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 March 13th, 2021, a new version of spikeinterface has been released (0.12.0). 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 11 March 2021 (according to the GitHub API):
Abhijith Krishnan
Achilleas Koutsou, Red Hat
Adam Lowet
Alan Liddell, Path Robotics
Alessio Buccino, ETH
Ben Dichter, CatalystNeuro
Cody Baker
Cole Hurwitz, University of Edinburgh
Emily Aery Jones, Stanford University
Fernando J. Chaure, University of Buenos Aires
Garcia Samuel, CNRS, Centre de recherche en neuroscience de Lyon
Giuliano Maggi
James Jun, Facebook, Agios-CTRL
Jasper Wouters
Jeremy Magland
John Hermiz
Joram van Rheede, University of Oxford
Jose Guzman, Austrian Academy of Sciences - OEAW
Josh Siegle, Allen Institute for Brain Science
Julia Sprenger, Institut de Neurosciences de la Timone (INT)
Kyu Hyun Lee
Luiz Tauffer, @kth
Manish Mohapatra
Matthias H. Hennig, University of Edinburgh
Mikkel Elle Lepperød
Peter Jones, NMI
Pierre Yger, Institut de la Vision
Roger Hurwitz
Roland Diggelmann, ETH Zurich
Saksham Sharda
Shawn Guo, School of Informatics, University of Edinburgh
Vincent Prevosto
Yaroslav Halchenko, Dartmouth College, @Debian, @DataLad, @PyMVPA, @fail2ban
catubc
wuffi
llobetv
Dradeliomecus
Michael Scudder
m-col, @DuguidLab
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