YASS: Yet Another Spike Sorter
Project description
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
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