Welcome to SpikeInterface’s documentation!

SpikeInterface is a Python module to analyze extracellular electrophysiology data.

With a few lines of code, SpikeInterface enables you to load and pre-process the recording, run several state-of-the-art spike sorters, post-process and curate the output, compute quality metrics, and visualize the results.

Warning

New features under construction! 🚧🚧🚧: after the 0.100.0 release (and related bug fixes), the next release will contain a major API improvement: the SortingAnalyzer. To read more about this, checkout the enhancement proposal. Please refer to the stable documentation here. Learn how to update your code here and read more about the SortingAnalyzer here.

Overview of SpikeInterface modules

SpikeInterface is made of several modules to deal with different aspects of the analysis pipeline:

• read/write many extracellular file formats.

• pre-process extracellular recordings.

• run many popular, semi-automatic spike sorters (also in Docker/Singularity containers).

• post-process spike sorted data.

• compare and benchmark spike sorting outputs.

• compute quality metrics to validate and curate spike sorting outputs.

• visualize recordings and spike sorting outputs.

• export a report and/or export to Phy.

• offer a powerful Qt-based viewer in a separate package spikeinterface-gui

• have some powerful sorting components to build your own sorter.

• have a full motion/drift correction framework (See Motion/drift correction)

Contents:

• Overview
• Installation
• Importing SpikeInterface
• Modules documentation
• How to guides
• Modules example gallery
• Installing Spike Sorters
• Viewers
• Development
• API
• Release notes
• Contact Us

Other resources

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 (spoiler alert: they strongly disagree with each other!).

  Note: the code-base and implementation have changed a lot since the “paper” version published in 2020.

  For detailed documentation we therefore suggest more recent resources, like this documentation and spiketutorials.