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](https://github.com/csn-le/wave_clus/wiki/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](https://github.com/csn-le/wave_clus/issues "Issues").
More instructions, details, FAQ and developer information: [wiki](https://github.com/csn-le/wave_clus/wiki "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](https://www.physiology.org/doi/full/10.1152/jn.00339.2018)
```bibtex
@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](http://www2.le.ac.uk/departments/engineering/research/bioengineering/neuroengineering-lab/Publications/spike%20sorting%20quick%20guide.pdf "quick guide")<br/>
Quian Quiroga, R.<br/>
Current Biology, Vol 22. R45–R46, 2012.
[Spike Sorting](https://www.scholarpedia.org/article/Spike_sorting "spike sorting in Scholarpedia")<br/>
R. Quian Quiroga<br/>
Scholarpedia 2 (12): 3583. 2007
