Extracellular recordings are an essential source of data in experimental and clinical neuroscience. Of particular interest in these recordings is the activity of single neurons which must be inferred using a blind source separation procedure called spike sorting.
Given the importance of spike sorting, much attention has been directed towards the development of tools and algorithms that can increase its performance and automation. These developments, however, introduce new challenges in software and file format incompatibility which reduce interoperability, hinder benchmarking, and preclude reproducible analysis.
To address these limitations, we developed SpikeInterface, a Python framework designed to unify preexisting spike sorting technologies into a single code base and to standardize extracellular data file handling. With a few lines of code, users can run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorted results; and more, regardless of the underlying data format.
In the following documentation, we provide an overview of SpikeInterface.
SpikeInterface consists of 5 main sub-packages which encapsulate all steps in a typical spike sorting pipeline:
- spikeinterface.extractors
- spikeinterface.toolkit
- spikeinterface.sorters
- spikeinterface.comparisons
- spikeinterface.widgets
Contrary to the previous version (<0.90.0), spikeinterface is now one unique package.
Before that, spikeinterface was a metapackage that depended on 5 independent packages.
- probeinterface is a python package to define and handle neural
- probes and the wiring to recording devices.
- spikeforest is a reproducible, continuously updating platform which benchmarks the performance of some spike sorting software (kilosort, herdingspike, ironclust, jrclust, klusta, mountainsort4, spykingcircus, tridesclous, waveclus) using many ground-truth datasets. The processing engine is based on SpikeInterface.
- spikely is a graphical user interface (GUI) that allows users to build and run SpikeInterface spike sorting pipelines on extracellular datasets.
- MEArec is a fast customizable biophysical simulation of extracellular recording.