Coronal PlotΒΆ

Plot a coronal slice (best fit) that contains a given probe track. As input, use an eID and probe label. environment installation guide

# Author: Olivier Winter

import numpy as np

import ibllib.atlas as atlas
from import ONE
import as bbone

# === Parameters section (edit) ===
eid = '614e1937-4b24-4ad3-9055-c8253d089919'
probe_label = 'probe00'
# === Code (do not edit) ===
ba = atlas.AllenAtlas(25)
one = ONE(base_url="")
traj ='trajectories', 'list', session=eid,
                     provenance='Histology track', probe=probe_label)[0]
channels = bbone.load_channel_locations(eid=eid, one=one, probe=probe_label)

picks ='insertions', 'read', id=traj['probe_insertion'])['json']
picks = np.array(picks['xyz_picks']) / 1e6
ins = atlas.Insertion.from_dict(traj)

cax = ba.plot_tilted_slice(xyz=picks, axis=1, volume='image')
cax.plot(picks[:, 0] * 1e6, picks[:, 2] * 1e6)
cax.plot(channels[probe_label].x * 1e6, channels[probe_label].z * 1e6, 'g*')
Connected to as mayo
2021-05-10 15:26:37.888 INFO     [] Channel locations for probe00 have not been resolved. Channel and cluster locations obtained from histology track.
[<matplotlib.lines.Line2D at 0x22081015448>]