Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

Spike sorting and ephys data analysis for 1000 channels and beyond

Project description

# phy project

[![Build Status](https://img.shields.io/travis/kwikteam/phy.svg)](https://travis-ci.org/kwikteam/phy) [![codecov.io](https://img.shields.io/codecov/c/github/kwikteam/phy.svg)](http://codecov.io/github/kwikteam/phy?branch=master) [![Documentation Status](https://readthedocs.org/projects/phy/badge/?version=latest)](https://readthedocs.org/projects/phy/?badge=latest) [![PyPI release](https://img.shields.io/pypi/v/phy.svg)](https://pypi.python.org/pypi/phy) [![GitHub release](https://img.shields.io/github/release/kwikteam/phy.svg)](https://github.com/kwikteam/phy/releases/latest) [![Join the chat at https://gitter.im/kwikteam/phy](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/kwikteam/phy?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)

[phy](https://github.com/kwikteam/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.manual: 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](https://github.com/kwikteam/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](http://klusta.readthedocs.org/en/latest/), 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](http://conda.pydata.org/miniconda.html) installed. You can choose the Python 3.5 64-bit version for your operating system (Linux, Windows, or OS X).

  2. Download the [environment file](https://raw.githubusercontent.com/kwikteam/phy/master/installer/environment.yml).

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

    `bash 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 `

## Links

## Credits

phy is developed by [Cyrille Rossant](http://cyrille.rossant.net), [Shabnam Kadir](https://iris.ucl.ac.uk/iris/browse/profile?upi=SKADI56), [Dan Goodman](http://thesamovar.net/), [Max Hunter](https://iris.ucl.ac.uk/iris/browse/profile?upi=MLDHU99), and [Kenneth Harris](https://iris.ucl.ac.uk/iris/browse/profile?upi=KDHAR02), in the [Cortexlab](https://www.ucl.ac.uk/cortexlab), University College London.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for phy, version 1.0.9
Filename, size File type Python version Upload date Hashes
Filename, size phy-1.0.9-py2.py3-none-any.whl (204.7 kB) File type Wheel Python version py2.py3 Upload date Hashes View hashes
Filename, size phy-1.0.9.tar.gz (166.3 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page