yass-algorithm 0.9

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

Contributors

Peter Lee, Eduardo Blancas, Nishchal Dethe, Shenghao Wu, Hooshmand Shokri, Calvin Tong, Catalin Mitelut