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index.qmd
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index.qmd
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---
title: Pachitariu + Stringer lab
---
Our lab is at [HHMI Janelia Research Campus](https://www.janelia.org/) (near DC), a fully-funded non-profit research institution. Janelia just received a $500 million investment for AI research 🤖, more info [here](https://ai.hhmi.org/).
We are recruiting [PhD students](positions.qmd)!
## 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://www.suite2p.org/static/images/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
* [Analysis methods for large-scale neuronal recordings](https://www.science.org/stoken/author-tokens/ST-2239/full) review published!
* Cellpose development highlighted in a Nature [technology feature](https://www.nature.com/articles/d41586-024-03344-y)!
* Rastermap paper is now out [here](https://www.nature.com/articles/s41593-024-01783-4)! [News coverage](https://medicalxpress.com/news/2024-10-visualization-method-large-neuronal-datasets.html)
* Congrats to Fengtong Du et al, preprint now out: [Towards a simplified model of primary visual cortex](https://www.biorxiv.org/content/10.1101/2024.06.30.601394.abstract)!
* Kilosort4 paper is now out [here](https://www.nature.com/articles/s41592-024-02232-7)!
* Congrats to Lin Zhong et al, preprint now out on [Distinct streams for supervised and unsupervised learning in the visual cortex](https://www.biorxiv.org/content/10.1101/2024.02.25.581990v1)!
* Facemap was featured in a Nature Methods [research highlight](https://www.nature.com/articles/s41592-023-02154-w)!
* Congrats to Atika Syeda et al for the publication of the Facemap [paper](https://www.nature.com/articles/s41593-023-01490-6)!
## Resources
* About [HHMI Janelia Research Campus](https://www.janelia.org/about-us)
* HHMI's [values](https://www.hhmi.org/about/values)
* HHMI’s [commitment to Diversity, Equity, and Inclusion](https://diversity.hhmi.org/)
* [Being a postdoc at Janelia](https://youtube.com/playlist?list=PLTHgpZlI_u0hSo_NO0wpzpMnt6BnOOaWl&feature=shared)
## Talks
* 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
- [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