{ "info": { "author": "Kwik Team", "author_email": "cyrille.rossant at gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Natural Language :: English", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5" ], "description": "# Klusta: automatic spike sorting up to 64 channels\n\n[![Build Status](https://img.shields.io/travis/kwikteam/klusta.svg)](https://travis-ci.org/kwikteam/klusta)\n[![codecov.io](https://img.shields.io/codecov/c/github/kwikteam/klusta.svg)](http://codecov.io/github/kwikteam/klusta?branch=master)\n[![Documentation Status](https://readthedocs.org/projects/klusta/badge/?version=latest)](http://klusta.readthedocs.org/en/latest/)\n[![PyPI release](https://img.shields.io/pypi/v/klusta.svg)](https://pypi.python.org/pypi/klusta)\n[![GitHub release](https://img.shields.io/github/release/kwikteam/klusta.svg)](https://github.com/kwikteam/klusta/releases/latest)\n\n[**klusta**](https://github.com/kwikteam/klusta) is an open source package for automatic spike sorting of multielectrode neurophysiological recordings made with probes containing up to a few dozens of sites.\n\nWe are also working actively on more sophisticated algorithms that will scale to hundreds/thousands of channels. This work is being done within the [phy project](https://github.com/kwikteam/phy), which is still experimental at this point.\n\n## Overview\n\n**klusta** implements the following features:\n\n* **Kwik**: An HDF5-based file format that stores the results of a spike sorting session.\n* **Spike detection** (also known as SpikeDetekt): an algorithm designed for probes containing tens of channels, based on a flood-fill algorithm in the adjacency graph formed by the recording sites in the probe.\n* **Automatic clustering** (also known as Masked KlustaKwik): an automatic clustering algorithm designed for high-dimensional structured datasets.\n\n\n## GUI\n\nYou will need a GUI to visualize the spike sorting results.\n\nWe have developed two GUI programs with the same features:\n\n* **phy KwikGUI**: newer project, scales to hundreds/thousands of channels, still relatively experimental. **It will be automatically installed if you follow the install instructions below.**\n* **[KlustaViewa](https://github.com/klusta-team/klustaviewa)**: widely used, but older and a bit hard to install since it relies on very old dependencies.\n\nBoth GUIs work with the same **Kwik** format.\n\n\n## Quick install guide\n\nThe following instructions will install both **klusta** and the **phy KwikGUI**.\n\n1. 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).\n2. [Download the environment file.](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment.yml)\n3. Open a terminal (on Windows, `cmd`, not Powershell) in the directory where you saved the file and type:\n\n ```bash\n conda env create -n klusta -f environment.yml\n ```\n\n4. **Done**! Now, to use klusta and the phy KwikGUI, enter the directory that contains your files and type:\n\n ```bash\n source activate klusta # omit the `source` on Windows\n klusta yourfile.prm # spikesort your data with a PRM file\n phy kwik-gui yourfile.kwik # open the GUI\n ```\n\n See the documentation for more details.\n\n\n### Updating the software\n\nTo get the latest version of the software, open a terminal and type:\n\n```\nsource activate klusta # omit the `source` on Windows\npip install klusta phy phycontrib --upgrade\n```\n\n\n## Technical details\n\n**klusta** is written in pure Python. The clustering code, written in Python and Cython, currently lives in [another repository](https://github.com/kwikteam/klustakwik2/).\n\n\n## Links\n\n* [Documentation](http://klusta.readthedocs.org/en/latest/) (work in progress)\n* [Paper in Nature Neuroscience (April 2016)](http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4268.html)\n* [Mailing list](https://groups.google.com/forum/#!forum/klustaviewas)\n* [Sample data repository](http://phy.cortexlab.net/data/) (work in progress)\n\n\n## Credits\n\n**klusta** 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.", "description_content_type": null, "docs_url": null, "download_url": 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