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README.md

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Rastermap is a discovery algorithm for neural data. The algorithm was written by Carsen Stringer and Marius Pachitariu. For support, please open an [issue](https://github.com/MouseLand/rastermap/issues). Please see install instructions [below](README.md/#Installation). Check out the [**paper**](https://www.nature.com/articles/s41593-024-01783-4) and the [**tutorial video**](https://youtu.be/oQHq7yUWn2k) for more info. Rastermap runs in python 3.8+ and has a [**graphical user interface (GUI)**](#gui) for running it easily.
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Here is what the output looks like for 34,000 neurons recorded simultaneously in mouse cortex during spontaneous activity, compared to random neural sorting:
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<img src="https://www.suite2p.org/static/images/rastermap_spont.png" width="600" alt="random sorting and rastermap sorting of spontaneous activity"/>
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**If you use Rastermap or analysis code in this repo in your work, please cite the paper:**
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Stringer C., Zhong L., Syeda A., Du F., Kesa M., & Pachitariu M. (2024). Rastermap: a discovery method for neural population recordings. *Nature Neuroscience*. https://doi.org/10.1038/s41593-024-01783-4.
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* [rastermap_interactive.ipynb](notebooks/rastermap_interactive.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MouseLand/rastermap/blob/main/notebooks/rastermap_interactive.ipynb) allows running Rastermap in an interactive way without a local installation
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* [tutorial.ipynb](notebooks/tutorial.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MouseLand/rastermap/blob/main/notebooks/tutorial.ipynb) is a guided tutorial for integrating rastermap and facemap to visualize behavioral representations. See the student/teacher versions [here](https://github.com/MouseLand/course-materials/tree/main/behavior_encoding).
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Also all notebooks to analyze the data and create the figures in the paper are [here](paper/). All data available [here](https://osf.io/xn4cm/).
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Here is what the output looks like for a segment of a mesoscope recording in a mouse during spontaneous activity (3.2Hz sampling rate), compared to random neural sorting:
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<img src="https://www.suite2p.org/static/images/rastermap_spont.png" width="800" alt="random sorting and rastermap sorting of spontaneous activity"/>
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Also all notebooks to analyze the data and create the figures in the paper are [here](paper/).
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# Installation
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