How to write a session YAML for one probe

This guide shows you how to list the dataset folders of a single-shank probe, when they are not all in one folder.

Steps

  1. Create a .yaml file. Give a top-level path for the folder most datasets sit under, so the dataset paths can be relative:

    path: /mnt/data/subject01/2025-01-15

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

  2. Add any optional datasets you have: histology or features (see Session YAML). output must always be given. picks can be left out if xyz_picks.json is in the spike sorting folder, and processed_ephys if the RMS and power spectrum files are in the raw_ephys or the spike sorting folder.

  3. Open the file (see How to open a session) and check that each figure shows data.