/phy

Modules for manual spike sorting GUIs, ephys data analysis, visualization

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

phy project

Build Status codecov.io Documentation Status PyPI release GitHub release Join the chat at https://gitter.im/kwikteam/phy

phy is an open source neurophysiological data analysis package in Python. It provides features for sorting, analyzing, and visualizing extracellular recordings made with high-density multielectrode arrays containing hundreds to thousands of recording sites.

Overview

phy contains the following subpackages:

  • phy.cluster: an API for manual sorting, used to create graphical interfaces for neurophysiological data
  • phy.gui: a generic API for creating desktop applications with PyQt.
  • phy.plot: a generic API for creating high-performance plots with VisPy (using the graphics processor via OpenGL)

phy targets developers and doesn't provide any I/O code. It only provides Python routines to process and visualize data.

phy-contrib

The phy-contrib repo contains a set of plugins with integrated GUIs that work with dedicated automatic clustering software. Currently it provides:

  • KwikGUI: a manual sorting GUI that works with data processed with klusta, an automatic clustering package.
  • TemplateGUI: a manual sorting GUI that works with data processed with Spyking Circus and KiloSort (not released yet), which are template-matching-based spike sorting algorithms.

Installation

Note: the installation instructions will be simplified soon.

  1. Make sure that you have miniconda installed. You can choose the Python 3.6 64-bit version for your operating system (Linux, Windows, or OS X).

  2. Download the environment file.

  3. Open a terminal (on Windows, cmd, not Powershell) in the directory where you saved the file and type:

    conda env create -n phy
source activate phy  # omit the `source` on Windows
pip install phy phycontrib

  4. Done! Now, to use phy, you have to first type source activate phy in a terminal (omit the source on Windows), and then call phy.

Updating the software

To get the latest version of the software, open a terminal and type:

source activate phy  # omit the `source` on Windows
pip install phy phycontrib --upgrade

Installing the development version

You first need to download and install git. Then, use the regular command line terminal (not the git shell) and type the following:

source activate phy  # omit the `source` on Windows
pip install git+https://github.com/kwikteam/phy git+https://github.com/kwikteam/phy-contrib --upgrade

Links

Credits

phy is developed by Cyrille Rossant, Shabnam Kadir, Dan Goodman, Max Hunter, and Kenneth Harris, in the Cortexlab, University College London.