How to open a session that has not been spike sorted

This guide shows you how to look at the raw data, RMS and power spectra along the track before spike sorting has been run, for example to check a recording or to start an alignment early.

Prerequisites

  • The SpikeGLX .ap.meta file. Without spike sorting it is the only source of the probe geometry, so the session cannot be opened without it.

  • The _iblqc_* RMS and power spectrum files, which are what you align against without spike sorting.

  • The traced trajectory, xyz_picks.json.

  • Optionally, the .ap.bin and .lf.bin files, for snippets of the raw signal.

Steps

  1. Write a session YAML with no spike_sorting dataset. raw_ephys points at the folder with the SpikeGLX .ap.meta file, and the RMS and power spectrum files are read from the same folder unless you give a processed_ephys folder. Without spike sorting, raw_ephys, picks and output must all be given:

    probes:
  probe00:
    datasets:
      raw_ephys:
        path: /path/to/spikeglx
      picks:
        path: /path/to/picks
      output:
        path: /path/to/output

  2. Load the session. The probe geometry is read from the .ap.meta file. The RMS and power spectrum plots are offered, and the raw data snippets when the .bin files are there. The plots that need spike sorting are not offered.