Metadata-Version: 1.1
Name: klusta
Version: 3.0.9
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: # Klusta: automatic spike sorting up to 64 channels
        
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        [![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/)
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        [**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:
        
        * **KlustaViewa**: older project, but widely used. **This will be automatically installed if you follow the installation instructions below.**
        * **phy KwikGUI**: newer project, scales to hundreds/thousands of channels, still experimental. You'll need to install [phy](https://github.com/kwikteam/phy) and [phy-contrib](https://github.com/kwikteam/phy-contrib) if you want to try the development version.
        
        Both GUIs work with the same **Kwik** format.
        
        
        ## 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/).
        
        
        ## Quick install guide
        
        **Note**: the installation instructions will be simplified soon.
        
        The following instructions will install both **klusta** and the **KlustaViewa GUI**.
        
        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:**
            * [Linux](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment-linux.yml)
            * [OS X](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment-osx.yml)
            * [Windows](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment-win.yml)
        3. **Open a terminal** (on Windows, `cmd`, not Powershell) in the directory where you saved the file and type:
        
            ```bash
            conda install conda=3 --yes
            conda env create -n klusta -f environment-XXX.yml  # replace `XXX` by your system
            source activate klusta  # omit the `source` on Windows
            conda install numpy=1.8 --yes
            ```
        
        4. **Done**! Now, to use klusta and KlustaViewa, you have to first type `source activate klusta` in a terminal (omit the `source` on Windows), and then call `klusta` or `klustaviewa`. 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 klustaviewa kwiklib --upgrade
        ```
        
        ## 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
