MarineChap/spikeextractors

Python-based module for extracting from, converting between, and interfacing with many common file formats in extracellular recording.

SpikeExtractors

SpikeExtractors is a package of the SpikeInterface project designed to address issues of file format compatibility within spike sorting pipelines without creating yet another file format.

SpikeExtractors provides functionality to extract data from, convert between, and interface with many common file formats in extracellular recording. File types that can be utilized with SpikeExtractors include recorded dataset files, sorted dataset files, and probe files (.csv and .prb).

Getting Started

To get started with SpikeExtractors, you can install it with pip:

pip install spikeextractors

You can also get SpikeExtractors through the spikeinterface package:

pip install spikeinterface

You can also install SpikeExtractors locally by cloning the repo into your code base. If you install SpikeExtractors locally, you need to run the setup.py file.

git clone https://github.com/SpikeInterface/spikeextractors.git
cd spikeextractors
python setup.py install

Examples

For more information about how to use SpikeExtractors, please checkout these examples.

Documentation

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

Authors

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

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

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 Cole Hurwitz at colehurwitz@gmail.com