Introduction

phy is an open-source Python library providing a graphical user interface for visualization and manual curation of large-scale electrophysiological data. It is optimized for high-density multielectrode arrays containing hundreds to thousands of recording sites (mostly Neuropixels probes).

Current release candidate: phy 2.1.0rc1 is available for testing on PyPI. This maintenance-focused release candidate aims to improve installation and GUI reliability on current systems. See the release notes for installation instructions, compatibility notes, and testing guidance.

Spike sorting programs

phy can open datasets spike-sorted with the following programs:

• KiloSort
• SpykingCircus
• klusta

KiloSort and SpykingCircus are spike sorting programs based on template matching. They use a file format based on .npy (NumPy binary arrays) and .tsv files (tab-separated files).

klusta is a legacy spike sorting program based on an automatic clustering algorithm. It uses the kwik format based on HDF5. While klusta and the kwik format are still supported by phy, they are no longer actively maintained.

Installation instructions

See the GitHub repository for stable-install instructions, or go to the release notes for the 2.1.0rc1 release-candidate install and testing instructions.