How to avoid repeating paths in a session YAML

This guide shows you how to shorten a session YAML whose probes share folders or folder names.

Steps

Move the parts every path shares into base paths. A path at the top of the file, on a configuration or on a probe is prepended to the relative dataset paths below it:

path: /mnt/data/subject01/2025-01-15
probes:
  probe00:
    path: probe00
    datasets:
      spike_sorting:
        path: kilosort       # /mnt/data/subject01/2025-01-15/probe00/kilosort

Move folders shared by every probe, such as the histology, into defaults as absolute paths.

Move folder names that are the same for every probe into defaults as relative paths. Each probe then resolves them against its own base path, and can leave the dataset out or give it as {}:

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

defaults:
  histology:
    path: /mnt/data/subject01/histology   # absolute: the same folder for every probe
  spike_sorting:
    path: kilosort                        # relative: joined onto each probe's base path
  raw_ephys:
    path: spikeglx
  picks:
    path: picks

probes:
  probe00:
    path: probe00
    # spike_sorting: /mnt/data/subject01/2025-01-15/probe00/kilosort
    # raw_ephys:     /mnt/data/subject01/2025-01-15/probe00/spikeglx
    # picks:         /mnt/data/subject01/2025-01-15/probe00/picks
    # histology:     /mnt/data/subject01/histology
    datasets:
      output:
        path: alignment   # /mnt/data/subject01/2025-01-15/probe00/alignment
  probe01:
    path: probe01
    # spike_sorting: /mnt/data/subject01/2025-01-15/probe01/kilosort
    # raw_ephys:     /mnt/data/subject01/2025-01-15/probe01/spikeglx
    # picks:         /mnt/data/subject01/2025-01-15/probe01/picks
    # histology:     /mnt/data/subject01/histology
    datasets:
      output:
        path: alignment   # /mnt/data/subject01/2025-01-15/probe01/alignment

Keep a dataset’s own path only where a probe differs from the default. A probe’s own relative path replaces the default; it is not joined onto it.