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Python toolkit for analysis, visualization, and comparison of spike sorting output

Project description

PyPI version

SpikeInterface

SpikeInterface is a Python framework designed to unify preexisting spike sorting technologies into a single code base.

spikeinterface is a meta-package that wraps 5 other Python packages from the SpikeInterface team:

  • spikeextractors: Data file I/O and probe handling. Build Status
  • spiketoolkit: Toolkit for pre-processing, post-processing, validation, and automatic curation. Build Status
  • spikesorters: Python wrappers to spike sorting algorithms. Build Status
  • spikecomparison: Comparison of spike sorting output (with and without ground-truth). Build Status
  • spikewidgets: Data visualization widgets. Build Status

On October 8, 2019, we have released the very first beta version of spikeinterface (0.9.1)

Please have a look at the preprint that describes in detail this project

Installation

You can install SpikeInterface from pip:

pip install spikeinterface

Alternatively, you can clone the repository and install from sources the development version:

git clone https://github.com/SpikeInterface/spikeinterface.git
cd spikeinterface
python setup.py develop

Important: installing with python setup.py develop DOES NOT install the latest version of the different modules. In order to get the latest updates, clone the above-mentioned repositories and install them from source.

Documentation

All documentation for SpikeInterface can be found here: https://spikeinterface.readthedocs.io/en/latest/.

You can also check out this 1-hour video tutorial for the NWB User Days 2019: https://www.youtube.com/watch?v=nWJGwFB7oII

Citation

If you find SpikeInterface useful in your research, please cite:

@article{buccino2019spikeinterface,
  title={SpikeInterface, a unified framework for spike sorting},
  author={Buccino, Alessio P and Hurwitz, Cole L and Magland, Jeremy and Garcia, Samuel and Siegle, Joshua H and Hurwitz, Roger and Hennig, Matthias H},
  journal={BioRxiv},
  pages={796599},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

SpikeInterface contributors

For any correspondence, contact Alessio Buccino (alessiop.buccino@gmail.com), Cole Hurwitz (colehurwitz@gmail.com), Samuel Garcia (samuel.garcia@cnrs.fr), Jeremy Magland (jmagland@flatironinstitute.org) or Matthias Hennig (m.hennig@ed.ac.uk), or just write an issue!

The following people have contributed code to the project as of 24 August 2020:

Project details


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