spikechef

Sorts multichannel arf data. Uses the klusta* suite.

For each program, try --help to see options

V 0.3

1. collect data using Intan's RHD2000 interface software, which creates *.rhd files in a single directory.
2. use rhd2arf.m (Matlab script) to create arf files. code You can run the script from the command line from within the *.rhd directory by typing matlab -nodisplay -r "path(path, '~/code/rhd2arf');rhd2arf;exit"
3. use label_stim to annotate arf file with stimulus times and dumber_sums.py to get an estimate of stimulus response.
4. convert those arf files to .kwd (hdf5 format for klusta suite) with arf2kwd.py.
5. also create/use appropriate .prm and prb files (see klusta suite docs). and run klusta EXPERIMENT.prm
6. merge spikes back into the arf file with ...(TODO)

V 0.2

Usage

1. run arftodat.py on .arf(s)
2. run detectspikes.py on generated .dat files
3. generate a clustering script with gen_klusta_command.py, then run the resulting script, which is very memory intensive and may take 1-2 days.
4. After clustering, use klustaviewer to review
5. use clutoarf.py to create spike-sorted arf file for analysis!