spikeinterface 0.10.0

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

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.
• 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 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 ([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 24 August 2020:

• Achilleas Koutsou, @G-Node
• Alan Liddell, Vidrio Technologies
• Alessio Buccino, ETH
• Alexander Morley, MRC BNDU (University of Oxford)
• 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, Computer Laboratory, University of Cambridge
• TRRuikes
• Yaroslav Halchenko, Dartmouth College, @Debian, @DataLad, @PyMVPA, @fail2ban
• Michael Scudder