yass-algorithm 0.1.1

YASS: Yet Another Spike Sorter

YASS is a state-of-the-art method for spike sorting.

Note: We are currently working on improving YASS to be usable in different types of neural data. The neural network detector currently only works in reduced use cases. We will add more models soon.

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 git+https://github.com/paninski-lab/yass

Example

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

# clone the repo and move to the main folder
git clone https://github.com/paninski-lab/yass
cd yass

# install package (this is the same as running
# pip install git+https://github.com/paninski-lab/yass)
pip install .

# move to the examples folder and run yass in the sample data
cd examples
yass 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

pytest

Building documentation

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

brew install graphviz

cd doc
make [format]

Mantainers

Peter Lee, Eduardo Blancas