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YASS: Yet Another Spike Sorter

Project description

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Note: YASS is in an early stage of development. Although it is stable, it has only been tested with the data in our lab, but we are working to make it more flexible. Feel free to send feedback through Gitter. Expect a lot of API changes in the near future.

Reference

Lee, J. et al. (2017). YASS: Yet another spike sorter. Neural Information Processing Systems. Available in biorxiv: https://www.biorxiv.org/content/early/2017/06/19/151928

Installation

Installing the last stable version:

pip install yass-algorithm

If you are feeling adventurous, you can install from the master branch:

pip install git+git://github.com/paninski-lab/yass@master

Example

Quick example of YASS using a sample of the neuropixel data from Nick Steinmetz:

# install last stable version
pip install yass-algorithm

# clone repo to get the sample data
git clone https://github.com/paninski-lab/yass

# move to the examples/ folder and run yass in the sample data
cd yass/examples
yass sort config_sample.yaml

# see the spike train
cat data/spike_train.csv

You can also use YASS in Python scripts. See the documentation for details.

Documentation

Documentation hosted at https://yass.readthedocs.io

Running tests

To run tests and flake8 checks (from the root folder):

pip install -r requirements.txt

make test

Building documentation

You need to install graphviz to build the graphs included in the documentation. On macOS:

brew install graphviz

To build the docs (from the root folder):

pip install -r requirements.txt

make docs

Project details


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