Python toolkit for analysis, visualization, and comparison of spike sorting output
Project description
SpikeInterface: a unified framework for spike sorting
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:rocket::rocket::rocket: New features!: after months of development and testing, we are happy to announce that the latest release (0.101.0) includes a major API improvement: the
SortingAnalyzer! To read more about why we did this, checkout the SpikeInterface Enhancement Proposal. Please follow this guide to transition from the old API to the new one: Updating from legacy.
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 (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.
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.
How to install spikeinterface
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 ..
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}
}
Please also cite other relevant papers for the specific components you use. For a ful list of references, please check the references page.
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