This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (pypi.python.org).
Help us improve Python packaging - Donate today!

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.

Release History

Release History

This version
History Node

1.0.9

History Node

1.0.8

History Node

1.0.7

History Node

1.0.6

History Node

1.0.5

History Node

1.0.4

History Node

1.0.3

History Node

1.0.2

History Node

1.0.1

History Node

1.0.0

History Node

0.2.2

History Node

0.2.2.dev0

History Node

0.2.1

History Node

0.2.0

History Node

0.2.0.dev1

History Node

0.2.0.dev0

History Node

0.1.0

Download Files

Download Files

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

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
phy-1.0.9-py2.py3-none-any.whl (204.7 kB) Copy SHA256 Checksum SHA256 py2.py3 Wheel Nov 10, 2016
phy-1.0.9.tar.gz (166.3 kB) Copy SHA256 Checksum SHA256 Source Nov 10, 2016

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting