Using probes with multiple shanks
Update: the latest version of the code addresses this issue. After getting feedback from users, this page will be removed if there are no further issues. For 2D arrays, you may want to set the new x_centers parameter (under “Extra Settings” in the GUI) for best results.
Currently, Kilosort4 does not process shanks separately. Until this is added, we recommend changing your probe layout to artificially stack the shanks in a single column with a bit of vertical space (~100um) between each shank.
If that option isn’t feasible for some reason, you can also try adjusting the min_template_size and/or dminx parameters in the GUI, or in the settings argument for run_kilosort if you’re using the API. Setting dminx to around half the total width of the probe seems to be a good starting point, and you can adjust from there.