 9:53 PM
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...
Reposted by Marius Pachitariu
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!
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
May 7, 2025 at 11:28 PM
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!
publicusaresearchbenefits.com
please share and re-share so we get more great stories in there!
🚀🔬🦠 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
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
May 3, 2025 at 7:12 PM
🚀🔬🦠 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
paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n
Reposted by Marius Pachitariu
🌟 Teaching Assistants are who make
Neuromatch Academy run! 🌟
Thinking of becoming a Teaching Assistant (TA) for
Neuromatch or Climatematch Academy? Here’s why you should GO
FOR IT! 🚀
Learn more and apply here: neuromatch.io/courses/
#Education #TA #TeachingOpportunity #mentorship
Neuromatch Academy run! 🌟
Thinking of becoming a Teaching Assistant (TA) for
Neuromatch or Climatematch Academy? Here’s why you should GO
FOR IT! 🚀
Learn more and apply here: neuromatch.io/courses/
#Education #TA #TeachingOpportunity #mentorship
March 17, 2025 at 5:05 PM
🌟 Teaching Assistants are who make
Neuromatch Academy run! 🌟
Thinking of becoming a Teaching Assistant (TA) for
Neuromatch or Climatematch Academy? Here’s why you should GO
FOR IT! 🚀
Learn more and apply here: neuromatch.io/courses/
#Education #TA #TeachingOpportunity #mentorship
Neuromatch Academy run! 🌟
Thinking of becoming a Teaching Assistant (TA) for
Neuromatch or Climatematch Academy? Here’s why you should GO
FOR IT! 🚀
Learn more and apply here: neuromatch.io/courses/
#Education #TA #TeachingOpportunity #mentorship
Reposted by Marius Pachitariu
🚨 Neuromatch Academy Course Applications are OPEN for 2025!! 🚨
Get your application in early to be a student or teaching assistant for this year’s courses!
Applications are due Sunday, March 23.
Apply & learn more: neuromatch.io/courses/
#mlsky #compneurosky #ai #climatesolutions #ScienceEdu 🧪
Get your application in early to be a student or teaching assistant for this year’s courses!
Applications are due Sunday, March 23.
Apply & learn more: neuromatch.io/courses/
#mlsky #compneurosky #ai #climatesolutions #ScienceEdu 🧪
February 24, 2025 at 5:58 PM
🚨 Neuromatch Academy Course Applications are OPEN for 2025!! 🚨
Get your application in early to be a student or teaching assistant for this year’s courses!
Applications are due Sunday, March 23.
Apply & learn more: neuromatch.io/courses/
#mlsky #compneurosky #ai #climatesolutions #ScienceEdu 🧪
Get your application in early to be a student or teaching assistant for this year’s courses!
Applications are due Sunday, March 23.
Apply & learn more: neuromatch.io/courses/
#mlsky #compneurosky #ai #climatesolutions #ScienceEdu 🧪
Reposted by Marius Pachitariu
Bring your samples into focus! A new version of the #Cellpose cell boundary mapping tool, developed at @hhmijanelia.bsky.social by @computingnature.bsky.social and @marius10p.bsky.social, now works on less-than-perfect microscopy images that are noisy, blurry, or undersampled.
Newest version of Cellpose can spot cell boundaries even in cloudy conditions
Picking out individual cells in distorted microscopy images is now as easy as clicking a button. A new version of Cellpose – the popular tool that maps the boundaries of diverse cells in microscopy
buff.ly
February 17, 2025 at 1:42 PM
Bring your samples into focus! A new version of the #Cellpose cell boundary mapping tool, developed at @hhmijanelia.bsky.social by @computingnature.bsky.social and @marius10p.bsky.social, now works on less-than-perfect microscopy images that are noisy, blurry, or undersampled.
Reposted by Marius Pachitariu
(1/11) Today I preprinted a lot of work from my postdoc with @dudman.bsky.social, which started with a question of how the nervous system balances flexibility with efficiency of learning. The thread below gives some background....
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Cortical control of innate behavior from subcortical demonstration
Motor control in mammals is traditionally viewed as a hierarchy of descending spinal-targeting pathways, with frontal cortex at the top. Many redundant muscle patterns can solve a given task, and this...
www.biorxiv.org
February 13, 2025 at 7:16 PM
(1/11) Today I preprinted a lot of work from my postdoc with @dudman.bsky.social, which started with a question of how the nervous system balances flexibility with efficiency of learning. The thread below gives some background....
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Marius Pachitariu
#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
February 12, 2025 at 11:10 AM
#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
Reposted by Marius Pachitariu
🖥️ A new version of #Cellpose – the popular tool developed by @computingnature.bsky.social & @marius10p.bsky.social that maps the boundaries of diverse cells in microscopy images – now works on less-than-perfect pictures that are noisy, blurry, or undersampled.
🔗 www.janelia.org/news/newest-...
🔗 www.janelia.org/news/newest-...
February 13, 2025 at 5:35 PM
🖥️ A new version of #Cellpose – the popular tool developed by @computingnature.bsky.social & @marius10p.bsky.social that maps the boundaries of diverse cells in microscopy images – now works on less-than-perfect pictures that are noisy, blurry, or undersampled.
🔗 www.janelia.org/news/newest-...
🔗 www.janelia.org/news/newest-...
The trilogy is complete.
#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
February 12, 2025 at 2:20 PM
The trilogy is complete.