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wave_clus

(★ 143)

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

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- - build_templates.m
  - fit_gaussian.m
  - force_membership_wc.m
  - ML_gaussian.m
  - nearest_neighbor.m
- amp_detect.m
- amp_detect_pol.m
- check_WC_params.m
- Do_clustering.m
- find_temp.m
- find_temp_old.m
- fix_filter.m
- fix_wavedec.m
- Get_spikes.m
- Get_spikes_pol.m
- index_detect_pol.m
- int_spikes.m
- int_spikes_pol.m
- readInData.m
- run_cluster.m
- spike_alignment.m
- spike_detection_filter.m
- test_ks.m
- update_parameters.m
- wave_features.m
- wc_polytrode_figs.m
- set_parameters_ui.fig
- wave_clus.fig
- wave_clus_aux.fig
- wave_clus_aux1.fig
- wave_clus_aux2.fig
- wave_clus_aux3.fig
- wave_clus_aux4.fig
- wave_clus_aux5.fig
- draw_histograms.m
- filelist_wc.xlj
- mark_clusters_temperature_diagram.m
- Plot_all_features.m
- Plot_amplitudes.m
- Plot_continuous_data.m
- plot_spikes.m
- plot_spikes_aux.m
- wave_clus_aux.m
- wave_clus_aux1.m
- wave_clus_aux2.m
- wave_clus_aux3.m
- wave_clus_aux4.m
- wave_clus_aux5.m
- dat_wc_reader.m
- h5_wc_reader.m
- intch_wc_reader.m
- mat_wc_reader.m
- nc5_wc_reader.m
- ncs_wc_reader.m
- pl2ch_wc_reader.m
- supported_wc_extensions.m
- tdtch_wc_reader.m
- cluster.exe
- cluster_64.exe
- cluster_linux.exe
- cluster_linux64.exe
- cluster_mac.exe
- cluster_maci.exe
- make_fwc_curve.m
- parse_data_int.m
- parse_data_NSx.m
- parse_data_pl2.m
- parse_data_tdt.m
- parse_intan_RHD2000.m
- 35191___.TTF
.gitignore
README.md
set_parameters.m
set_parameters_DEFAULT.m
set_parameters_ui.m
version.txt
wave_clus.m

// repository documentation

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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