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SpikeInterface is a Python framework designed to unify preexisting spike sorting technologies into a single code base.
Please Star the project to support us and Watch to always stay up-to-date!
With SpikeInterface, users can:
- read/write many extracellular file formats.
- pre-process extracellular recordings.
- run many popular, semi-automatic spike sorters (kilosort1-4, mountainsort4-5, spykingcircus, tridesclous, ironclust, herdingspikes, yass, waveclus)
- run sorters developed in house (lupin, spkykingcicus2, tridesclous2, simple) that compete with kilosort4
- run theses polar sorters without installation using containers (Docker/Singularity).
- post-process sorted datasets using th SortingAnalyzer
- 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
- curate your sorting with several strategies (ml-based, metrics based, manual, ...)
- offer a powerful Qt-based or we-based viewer in a separate package spikeinterface-gui for manual curation that replace phy.
- have powerful sorting components to build your own sorter.
- have a full motion/drift correction framework
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.
Checkout our YouTube channel for video tutorials: SpikeInterface YouTube Channel.
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.
You can install the latest version of spikeinterface version with pip (using quotes ensures pip install works in all terminals/shells):
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 ..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}
}Please also cite other relevant papers for the specific components you use. For a full list of references, please check the references page.