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---
title: Pachitariu + Stringer lab
resources:
- .nojekyll
---
Our lab is at [HHMI Janelia Research Campus](https://www.janelia.org/) (near DC), a fully-funded non-profit research institution.
## Research
Our lab combines machine learning / AI techniques and large-scale imaging to investigate plasticity rules and sensory representations in cortical circuits. Example recording of 50,000+ neurons simultaneously at 3Hz, using two-photon calcium imaging:
<video width="100%" autoplay loop muted playsinline controls alt="50,000 neurons recorded with two-photon calcium imaging from mouse visual cortex">
<source src="https://github.com/MouseLand/MouseLand.github.io/releases/download/v0.1/Movie1.mp4" type="video/mp4">
</video>
Learn more about our research [here](research/index.qmd) and see all publications [here](research/publications.qmd). We share all the data generated by our studies, linked [here](code_and_data.qmd). We also have developed several data processing packages for the bio/neuro community: [cellpose](research/posts/cellpose.qmd), [kilosort](research/posts/kilosort.qmd), [suite2p](research/posts/suite2p.qmd), [facemap](research/posts/rastermap.qmd), and [rastermap](research/posts/rastermap.qmd).
## News
* Congrats to Miguel Angel Nuñez-Ochoa et al, preprint now out on [Linking neural representations to behavior using generalization](https://www.biorxiv.org/content/10.64898/2026.04.21.719991v1.abstract)!
* Congrats to Paul K LaFosse et al, preprint now out on [Raster photostimulation of large-scale neural populations](https://www.biorxiv.org/content/10.64898/2026.04.21.719951v1.abstract)!
* [Critical initialization of biological neural networks](https://www.nature.com/articles/s41586-026-10528-1) now published! + all [data](https://doi.org/10.25378/janelia.27854448) and [code](https://github.com/MouseLand/critical_init) shared!
* Congrats to Atika Syeda et al, preprint now out on [Orofacial behaviors, not eye movements, govern neural activity in mouse visual cortex](https://www.biorxiv.org/content/10.64898/2026.02.04.703800v1.abstract)! Also she presented this work at Cosyne!
* [Suite2p](https://www.biorxiv.org/content/10.64898/2026.02.04.703741v1.abstract) now out as a preprint!
* Check out our lab's SfN posters:
* **Nov 17 PM Q2**: PSTR224.08. Train/test behavioral cross-validation reveals neural correlates in mice
* **Nov 19 AM R8**: PSTR394.02. Impact of eye movements and orofacial movements on mouse visual cortex
* **Nov 19 PM Q9**: PSTR450.05. Spatial or temporal prediction in mouse visual cortex
* Congrats to Qingqing Zhang et al, preprint now out on [Spatial predictive coding in visual cortical neurons](https://www.biorxiv.org/content/10.1101/2025.09.17.676794v1)!
* Fengtong Du's [paper](https://www.nature.com/articles/s41467-025-61171-9) on minimodels of visual cortical neurons in mice and monkeys now published! [News coverage](https://www.janelia.org/news/new-computational-model-could-help-shed-light-on-how-we-see)
* Lin Zhong's [paper](https://www.nature.com/articles/s41586-025-09180-y) on unsupervised learning now published! [News coverage](https://www.janelia.org/news/zoning-out-could-be-beneficial%E2%80%94and-may-actually-help-us-learn-faster)
## Resources
* About [HHMI Janelia Research Campus](https://www.janelia.org/about-us)
* HHMI's [values](https://www.hhmi.org/about/values)
* [Being a postdoc at Janelia](https://youtube.com/playlist?list=PLTHgpZlI_u0hSo_NO0wpzpMnt6BnOOaWl&feature=shared)
## Talks
* Cellpose3 [talk+tutorial](https://www.youtube.com/watch?v=TZZZlGk6AKo)
* Rastermap [tutorial](https://youtu.be/oQHq7yUWn2k)
* Facemap [tutorial](https://youtu.be/aO_kXkOuadg)
* Kilosort 4 [talk](https://youtu.be/LTSmoACr918?feature=shared)
* Making sense of large-scale neural and behavioral data with Facemap and Rastermap [talk](https://www.youtube.com/watch?v=4fIXfSBKWu8)
* Cellpose 2.0: how to train your own model [talk](https://youtu.be/3ydtAhfq6H0), [talk+tutorial](https://youtu.be/5qANHWoubZU)
* Cellpose [talk](https://youtu.be/7y9d4VIKiS8), [talk+tutorial](https://www.youtube.com/watch?v=DL-j-hPFixk)
* Suite2p [talk](https://www.youtube.com/watch?v=L0cX6V2wFUU)
* Kilosort 1, 2, 2.5 & 3 [talk](https://youtu.be/cmrAhhquC9E?feature=shared)
* High precision coding in visual cortex [short talk](https://youtu.be/5-DkXplTFuY), [long talk](https://www.youtube.com/watch?v=ob48PKoIbfA)
* High-dimensional geometry of population responses in visual cortex [talk](https://www.youtube.com/watch?v=fAFHJiqYwb8)
* High-dimensional problems in neuroscience [talk](https://youtu.be/NzdynFTp7fY)
* Spontaneous behaviors drive multidimensional, brainwide activity [talk](https://youtu.be/1FCCh4COiCM?feature=shared&t=196)
## Media Coverage
- [How Brains Learn & Compute: Neuroscience Meets AI with Dr. Marius Pachitariu](https://youtu.be/dl_xnOsGp4E?si=65uU8IXqMm0GhXme), Mind & Matter Podcast
- [New computational model could help shed light on how we see](https://www.janelia.org/news/new-computational-model-could-help-shed-light-on-how-we-see), Howard Hughes Medical Institute
- [Doing This Might Actually Make You Smarter](https://www.vice.com/en/article/doing-this-might-actually-make-you-smarter/), Vice
- ["Zoning Out" Actually Helps You Learn? Data From Up To 90,000 Brain Cells Says So](https://www.iflscience.com/zoning-out-actually-helps-you-learn-data-from-up-to-90000-brain-cells-says-so-79986), IFL Science
- [Zoning out could be beneficial—and may actually help us learn faster](https://www.janelia.org/news/zoning-out-could-be-beneficial%E2%80%94and-may-actually-help-us-learn-faster), Howard Hughes Medical Institute
- [Newest version of Cellpose can spot cell boundaries even in cloudy conditions](https://www.janelia.org/news/newest-version-of-cellpose-can-spot-cell-boundaries-even-in-cloudy-conditions), Howard Hughes Medical Institute
- [Novel visualization method helps make sense of large neuronal activity datasets](https://medicalxpress.com/news/2024-10-visualization-method-large-neuronal-datasets.html), Medical Xpress
- [New tool helps scientists spot patterns in mountains of data](https://www.janelia.org/news/new-tool-helps-scientists-spot-patterns-in-mountains-of-data), Howard Huges Medical Institute
- [Six tips for going public with your lab’s software](https://www.nature.com/articles/d41586-024-03344-y), Nature
- [Janelia scientists release state-of-the-art spike-sorting software Kilosort4](https://www.janelia.org/news/janelia-scientists-release-state-of-the-art-spike-sorting-software-kilosort4), Howard Hughes Medical Institute
- [Predicting neural activity from facial expressions](https://www.nature.com/articles/s41592-023-02154-w), Nature Methods
- [Tiny faces, big expressions: Reading rodent faces](https://pennneuroknow.com/2023/12/19/tiny-faces-big-expressions-reading-rodent-faces/), Penn NeuroKnow
- [Reading the mouse mind from its face: New tool decodes neural activity using facial movements](https://www.janelia.org/news/reading-the-mouse-mind-from-its-face-new-tool-decodes-neural-activity-using-facial-movements), Howard Hughes Medical Institute
- [Noisy solo neurons show consistency in groups](https://www.janelia.org/news/noisy-solo-neurons-show-consistency-in-groups), Howard Hughes Medical Institute
- [High precision coding: How the visual cortex processes information about the world](https://www.scientifica.uk.com/neurowire/high-precision-coding-how-the-visual-cortex-processes-information-about-the-world), Scientifica
- [New tool maps boundaries of diverse cells in microscope images](https://www.janelia.org/news/new-tool-maps-boundaries-of-diverse-cells-in-microscope-images), Howard Hughes Medical Institute
- [Python power-up: new image tool visualizes complex data](https://www.nature.com/articles/d41586-021-03628-7), Nature
- [A Power Law Keeps the Brain's Perceptions Balanced](https://www.quantamagazine.org/a-power-law-keeps-the-brains-perceptions-balanced-20191022/), Quanta magazine
- [Power Law Discovery May Explain Why You Can See the Forest and the Trees](https://www.simonsfoundation.org/2019/06/26/power-law-discovery-may-explain-why-you-can-see-the-forest-and-the-trees/), Simons Foundation
- ['Noise' in the Brain Encodes Surprisingly Important Signals](https://www.quantamagazine.org/noise-in-the-brains-vision-areas-encodes-body-movements-20191107/), Quanta magazine
- [Thinking on the Go: Why Does the Whole Brain Light Up for Just the Smallest Movements?](https://www.simonsfoundation.org/2019/11/26/thinking-on-the-go-why-does-the-whole-brain-light-up-for-just-the-smallest-movements/), Simons Foundation
- [profile + podcast](https://www.storiesofwin.org/profiles/2021/6/2/dr-carsen-stringer), Stories of Women in Neuroscience (WIN) by Daniela Cassataro
- [Understanding 40,000 neurons](https://braininspired.co/podcast/91/), Brain Inspired podcast by Paul Middlebrooks