Dear forum users,
I am struggling to find a meaningful name for those 3D regions in an annotated nrrd volume (Mouse CCFv2 or v3) which are labeled by an identifier which is not a leaf of the hierarchy tree described in 1.json.
Here is an example. In the file annotation_25.nrrd, the Thalamus contains 58834 voxels with id 549, that is, the identifier of the Thalamus in 1.json. This represents approximately 4.5% of the volume of the Thalamus which is not annotated by a name more precise than “Thalamus”.
I would like to understand the circumstances under which such voxels are labeled by a non-leaf identifier (“leaf” refers to the hierarchy tree of 1.json, this means that the “children” list is empty).
Here are my questions:
- Ideally, should these voxels with non-leaf identifiers be re-distributed in regions with leaf identifiers?
- Ideally, should these voxels be included in new child regions with new names and new identifiers?
- Or is it a bit of both?
Visual inspection suggests that it is a bit of both, but I would be very happy to get the opinion of those who created the annotated volumes.
Thanks in advance for your answer.