navis-org / pymaid

Python library to interface with CATMAID servers. Fully interoperable with navis.
https://pymaid.readthedocs.io/en/latest/
GNU General Public License v3.0
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get_volume uses mesh IDs, not volume IDs #233

Open clbarnes opened 1 year ago

clbarnes commented 1 year ago

Volumes are semantic objects (i.e. can be annotated); meshes are spatial objects which model volumes. This is the same as the relationship between (semantic) neurons and (spatial) skeletons. Using skeleton IDs for neurons is pretty common in pymaid (and indeed CATMAID); the semantic object ID is more of an implementation detail. get_entity_graph does explicitly distinguish between neurons and skeletons, but not between volumes and meshes: this is partially because the CATMAID backend get_annotated_entities function returns skeletons modelling neurons, but not meshes modelling volumes.

This is probably not much of a problem in daily usage and may be a can of worms to unpick, but I came across it so thought I'd note it in case anyone else did.