An online solution for spike sorting of large-scale extracellular recordings
SpyKING CIRCUS ORT is a python code to allow online spike sorting on multi channel recordings. A preprint with the details of the offline algorithm can be found on BioRxiv at http://biorxiv.org/content/early/2016/08/04/067843. It has been tested on datasets coming from in vitro retina with 252 electrodes MEA, from in vivo hippocampus with tetrodes, in vivo and in vitro cortex data with 30 and up to 4225 channels, with good results. Synthetic tests on these data show that cells firing at more than 0.5Hz can be detected, and their spikes recovered with error rates at around 1%, even resolving overlapping spikes and synchronous firing. It seems to be compatible with optogenetic stimulation, based on experimental data obtained in the retina.
This online implementation of SpyKING CIRCUS is currently still under active development. Please do not hesitate to report issues with the issue tracker
- copyright
Copyright 2006-2018 by the SpyKING CIRCUS team, see AUTHORS.
- license
CeCILL, see LICENSE for details.
The easiest way to install spyking-circus-ort for development purpose is using pip. First you need to check that you have all the necessary header files on your system to be able to build Python extensions. The access to these files is necessary during the compilation of pyopencl. To do so run:
sudo apt-get install python-devAdditionally, if you will use pyopencl on Intel CPUs and GPUs.
sudo apt-get install beignet-devThen you will have to install TkInter.
sudo apt-get install python-tkOnce you have all the necessary header files, to install spyking-circus-ort run:
pip install -e .