Python toolkit for analysis, visualization, and comparison of spike sorting output
Project description
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.
- spiketoolkit: Toolkit for pre-processing, post-processing, validation, and automatic curation.
- spikesorters: Python wrappers to spike sorting algorithms.
- spikecomparison: Comparison of spike sorting output (with and without ground-truth).
- spikewidgets: Data visualization widgets.
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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