Open CodyCBakerPhD opened 1 year ago
Although, looking deeper, it seems as if the Allen Brain Atlas itself does not lateralize region references (annotated symmetrically)...
In which case we would have to further clarify how we intend left vs. right hemispheres to be differentiated for symmetric ontologies
Here are some suggestions for how we could distinguish this, using MDm (Mediodorsal nucleus of the thalamus, medial part) as an example...
a) left-MDm/right-MDm b) MDm-left/MDm-right c) MDm-lh/MDm-rh d) lhMDm/rhMDm e) lMDm/rMDm - note the prefix 'l' is hard to distinguish from an I there
Or if anyone knows of any more official way of handling this according to the Allen folks or other experts on this topic?
What would you like changed or added to the documentation and why?
While working on the IBL conversion, a question has come up regarding our best practice convention for brain region references on the electrodes and units tables
The best practice now: https://nwbinspector.readthedocs.io/en/dev/best_practices/ecephys.html#ontologies
and while the IBL uses Allen as the default, they have two separate conventions when using it: lateralized and non-lateralized
As I interpret their approach, non-lateralized is essentially just wrapping the brain along the midline so that referring to a brain region does not reflect which hemisphere it belongs to
As I understand our best practice (and consistency with the
x/y/z
section below it), I would lean towards the lateralized interpretation for NWB, and should therefore add some clarification of that in the Best Practice sectionCurious what the rest of you think, though @bendichter @rly @oruebel @alejoe91
Do you have any interest in helping write or edit the documentation?
Yes.
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