AllenSDK contains useful tools for querying the CCF ontology and visualizing brain regions. Make a simple, dedicated tool that:
Creates a dataframe containing all brain regions and their properties (fixing this is brainglobe-atlas-api)
Simplifies hierarchical queries (this is going into brainglobe-atlas-api)
determine if region A is inside region B
given a region, list all subregions
Creates axis-oriented plots (this is moving into its own library - atlas-plots)
anatomical template
parcellations colored by CCF colors
anatomical template colored by CCF parcellation colors
Visualizes the ontology (this is done)
display a tree (or subtree) in a notebook-friendly way
Acceptance criteria
Determine if such a tool already exists (e.g. brainglobe, IBL, etc)
If not
create atlas-plots based on aind-library-template
pull over relevant plotting utilities from allensdk (should either use the OME-NGFF or NIFTI version of the atlas)
document how to download the CCF from a well known location (soon: s3://allen-atlas-assets).
copying from atlas-utils
AllenSDK contains useful tools for querying the CCF ontology and visualizing brain regions. Make a simple, dedicated tool that:
Acceptance criteria