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Spike sorting and ephys data analysis for 1000 channels and beyond

Project description

# 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 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, 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.

## Getting started

You will find installation instructions and a quick start guide in the [documentation](http://phy.readthedocs.org/en/latest/) (work in progress).

## 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.

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