API reference

Information on specific functions, classes, and methods.

Modules

brainglobe_atlasapi.utils	Provide utility functions for brainglobe-atlasapi.
brainglobe_atlasapi.structure_class	Provide a class for representing hierarchical structures, such as brain regions in an atlas.
brainglobe_atlasapi.list_atlases	Functionality to list all available and downloaded brainglobe atlases.
brainglobe_atlasapi.structure_tree_util	Utility functions for working with structure trees.
brainglobe_atlasapi.update_atlases	Provides functionality to update the atlas.
brainglobe_atlasapi.config	Utilities for reading and modifying brainglob configuration.
brainglobe_atlasapi.core	Module containing the core Atlas class.
brainglobe_atlasapi.descriptors	Module containing property descriptors for brainglobe-atlasapi.
brainglobe_atlasapi.cli	Command-line interface for brainglobe_atlasapi.
brainglobe_atlasapi.bg_atlas	Defines the BrainGlobeAtlas class for accessing brain atlas data.
brainglobe_atlasapi.atlas_generation.volume_utils	Code useful for dealing with volumetric data (e.g. allen annotation volume for the mouse atlas) extracting surfaces from volumetric data .
brainglobe_atlasapi.atlas_generation.metadata_utils	Provides tools to create and manage the metadata dictionaries and README files associated with atlases packaged within the BrainGlobe ecosystem.
brainglobe_atlasapi.atlas_generation.stacks	Functions for handling and processing image stacks related to atlas generation.
brainglobe_atlasapi.atlas_generation.annotation_utils	Helper functions to read annotation metadata from common formats.
brainglobe_atlasapi.atlas_generation.wrapup	Tools to finalise the atlas creation process.
brainglobe_atlasapi.atlas_generation.structures	Handle structure information for atlas generation.
brainglobe_atlasapi.atlas_generation.validate_atlases	Script to validate atlases.
brainglobe_atlasapi.atlas_generation.structure_json_to_csv	Convert structure JSON files to CSV format.