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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

1.0.9

This version

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1.0.8

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1.0.7

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1.0.6

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1.0.5

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1.0.4

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1.0.3

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1.0.2

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1.0.1

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1.0.0

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0.2.2

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0.2.2.dev0

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0.2.1

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0.2.0

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0.2.0.dev1

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0.2.0.dev0

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0.1.0

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Download Files

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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

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