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...

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/...

💻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 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. 🥼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).

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. 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

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...

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!

🚀🔬🦠 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

🌟 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 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 🧪

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.

(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...

#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...

🖥️ 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-...

The trilogy is complete.

Tutorial talk here: youtu.be/TZZZlGk6AKo?... ; Code is here: github.com/MouseLand/ce...

Interested in understanding how things work? In particular the tools you use to study the brain? Join us at TENSS 2025 where we brainstorm ideas, build and debug microscopes, electrophysiology and behavior rigs amidst the picturesque Transylvanian hills! tenss.ro Apply by: February 16th!

What if… spontaneous neural activity 🧠 reflects the baseline rumblings of a brainwide dynamical system initialized for learning? We find that the rumblings have macroscopic properties like those emerging from linear symmetric, critical systems 🧵 #neuroscience #neuroAI www.biorxiv.org/content/10.1...

In a new review, Group Leaders @computingnature.bsky.social & @marius10p.bsky.social examine methods for analyzing large-scale neuronal recordings, how these tools have enabled progress in answering longstanding questions in neuroscience, and what advances & challenges lie ahead. hhmi.news/3Di0Bcz

Subspace communication to me is essentially correlation on crack.

Here are some things that neuroscientists don't like to call "correlation": 1990s: "reverse correlation" 2000s: "granger causality" 2010s: "functional connectivity" 2020s: "subspace communication"

Be successful, run a big lab. Have many (12) grad students. Play the numbers game. Some are bound to get a paper, the others we dont talk about, they're dead to us. post-hoc test, survivors used git

We are looking for exceptional #AIScientist|s to join our #AI@HHMI initiative at #HHMIJanelia. We want to uncover fundamental principles underlying complex biological systems that are inaccessible without new innovations that combine #AI with experimental design. ai.hhmi.org#join-our-team 1/4

We wrote a review on analysis methods for large-scale neural recordings www.science.org/stoken/autho... @marius10p.bsky.social #neuroscience 🧪🧠 Anything we missed? Reply w/ your fav method!

Ultrasound Localization Microscopy #ULM pushes cardiac imaging to the next level: Coronary hemodynamics revealed in 3D down to the micron scale published in #JACCImaging, the paper: www.sciencedirect.com/science/arti... Animation made with #houdini #sidefx. #scicom #dataviz #cardiology #science

📢 #rastermap paper out now, easily explore and visualize your neural recordings 🐭🐒🐟 and ANNs 🤖 https://nature.com/articles/s41593-024-01783-4. Updates from preprint include analyses of primate data and IBL task data. Video tutorial: https://youtu.be/oQHq7yUWn2k #neuroscience #machinelearning

Six tips for going public with your lab’s software: https://www.nature.com/articles/d41586-024-03344-y 1) make time for maintenance 2) simplify installation 3) add a GUI or good CLI 4) good documentation 5) use github/git 6) automated testing Any other tips people have? #softwareengineering

The first preprint of my postdoc with @dudman.bsky.social is now online! Here we wanted to understand the algorithms mice use when learning to forage in large environments with many potential resources. www.biorxiv.org/content/10.1...