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Marius Pachitariu

@marius10p.bsky.social
2K followers 698 following 22 posts

Lab head @HHMIJanelia neuroscience, deep learning, large-scale recordings #Kilosort, #Suite2p, #Cellpose, #Rastermap, #Facemap

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Nicole Rust @nicolecrust.bsky.social · 07/08/2026
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
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Keri Martinowich @martinowk.bsky.social · 08/08/2026
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.
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Talia Lerner @talialerner.bsky.social · 09/08/2026
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.”
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Jed Brown @jedbrown.org · 17/07/2026
Editor in Chief of Science: AI in scientific publishing: Slower, worse, and more expensive.
doi.org
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...
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Dimitra Maoutsa @dimma.bsky.social · 06/07/2026
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
Schematic of the experimental setup and our analysis. Mice experienced visual corridors containing leaf or circle patterns, with reward available only for one pattern in the rewarded cohort and no reward in the unrewarded cohort. Large-scale calcium imaging sampled neurons across V1 and higher visual areas before and after learning. Neural activity was organised into neuron × time × trial tensors and analysed with tensor component analysis. Example factors show differences between rewarded and unrewarded mice before versus after learning, including stronger separation of leaf and circle trials after rewarded learning.
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Sonja Blumenstock @sblumenstock.bsky.social · 01/07/2026
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.
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The Transmitter @thetransmitter.bsky.social · 22/06/2026
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...
thetransmitter.org
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…
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jonny (leachate composite form) @jo.nny.rip · 07/06/2026
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.
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Matteo Carandini @carandinilab.net · 01/06/2026
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.
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Miguel Nunez @nunezkant.bsky.social · 26/05/2026
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
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Carsen Stringer @computingnature.bsky.social · 22/05/2026
🚨🧠 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
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Kristin Branson @kristinmbranson.bsky.social · 18/05/2026
New preprint with @lingqiz.bsky.social: Neurodata Without Boredom: Benchmarking Agentic AI for Data Reuse arxiv.org/abs/2605.12808 1/10
Overview of the data conversion task. The benchmark includes eight datasets spanning a range of neural recording modalities, behavioral tasks, measurements, experiment protocols, and data formats. For each dataset, agents were also given the released paper, methods, and code, together with a structured prompt. The agent’s goal was to convert each heterogeneous source dataset into a common format suitable for a neural decoding task. 
Diagram has a column for each of 8 papers from mouse systems neuroscience. The first row shows the name of the dataset and a description of the focus of that work: 1) Allen2P: Visual change detection,2) Lee2025: Spatial coding & remapping, 3) Majnik2025: Cortical development, 4) Sosa2024: Spatial reward learning,  5) Chen2024: Memory-guided decision, 6) Hasnain2024: Context-based decision, 7) Zhang2025: Visual-motor decision, 8) Zhong2025: Visual learning. 
The next row shows the type of neural recording data: 1, 3, 4, 8: head-fixed calcium imaging, 2: miniprobe, 5-7: neuropixels or other silicon probes
The next row shows the types of behavioral and task variables. These are different for every task
The next row shows a visualization of the experiment protocol for each task. Again, these are different for every task
The next row shows that this information is all condensed into data, paper, and code. Data has the different types of information in different orders and structures. It also shows the type of files: 1: NWB files & SDK, 2,6: MATLAB files, 3, 7: Python files, 4-5: NWB files, 8: Various + API
The next part of the diagram shows the task, which is for agents to convert the data to a common data format for a downstream decoder task.
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Paul Kristian LaFosse @lafosse.bsky.social · 15/05/2026
🚨 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
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Stories of WiN @storiesofwin.bsky.social · 23/03/2026
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...
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Spencer LaVere Smith @spencerlaveresmith.bsky.social · 27/02/2026
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
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Carsen Stringer @computingnature.bsky.social · 16/03/2026
👋 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
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Ruairidh McLennan Battleday @battleday.bsky.social · 05/03/2026
📢📢 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
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Neuromatch @neuromatch.bsky.social · 25/02/2026
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/
"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
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Carsen Stringer @computingnature.bsky.social · 12/02/2026
🔬🧠 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...
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Carsen Stringer @computingnature.bsky.social · 09/02/2026
🚨 new work from the lab on how eye movements 👀 versus orofacial movements influence 🐭 visual cortex activity 🧠 #neuroscience #behavior #neuroAI
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Konrad Kording @kordinglab.bsky.social · 09/02/2026
Planyourscience.com now applauds the good changes you make - and pushes back on the less good one.
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Atika Syeda @atika-syeda.bsky.social · 05/02/2026
Excited to share “Orofacial behaviors, not eye movements, govern neural activity in mouse visual cortex” www.biorxiv.org/content/10.6... Summary below...
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 02/01/2026
A System for Live Sorting of Neuronal Spiking Activity from Large-scale Recordings www.biorxiv.org/content/10.64898/20…
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 07/01/2026
High performance sorting of motor unit action potentials with EMUsort www.biorxiv.org/content/10.64898/20…
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Konrad Kording @kordinglab.bsky.social · 18/11/2025
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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Konrad Kording @kordinglab.bsky.social · 29/10/2025
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
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.
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Spencer LaVere Smith @spencerlaveresmith.bsky.social · 09/10/2025
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
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Carsen Stringer @computingnature.bsky.social · 23/09/2025
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...
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Marius Pachitariu @marius10p.bsky.social · 22/09/2025
New work from the lab, mismatch responses consistent with spatial but not temporal predictive coding theory.
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Qingqing Zhang @qqzhang.bsky.social · 22/09/2025
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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Janelia Research Campus @hhmijanelia.bsky.social · 02/07/2025
💻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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Carsen Stringer @computingnature.bsky.social · 02/07/2025
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...
vice.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...
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Janelia Research Campus @hhmijanelia.bsky.social · 24/06/2025
🧠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-...
janelia.org
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...
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Marius Pachitariu @marius10p.bsky.social · 24/06/2025
Your brain learns for you even when you're not actively learning. Maybe. (in mice).
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Gabriel Stine @gabrielmstine.bsky.social · 23/06/2025
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
tinyurl.com
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.
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Dr Nick @nmwilkinson.eurosky.social · 23/06/2025
AI doesn't have to be shit
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Janelia Research Campus @hhmijanelia.bsky.social · 23/06/2025
🚶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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Helen Matthews @helenkmatthews.bsky.social · 23/06/2025
Everyone in the lab is raving about Cellpose-SAM. Segmenting the previously unsegmentable across a range of different cell types and markers.
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Michał Januszewski @michalwj.bsky.social · 22/05/2025
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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Princeton University Press @princetonupress.bsky.social · 21/05/2025
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
A neuroscientist's bold proposal for tackling one of the greatest challenges of our time--brain and mental illnesses
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Markus Meister @mameister4.bsky.social · 21/05/2025
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...
mitpress.mit.edu
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...
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Carlos Brody @carlosbrody.bsky.social · 08/05/2025
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
Searchable database of tangible benefits that federally-funded research gave us.
A crowd-sourced site. Health and Well-being. National Security. Prosperity.
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Marius Pachitariu @marius10p.bsky.social · 03/05/2025
🚀🔬🦠 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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Neuromatch @neuromatch.bsky.social · 17/03/2025
🌟 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
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Neuromatch @neuromatch.bsky.social · 24/02/2025
🚨 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 🧪
Applications are now open! 3-week courses: Comp Neuro and Deep Learning. 2-week courses: NeuroAI and Comp Tools for Climate Science.
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HHMI @hhmi-science.bsky.social · 17/02/2025
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.
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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
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Jason Keller @neurojak.bsky.social · 13/02/2025
(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...
biorxiv.org
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...
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Carsen Stringer @computingnature.bsky.social · 12/02/2025
#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...
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Janelia Research Campus @hhmijanelia.bsky.social · 13/02/2025
🖥️ 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-...
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Marius Pachitariu @marius10p.bsky.social · 12/02/2025
The trilogy is complete.
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