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| working_dir = Path.home() / "brainglobe_workingdir/" | ||
| atlas_name = "eurasian_blackcap" | ||
| resolution = 25 | ||
| minor_version = 5 |
adamltyson
approved these changes
Jan 27, 2026
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Description
Why is this PR needed?
As part of the latest round of reviews of the blackcap paper, we need to add an additional region (MC, caudal mesopallium) to the blackcap atlas
What does this PR do?
This PR
atlas_generations/annotation_utils.pymesh_utils.pylogging message)Unlike previous annotations, MC was annotated in the male atlas space (not the previous mixed atlas space) so we can't easily incorporate directly with the previous annotation combinations scripts.
I have therefore chosen to integrate the region during packaging, where we are already in the correct space.
Atlas validation functions all pass.
@simonweiler has confirmed he is happy with the new region based on the two screenshots below
The coronal section shows MC (light green) as a child region of M. The 3D view shows the root mesh, the M mesh and the MC mesh.