How to align an IBL insertion from Alyx

This guide shows you how to load a probe insertion from the IBL Alyx database, align it, and upload the alignment and its quality assessment back to Alyx.

Prerequisites

  • The ibl extra installed (see How to install the optional extras).

  • An Alyx account, with ONE set up for it. The first time ONE is used it asks for the database URL and your credentials.

Steps

  1. Start the GUI in IBL mode. To go straight to one insertion, pass its probe insertion id:

    alignment-gui-ibl -p <pid>

    Without -p, choose the subject, the session and probe, and the shank from the dropdowns, and click Load. Only insertions with spike sorting are listed.

  2. Align as usual. The data is downloaded through ONE and cached locally, so later loads are faster.

  3. Upload (Shift+U). For each shank, a QC dialog asks for:

    • the confidence of the alignment: High, Medium or Low

    • the QC of the recording: Pass, Warning or Critical, with at least one problem ticked for Warning or Critical

    • whether to resolve the insertion’s alignment with this one

    With more than one shank, tick Apply to all shanks to give the remaining shanks the same assessment. Cancelling the dialog cancels the upload.

  4. The channel locations, the alignment and the assessment are saved to Alyx, under your Alyx user name.

Previous alignments of the insertion, by any user, are in the alignment dropdown (see How to continue from a previous alignment).