spikeinterface 0.11.0

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

SpikeInterface: a unified framework for spike sorting

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

On December 10, 2020, a new version of spikeinterface has been released (0.11.0). Check out the release notes

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

Installation

You can install SpikeInterface from pip:

pip install spikeinterface

The pip installation will install a specific and fixed version of the spikeinterface packages.

To use the latest updates, install spikeinterface and the related packages from source:

git clone https://github.com/SpikeInterface/spikeinterface.git
cd spikeinterface
python setup.py install (or develop)

Then you can install the latest releases of the spikeinterface packages:

pip install --upgrade spikeextractors spiketoolkit spikesorters spikecomparison spikewidgets

You can also install the five packages from sources (e.g. for spikeextractors):

git clone https://github.com/SpikeInterface/spikeextractors.git
cd spikeextractors
python setup.py install (or develop)

Documentation

All documentation for SpikeInterface can be found here.

You can also check out this 1-hour video tutorial for the NWB User Days 2020:

Citation

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

@article{buccino2020spikeinterface,
  title={SpikeInterface, a unified framework for spike sorting},
  author={Buccino, Alessio Paolo and Hurwitz, Cole Lincoln and Garcia, Samuel and Magland, Jeremy and Siegle, Joshua H and Hurwitz, Roger and Hennig, Matthias H},
  journal={Elife},
  volume={9},
  pages={e61834},
  year={2020},
  publisher={eLife Sciences Publications Limited}
}

SpikeInterface contributors

For any correspondence, contact Alessio Buccino ([e-mail]), Cole Hurwitz ([e-mail]), Samuel Garcia ([e-mail]), Jeremy Magland ([e-mail]) or Matthias Hennig ([e-mail]), or just write an issue!

The following people have contributed code to the project as of 10 Nov 2020:

• Achilleas Koutsou, @G-Node
• Alan Liddell, Vidrio Technologies
• Alessio Buccino, ETH
• Alexander Morley, Babylon Health
• Ben Dichter, CatalystNeuro
• Cody Baker
• Cole Hurwitz, University of Edinburgh
• Fernando J. Chaure, University of Buenos Aires
• Garcia Samuel, CNRS, Centre de recherche en neuroscience de Lyon
• James Jun, Facebook, Agios-CTRL
• Jasper Wouters
• Jeremy Magland
• Jose Guzman, Austrian Academy of Sciences - OEAW
• Josh Siegle, Allen Institute for Brain Science
• Luiz Tauffer, @kth
• Manish Mohapatra
• Martino Sorbaro, Neuroinformatics, UZH & SynSense.ai
• Matthias H. Hennig, University of Edinburgh
• Mikkel Elle Lepperød
• NMI Biomedical Micro and Nano Engineering
• Pierre Yger, Institut de la Vision
• Roger Hurwitz
• Roland Diggelmann, ETH Zurich
• Shawn Guo, School of Informatics, University of Edinburgh
• TRRuikes
• Yaroslav Halchenko, Dartmouth College, @Debian, @DataLad, @PyMVPA, @fail2ban
• Michael Scudder