Welcome to SpikeInterface’s documentation!¶
Spikeinterface is a Python module designed to improve the accessibility, reliability, and reproducibility of spike sorting and all its associated computations.
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.
export report and export to Phy.
offer a powerful Qt-based viewer in separate package spikeinterface-gui
have some powerful sorting components to build your own sorter.
Overview of SpikeInterface modules¶
To get started with SpikeInterface, you can take a look at the following additional resources:
spiketutorials is a collection of basic and advanced tutorials,
It includes links to videos to dive into the SpikeInterface framework.
SpikeInterface Reports contains several notebooks to reproduce analysis figures
of SpikeInterface-based papers and to showcase the latest features of SpikeInterface.
The 2020 eLife paper introduces the concept and motivation and performs
an in-depth comparison of multiple sorters (spolier alert: they strongly disagree between each other!). Note: the
code-base and implementation have changed a lot since the “paper” version in published in 2020.
For detailed documentation we therefore suggest more recent resources, like this documentation and
Versions and compatibility¶
We released a major version of SpikeInterface (referred to as new API) in July 2021 (version>=0.90) which:
breaks backward compatibility with 0.10/0.11/0.12/0.13 series (old API)
is not a metapackage anymore
doesn’t depend on spikeextractors/spiketoolkit/spikesorters/spikecomparison/spikewidgets sub-packages
Please see the release notes here: SpikeInterface 0.90.0 release notes.
For other version release notes check the Release notes.
See the documentation for the version old API (version<=0.13) here.