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A Python-based module for creating flexible and robust spike sorting pipelines.
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README.md

PyPI version

SpikeInterface

SpikeInterface is a Python framework designed to unify preexisting spike sorting technologies into a single code base.

spikeinterface is a meta-package that wraps 5 other Python packages from the SpikeInterface team:

  • spikeextractors: Data file I/O and probe handling. Build Status
  • spiketoolkit: Toolkit for pre-processing, post-processing, validation, and automatic curation. Build Status
  • spikesorters: Python wrappers to spike sorting algorithms. Build Status
  • spikecomparison: Comparison of spike sorting output (with and without ground-truth). Build Status
  • spikewidgets: Data visualization widgets. Build Status

On October 8, 2019, we have released the very first beta version of spikeinterface (0.9.1)

Please have a look at the preprint that describes in detail this project

Installation

You can install SpikeInterface from pip:

pip install spikeinterface

Alternatively, you can clone the repository and install from sources the development version:

git clone https://github.com/SpikeInterface/spikeinterface.git
cd spikeinterface
python setup.py develop

Important: installing with python setup.py develop DOES NOT install the latest version of the different modules. In order to get the latest updates, clone the above-mentioned repositories and install them from source.

Examples

For using SpikeInterface, please checkout these examples.

Also, you can checkout this tutorial for getting started with SpikeInterface.

Documentation

All documentation for SpikeInterface can be found here: https://spikeinterface.readthedocs.io/en/latest/.

Authors

Alessio Paolo Buccino - Center for Inegrative Neurolasticity (CINPLA), Department of Biosciences, Physics, and Informatics, University of Oslo, Oslo, Norway

Cole Hurwitz - The Institute for Adaptive and Neural Computation (ANC), University of Edinburgh, Edinburgh, Scotland

Jeremy Magland - Center for Computational Biology (CCB), Flatiron Institute, New York, United States

Matthias Hennig - The Institute for Adaptive and Neural Computation (ANC), University of Edinburgh, Edinburgh, Scotland

Samuel Garcia - Centre de Recherche en Neuroscience de Lyon (CRNL), Lyon, France


For any correspondence, contact Alessio Buccino (alessiop.buccino@gmail.com), Cole Hurwitz (cole.hurwitz@ed.ac.uk), or just write an issue!
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