Metadata-Version: 1.1
Name: klusta
Version: 3.0.16
Summary: Spike detection and automatic clustering for spike sorting
Home-page: https://klusta.cortexlab.net
Author: Kwik Team
Author-email: cyrille.rossant at gmail.com
License: BSD
Description-Content-Type: UNKNOWN
Description: # Klusta: automatic spike sorting up to 64 channels
        
        [![Build Status](https://img.shields.io/travis/kwikteam/klusta.svg)](https://travis-ci.org/kwikteam/klusta)
        [![codecov.io](https://img.shields.io/codecov/c/github/kwikteam/klusta.svg)](http://codecov.io/github/kwikteam/klusta?branch=master)
        [![Documentation Status](https://readthedocs.org/projects/klusta/badge/?version=latest)](http://klusta.readthedocs.org/en/latest/)
        [![PyPI release](https://img.shields.io/pypi/v/klusta.svg)](https://pypi.python.org/pypi/klusta)
        [![GitHub release](https://img.shields.io/github/release/kwikteam/klusta.svg)](https://github.com/kwikteam/klusta/releases/latest)
        
        [**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.
        
        We 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.
        
        ## Overview
        
        **klusta** implements the following features:
        
        * **Kwik**: An HDF5-based file format that stores the results of a spike sorting session.
        * **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.
        * **Automatic clustering** (also known as Masked KlustaKwik): an automatic clustering algorithm designed for high-dimensional structured datasets.
        
        
        ## GUI
        
        You will need a GUI to visualize the spike sorting results.
        
        We have developed two GUI programs with the same features:
        
        * **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.**
        * **[KlustaViewa](https://github.com/klusta-team/klustaviewa)**: widely used, but older and a bit hard to install since it relies on very old dependencies.
        
        Both GUIs work with the same **Kwik** format.
        
        
        ## Quick install guide
        
        The following instructions will install both **klusta** and the **phy KwikGUI**.
        
        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/klusta/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 klusta -f environment.yml
            ```
        
        4. **Done**! Now, to use klusta and the phy KwikGUI, enter the directory that contains your files and type:
        
            ```bash
            source activate klusta  # omit the `source` on Windows
            klusta yourfile.prm  # spikesort your data with a PRM file
            phy kwik-gui yourfile.kwik  # open the GUI
            ```
        
            See the documentation for more details.
        
        
        ### Updating the software
        
        To get the latest version of the software, open a terminal and type:
        
        ```
        source activate klusta  # omit the `source` on Windows
        pip install klusta phy phycontrib --upgrade
        ```
        
        
        ## Technical details
        
        **klusta** is written in pure Python. The clustering code, written in Python and Cython, currently lives in [another repository](https://github.com/kwikteam/klustakwik2/).
        
        
        ## Links
        
        * [Documentation](http://klusta.readthedocs.org/en/latest/) (work in progress)
        * [Paper in Nature Neuroscience (April 2016)](http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4268.html)
        * [Mailing list](https://groups.google.com/forum/#!forum/klustaviewas)
        * [Sample data repository](http://phy.cortexlab.net/data/) (work in progress)
        
        
        ## Credits
        
        **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.
        
Keywords: klusta,neuroscience,spike sorting,klustakwik
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
