Python toolkit for analysis, visualization, and comparison of spike sorting output
Project description
SpikeInterface: a unified framework for spike sorting
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:warning::warning::warning: PRs with new features are frozen!: after the 0.100.0 release, we will not accept PRs with new features (only bug fixes) until February 21st 2024.
SpikeInterface is a Python framework designed to unify preexisting spike sorting technologies into a single code base.
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With SpikeInterface, users can:
- read/write many extracellular file formats.
- pre-process extracellular recordings.
- run many popular, semi-automatic spike sorters (also in Docker/Singularity containers).
- post-process sorted datasets.
- compare and benchmark spike sorting outputs.
- compute quality metrics to validate and curate spike sorting outputs.
- visualize recordings and spike sorting outputs in several ways (matplotlib, sortingview, jupyter, ephyviewer)
- export a report and/or export to phy
- offer a powerful Qt-based viewer in a separate package spikeinterface-gui
- have powerful sorting components to build your own sorter.
Documentation
Detailed documentation of the latest PyPI release of SpikeInterface can be found here.
Detailed documentation of the development version of SpikeInterface can be found here.
Several tutorials to get started can be found in spiketutorials.
There are also some useful notebooks on our blog that cover advanced benchmarking and sorting components.
You can also have a look at the spikeinterface-gui.
How to install spikeinterface
You can install the latest version of spikeinterface version with pip:
pip install spikeinterface[full]
The [full] option installs all the extra dependencies for all the different sub-modules.
To install all interactive widget backends, you can use:
pip install spikeinterface[full,widgets]
To get the latest updates, you can install spikeinterface from source:
git clone https://github.com/SpikeInterface/spikeinterface.git
cd spikeinterface
pip install -e .
cd ..
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}
}
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