Index

A

add_atlas_to_row() (in module brainglobe_atlasapi.list_atlases) AdditionalRefDict (class in brainglobe_atlasapi.core) annotation (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property)

Atlas (class in brainglobe_atlasapi.core) atlas_name_from_repr() (in module brainglobe_atlasapi.utils) atlas_repr_from_name() (in module brainglobe_atlasapi.utils)

B

brainglobe_atlasapi.atlas_generation.annotation_utils module brainglobe_atlasapi.atlas_generation.metadata_utils module brainglobe_atlasapi.atlas_generation.stacks module brainglobe_atlasapi.atlas_generation.structure_json_to_csv module brainglobe_atlasapi.atlas_generation.structures module brainglobe_atlasapi.atlas_generation.validate_atlases module brainglobe_atlasapi.atlas_generation.volume_utils module brainglobe_atlasapi.atlas_generation.wrapup module brainglobe_atlasapi.bg_atlas module

brainglobe_atlasapi.cli module brainglobe_atlasapi.config module brainglobe_atlasapi.core module brainglobe_atlasapi.descriptors module brainglobe_atlasapi.list_atlases module brainglobe_atlasapi.structure_class module brainglobe_atlasapi.structure_tree_util module brainglobe_atlasapi.update_atlases module brainglobe_atlasapi.utils module BrainGlobeAtlas (class in brainglobe_atlasapi.bg_atlas)

C

catch_missing_mesh_files() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) catch_missing_structures() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) check_gin_status() (in module brainglobe_atlasapi.utils) check_internet_connection() (in module brainglobe_atlasapi.utils) check_latest_version() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) check_struct_consistency() (in module brainglobe_atlasapi.atlas_generation.structures) child_ids() (in module brainglobe_atlasapi.structure_tree_util) clear() (brainglobe_atlasapi.core.AdditionalRefDict method) (brainglobe_atlasapi.structure_class.Structure method) (brainglobe_atlasapi.structure_class.StructuresDict method)

cli_modify_config() (in module brainglobe_atlasapi.config) conf_from_file() (in module brainglobe_atlasapi.utils) conf_from_url() (in module brainglobe_atlasapi.utils) convert_structure_json_to_csv() (in module brainglobe_atlasapi.atlas_generation.structure_json_to_csv) create_masked_array() (in module brainglobe_atlasapi.atlas_generation.volume_utils) create_metadata_files() (in module brainglobe_atlasapi.atlas_generation.metadata_utils) create_readme() (in module brainglobe_atlasapi.atlas_generation.metadata_utils) create_structures_csv() (in module brainglobe_atlasapi.atlas_generation.metadata_utils)

D

download_extract_file() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method)

F

filter_structures_not_present_in_annotation() (in module brainglobe_atlasapi.atlas_generation.wrapup)

G

generate_metadata_dict() (in module brainglobe_atlasapi.atlas_generation.metadata_utils) get() (brainglobe_atlasapi.core.AdditionalRefDict method) (brainglobe_atlasapi.structure_class.Structure method) (brainglobe_atlasapi.structure_class.StructuresDict method) get_all_atlases_lastversions() (in module brainglobe_atlasapi.list_atlases) get_all_validation_functions() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) get_atlases_lastversions() (in module brainglobe_atlasapi.list_atlases) get_brainglobe_dir() (in module brainglobe_atlasapi.config) get_download_size() (in module brainglobe_atlasapi.utils) get_downloaded_atlases() (in module brainglobe_atlasapi.list_atlases)

get_local_atlas_version() (in module brainglobe_atlasapi.list_atlases) get_parent_id() (in module brainglobe_atlasapi.atlas_generation.structure_json_to_csv) get_structure_ancestors() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) get_structure_children() (in module brainglobe_atlasapi.atlas_generation.structures) get_structure_descendants() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) get_structure_mask() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) get_structure_terminal_nodes() (in module brainglobe_atlasapi.atlas_generation.structures) get_structures_tree() (in module brainglobe_atlasapi.structure_tree_util)

H

hemisphere_from_coords() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) hemispheres (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property)

hierarchy (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property)

I

install_atlas() (in module brainglobe_atlasapi.update_atlases) items() (brainglobe_atlasapi.core.AdditionalRefDict method) (brainglobe_atlasapi.structure_class.Structure method) (brainglobe_atlasapi.structure_class.StructuresDict method)

K

keys() (brainglobe_atlasapi.core.AdditionalRefDict method) (brainglobe_atlasapi.structure_class.Structure method) (brainglobe_atlasapi.structure_class.StructuresDict method)

L

local_full_name (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) local_version (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property)

lookup_df (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property)

M

mesh_from_structure() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) meshfile_from_structure() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) module brainglobe_atlasapi.atlas_generation.annotation_utils brainglobe_atlasapi.atlas_generation.metadata_utils brainglobe_atlasapi.atlas_generation.stacks brainglobe_atlasapi.atlas_generation.structure_json_to_csv brainglobe_atlasapi.atlas_generation.structures brainglobe_atlasapi.atlas_generation.validate_atlases brainglobe_atlasapi.atlas_generation.volume_utils brainglobe_atlasapi.atlas_generation.wrapup brainglobe_atlasapi.bg_atlas brainglobe_atlasapi.cli brainglobe_atlasapi.config brainglobe_atlasapi.core brainglobe_atlasapi.descriptors brainglobe_atlasapi.list_atlases brainglobe_atlasapi.structure_class brainglobe_atlasapi.structure_tree_util brainglobe_atlasapi.update_atlases brainglobe_atlasapi.utils

O

open_for_visual_check() (in module brainglobe_atlasapi.atlas_generation.validate_atlases)

orientation (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property)

P

pop() (brainglobe_atlasapi.core.AdditionalRefDict method) (brainglobe_atlasapi.structure_class.Structure method) (brainglobe_atlasapi.structure_class.StructuresDict method)

popitem() (brainglobe_atlasapi.core.AdditionalRefDict method) (brainglobe_atlasapi.structure_class.Structure method) (brainglobe_atlasapi.structure_class.StructuresDict method)

R

read_config() (in module brainglobe_atlasapi.config) read_itk_labels() (in module brainglobe_atlasapi.atlas_generation.annotation_utils) read_json() (in module brainglobe_atlasapi.utils) read_tiff() (in module brainglobe_atlasapi.utils) reference (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property) remote_url (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property)

remote_version (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) resolution (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property) retrieve_over_http() (in module brainglobe_atlasapi.utils) root_mesh() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) root_meshfile() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method)

S

save_annotation() (in module brainglobe_atlasapi.atlas_generation.stacks) save_hemispheres() (in module brainglobe_atlasapi.atlas_generation.stacks) save_reference() (in module brainglobe_atlasapi.atlas_generation.stacks) save_secondary_reference() (in module brainglobe_atlasapi.atlas_generation.stacks) setdefault() (brainglobe_atlasapi.core.AdditionalRefDict method) (brainglobe_atlasapi.structure_class.Structure method) (brainglobe_atlasapi.structure_class.StructuresDict method) shape (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property)

shape_um (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property) show_atlases() (in module brainglobe_atlasapi.list_atlases) split_label_text() (in module brainglobe_atlasapi.atlas_generation.annotation_utils) Structure (class in brainglobe_atlasapi.structure_class) structure_from_coords() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) structure_id_path_to_string() (in module brainglobe_atlasapi.atlas_generation.structure_json_to_csv) StructuresDict (class in brainglobe_atlasapi.structure_class)

U

update() (brainglobe_atlasapi.core.AdditionalRefDict method) (brainglobe_atlasapi.structure_class.Structure method) (brainglobe_atlasapi.structure_class.StructuresDict method)

update_atlas() (in module brainglobe_atlasapi.update_atlases)

V

validate_additional_references() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) validate_annotation_symmetry() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) validate_atlas() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) validate_atlas_files() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) validate_atlas_name() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) validate_checksum() (in module brainglobe_atlasapi.atlas_generation.validate_atlases)

validate_image_dimensions() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) validate_mesh_matches_image_extents() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) validate_metadata() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) validate_reference_image_pixels() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) values() (brainglobe_atlasapi.core.AdditionalRefDict method) (brainglobe_atlasapi.structure_class.Structure method) (brainglobe_atlasapi.structure_class.StructuresDict method)

W

wrapup_atlas_from_data() (in module brainglobe_atlasapi.atlas_generation.wrapup) write_config_value() (in module brainglobe_atlasapi.config)

write_default_config() (in module brainglobe_atlasapi.config) write_itk_labels() (in module brainglobe_atlasapi.atlas_generation.annotation_utils) write_stack() (in module brainglobe_atlasapi.atlas_generation.stacks)