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