How to load shanks that were sorted together

This guide shows you how to load a probe whose shanks were spike sorted together, so that one spike sorting output holds every shank.

Prerequisites

  • One traced trajectory per shank.

Steps

  1. Name the trajectory files with the shank number, counting from 1, and put them in the picks folder:

    xyz_picks_shank1.json
xyz_picks_shank2.json
xyz_picks_shank3.json
xyz_picks_shank4.json

  2. Give the probe a single entry in the session YAML, as for a single-shank probe:

    path: /path/to/session

probes:
  probe00:
    datasets:
      spike_sorting:
        path: probe00/kilosort
      raw_ephys:
        path: probe00/spikeglx
      picks:
        path: probe00/picks
      output:
        path: probe00/alignment

  3. Open the session. The GUI finds the shanks from the probe geometry and shows them side by side in a grid.

The results are written per shank, as channel_locations_shank1.json and so on, so all the shanks can share one output folder.