phy 1.0.9

Spike sorting and ephys data analysis for 1000 channels and beyond

# phy project

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[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

• [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)

## 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.