How to export a track from brainreg-segment

This guide shows you how to turn a track traced with brainreg-segment into xyz_picks.json.

Prerequisites

  • The histology registered to the Allen atlas with brainreg.

  • iblatlas, which is installed with the GUI.

Steps

  1. Trace the track in brainreg-segment, following its tutorial, with these settings:

    Setting

    Value

    Tracing space

    Registered atlas space, not the original sample space

    Spline points

    Fewer than 100 when fitting the track

  2. Click To brainrender to save the track as a .npy file. It is written to the segmentation/atlas_space/tracks folder of the brainreg output, named after the track.

  3. Convert it to IBL coordinates and save it:

    import json
from pathlib import Path

import numpy as np
from iblatlas.atlas import AllenAtlas

atlas = AllenAtlas(25)
picks_path = Path('/path/to/picks')

# brainreg track: CCF coordinates in µm, ordered AP, DV, ML
xyz_apdvml = np.load('/path/to/brainreg/output/segmentation/atlas_space/tracks/track_0.npy')

# IBL coordinates: ML, AP, DV relative to bregma, converted from m to µm
xyz_mlapdv = atlas.ccf2xyz(xyz_apdvml, ccf_order='apdvml') * 1e6

with open(picks_path / 'xyz_picks.json', 'w') as f:
    json.dump({'xyz_picks': xyz_mlapdv.tolist()}, f, indent=2)

  4. For a multi-shank probe, trace each shank and save each as xyz_picks_shank<N>.json, counting from 1.

  5. In the session YAML, use picks_path as the picks folder (see How to write a session YAML for one probe).