Package: phy
# phy project[![Build Status](https://img.shields.io/travis/kwikteam/phy.svg)](https://travis-ci.org/kwikteam/phy)
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[![Join the chat athttps://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.## Overviewphycontains the following subpackages:phy.cluster.manual: an API for manual sorting, used to create graphical interfaces for neurophysiological dataphy.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-contribThe [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 withSpyking CircusandKiloSort(not released yet), which are template-matching-based spike sorting algorithms.## InstallationNote: the installation instructions will be simplified soon.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).Download the [environment file](https://raw.githubusercontent.com/kwikteam/phy/master/installer/environment.yml).Open a terminal(on Windows,cmd, not Powershell) in the directory where you saved the file and type:`bash conda env create-nphy source activate phy  # omit the `source` on Windows pip install phy phycontrib `Done! Now, to use phy, you have to first typesource activate phyin a terminal (omit thesourceon Windows), and then callphy.### Updating the softwareTo 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[User documentation of the Template GUI](http://phy-contrib.readthedocs.io/en/latest/template-gui/)[Developer documentation](http://phy.readthedocs.org/en/latest/) (work in progress)[Mailing list](https://groups.google.com/forum/#!forum/phy-users)[Sample data repository](http://phy.cortexlab.net/data/) (work in progress)## Creditsphyis 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.