README.md

klusta-pipeline

Data pipeline for analyzing spike2 collected data in phy

phy helper scripts

There is one script which will get your data from probe-the-broab into the KWD format that phy requires.

Make KWD file from spike2 matfiles

1. Run make_kwd {rig} {probe} {path_to_matfiles} {path_to_save_kwd}
2. See make_kwd.py for a list of other arguments you may supply.
3. make_kwd will spit out all the data and config files necessary for phy in the directory you specified.
4. You may now run phy spikesort params.prm to begin automatic clustering.
5. Run phy cluster-manual {output.kwik} to begin manual sorting.

Merging Stimuli Information

1. After manual sorting, run merge_stim_kwik {path_to_matfiles} {path_to_kwikfile} to merge events into the kwikfile
2. All of the auxiliary files (such as the .json, .kwd, etc.) are necessary for merge_stim_kwik to run successfully
3. Your kwikfile now contains all the event times from your experiment.