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