How to export a track from Lasagna

This guide shows you how to turn a track traced with Lasagna into xyz_picks.json.

Prerequisites

Steps

  1. Trace the track in Lasagna, following its guide, and:

    • do not rotate, flip or mirror the images while tracing

    • trace in histology already registered to the Allen atlas, or apply the registration transform to the points afterwards if you trace in the original image space

  2. Save the _pts line, not the _fit line.

  3. Convert it to IBL coordinates and save it:

    import json
from pathlib import Path

from ibllib.pipes.histology import load_track_csv

picks_path = Path('/path/to/picks')

# Returns ML, AP, DV relative to bregma in m; converted to µm
xyz = load_track_csv('/path/to/lasagna/tracing_pts.csv') * 1e6

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

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