Output files

This page lists the files the GUI writes. They go in the output folder of the session YAML.

Files

channel_locations.json

Written when an alignment is uploaded. The location of every channel after the alignment, keyed channel_0, channel_1, …, plus an origin entry.

Field	Units	Description
x, y, z	µm	ML, AP and DV coordinates relative to bregma
axial	µm	Position along the probe (see Probe geometry)
lateral	µm	Position across the probe
brain_region_id		Allen atlas region id
brain_region		Allen atlas region acronym
original_channel_idx	index	Row of the channel in channels.localCoordinates, or of the electrode in the metadata if there is no spike sorting

The origin entry gives the position of bregma in the Allen CCF, in µm, as {"bregma": [ML, AP, DV]}.

{
  "channel_0": {
    "x": -2453.87, "y": -4189.74, "z": -3415.69,
    "axial": 20.0, "lateral": 43.0,
    "brain_region_id": 0, "brain_region": "void",
    "original_channel_idx": 0
  },
  "origin": {"bregma": [5739.0, 5400.0, 332.0]}
}

prev_alignments.json

Written when an alignment is uploaded. Every alignment made for the probe, so that any of them can be reloaded from the alignment dropdown. Each key is the date and time of the alignment, followed by _<user> when a user name is known. Each value is a pair of lists: the depths of the reference lines in the electrophysiology, and the matching depths along the histology track.

alignment_progress.json

Written by Save Progress (Shift+S). An alignment that has not been uploaded yet. The next time the session is loaded it is offered in the alignment dropdown under a recovered key and chosen as the starting alignment. Deleted when the alignment is uploaded.

Multi-shank probes

For a probe with more than one shank, each shank is aligned separately and every file gets a shank suffix, counting from 1 with no separator before the number:

channel_locations_shank1.json
prev_alignments_shank1.json
alignment_progress_shank1.json

The suffix is only added when the shanks come from one probe entry in the session YAML. When each shank is given as its own probe entry, each entry writes files without a suffix, so each entry needs its own output path.