AllenNeuralDynamics / brainglobe-atlasapi

A lightweight python module to interact with atlases for systems neuroscience
https://brainglobe.info/documentation/brainglobe-atlasapi/index.html
BSD 3-Clause "New" or "Revised" License
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Extract ontology- and annotation-related methods from allensdk into its own package #1

Closed dbirman closed 4 weeks ago

dbirman commented 1 month ago

copying from atlas-utils

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).
dbirman commented 4 weeks ago

This has been broken down into sub-tasks, closing