liyipeng-moon/wave_clus

A fast and unsupervised algorithm for spike detection and sorting using wavelets and super-paramagnetic clustering

Wave_clus 3

Wave_clus is a fast and unsupervised algorithm for spike detection and sorting that runs under Windows, Mac or Linux operating systems.

To install, download this repository into a folder. In MATLAB (R2009b or higher) go to Set Path and add the directory wave_clus with the subfolders to the MATLAB path.

How to use

There are two ways to use Wave_clus:

1. To open the GUI, type wave_clus in the MATLAB command prompt.

2. To use the batch functions, type Get_spikes('filename.ext'), where .ext is a file extension (eg. .mat), for the spike detection; this will save a file filename_spikes.mat in the current directory. Subsequently, run Do_clustering('filename_spikes.mat') to do the sorting. You can process multiple files at once or specific channels of multiple files.

Wave_clus can read raw data or already detected spikes generated with electrophysiology data acquisition systems (Blackrock, Neuralynx, Plexon, TDT, Intan, etc) or saved as matlab files (*.mat). It can also deal with tetrodes and high-density probes. See the Wiki page for Input Files for more details.

Either way, wave_clus generates a file times_filename.mat, with a variable cluster_class of two columns: the first column is the class of the spike and the second one is the spike time in ms.

Wave_clus is free (and therefore without any warranty) for any non-commercial applications. For any commercial application please contact Prof. Rodrigo Quian Quiroga.

Important links

Questions, problems and suggestions: issues section.

More instructions, details, FAQ and developer information: wiki.

References

How to cite

A novel and fully automatic spike sorting implementation with variable number of features. F. J. Chaure, H. G. Rey and R. Quian Quiroga. Journal of Neurophysiology; 2018. https://doi.org/10.1152/jn.00339.2018

@article{doi:10.1152/jn.00339.2018,
  title={A novel and fully automatic spike sorting implementation with variable number of features},
  author={Chaure, F. J. and Rey, H. G. and Quian Quiroga, R.},
  journal={Journal of Neurophysiology},
  year={2018},
  volume={120}, 
  number={4}, 
  pages={1859-1871}, 
  doi = {10.1152/jn.00339.2018},
}

For a non technical reference about spike sorting see:

Quick guide: Spike Sorting
Quian Quiroga, R.
Current Biology, Vol 22. R45–R46, 2012.

Spike Sorting
R. Quian Quiroga
Scholarpedia 2 (12): 3583. 2007