Index

A

Actor (class in brainrender.actor) add() (brainrender.scene.Scene method) add_atlas_to_row() (in module brainglobe_atlasapi.list_atlases) add_brain_region() (brainrender.scene.Scene method) add_keyframe() (brainrender.video.Animation method) additional_metadata (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) additional_references (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) AdditionalRefDict (class in brainglobe_atlasapi.core) Animation (class in brainrender.video) annotation (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property) (brainrender.atlas.Atlas property)

annotation_stack (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) AnnotationInfo (class in brainglobe_atlasapi.atlas_generation.atlas_packaging_data) apply_modal_filter() (in module brainglobe_atlasapi.atlas_generation.annotation_utils) Atlas (class in brainglobe_atlasapi.core) (class in brainrender.atlas) atlas_link (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) atlas_minor_version (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) atlas_name (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) atlas_name_from_repr() (in module brainglobe_atlasapi.utils) atlas_packager (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) atlas_repr_from_name() (in module brainglobe_atlasapi.utils) AtlasPackagingData (class in brainglobe_atlasapi.atlas_generation.atlas_packaging_data)

B

brainglobe_atlasapi.atlas_generation.annotation_utils module brainglobe_atlasapi.atlas_generation.atlas_packaging_data module brainglobe_atlasapi.atlas_generation.mesh_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.atlas_name 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) brainrender.actor module brainrender.actors.cylinder module brainrender.actors.line module brainrender.actors.neurons module brainrender.actors.points module brainrender.actors.streamlines module brainrender.actors.volume module brainrender.atlas module brainrender.atlas_specific.allen_brain_atlas.gene_expression.api module brainrender.atlas_specific.allen_brain_atlas.gene_expression.ge_utils module brainrender.atlas_specific.allen_brain_atlas.streamlines module brainrender.camera module brainrender.cameras module brainrender.render module brainrender.scene module brainrender.settings module brainrender.video module

C

catch_missing_mesh_files() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) catch_missing_structures() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) center (brainrender.actor.Actor property) (brainrender.actors.cylinder.Cylinder property) (brainrender.actors.line.Line property) (brainrender.actors.neurons.Neuron property) (brainrender.actors.points.Point property) (brainrender.actors.points.Points property) (brainrender.actors.points.PointsDensity property) (brainrender.actors.streamlines.Streamlines property) (brainrender.actors.volume.Volume property) check_camera_param() (in module brainrender.camera) check_gene_cached() (in module brainrender.atlas_specific.allen_brain_atlas.gene_expression.ge_utils) check_internet_connection() (in module brainglobe_atlasapi.utils) check_latest_version() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainrender.atlas.Atlas method) check_requested_component() (in module brainglobe_atlasapi.atlas_generation.atlas_packaging_data) check_s3_status() (in module brainglobe_atlasapi.utils) check_struct_consistency() (in module brainglobe_atlasapi.atlas_generation.structures) child_ids() (in module brainglobe_atlasapi.structure_tree_util) citation (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) clean_actors (brainrender.scene.Scene property)

clean_renderables (brainrender.scene.Scene property) 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) close() (brainrender.render.Render method) (brainrender.scene.Scene method) ComponentInfo (class in brainglobe_atlasapi.atlas_generation.atlas_packaging_data) compress() (brainrender.video.Animation method) (brainrender.video.VideoMaker method) conf_from_file() (in module brainglobe_atlasapi.utils) conf_from_url() (in module brainglobe_atlasapi.utils) construct_meshes_from_annotation() (in module brainglobe_atlasapi.atlas_generation.mesh_utils) content (brainrender.scene.Scene property) convert_structure_json_to_csv() (in module brainglobe_atlasapi.atlas_generation.structure_json_to_csv) CoordinateSpaceInfo (class in brainglobe_atlasapi.atlas_generation.atlas_packaging_data) create_masked_array() (in module brainglobe_atlasapi.atlas_generation.volume_utils) create_masked_array_numba() (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_region_mesh() (in module brainglobe_atlasapi.atlas_generation.mesh_utils) create_structures_csv() (in module brainglobe_atlasapi.atlas_generation.metadata_utils) Cylinder (class in brainrender.actors.cylinder)

D

download() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainrender.atlas.Atlas method)

download_and_cache() (in module brainrender.atlas_specific.allen_brain_atlas.gene_expression.ge_utils)

E

existing_stub (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo attribute) existing_version (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo attribute) experiments_source_search() (in module brainrender.atlas_specific.allen_brain_atlas.streamlines)

export() (brainrender.render.Render method) (brainrender.scene.Scene method) extract_mesh_from_mask() (in module brainglobe_atlasapi.atlas_generation.mesh_utils)

F

file_name (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AnnotationInfo attribute) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo attribute) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.CoordinateSpaceInfo attribute) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.TemplateInfo attribute) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.TerminologyInfo attribute)

filter_structures_not_present_in_annotation() (in module brainglobe_atlasapi.atlas_generation.structures) folder_version_to_dotted() (in module brainglobe_atlasapi.list_atlases) format_component_stub() (in module brainglobe_atlasapi.descriptors) format_hemispheres_stub() (in module brainglobe_atlasapi.descriptors) format_meshes_stub() (in module brainglobe_atlasapi.descriptors) FrameGenerator (class in brainrender.video)

G

GeneExpressionAPI (class in brainrender.atlas_specific.allen_brain_atlas.gene_expression.api) generate_frames() (brainrender.video.Animation method) (brainrender.video.VideoMaker method) generate_metadata_dict() (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AnnotationInfo method) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo method) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.CoordinateSpaceInfo method) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.TemplateInfo method) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.TerminologyInfo method) (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_actors() (brainrender.scene.Scene 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_camera() (in module brainrender.camera) get_camera_params() (in module brainrender.camera) get_download_size() (in module brainglobe_atlasapi.utils) get_downloaded_atlases() (in module brainglobe_atlasapi.list_atlases) get_frame_params() (brainrender.video.Animation method) get_gene_data() (brainrender.atlas_specific.allen_brain_atlas.gene_expression.api.GeneExpressionAPI method) get_gene_id_by_name() (brainrender.atlas_specific.allen_brain_atlas.gene_expression.api.GeneExpressionAPI method)

get_gene_symbol_by_id() (brainrender.atlas_specific.allen_brain_atlas.gene_expression.api.GeneExpressionAPI method) get_keyframe_framenumber() (brainrender.video.Animation method) get_latest_version() (in module brainglobe_atlasapi.utils) get_local_atlas_version() (in module brainglobe_atlasapi.list_atlases) get_parent_id() (in module brainglobe_atlasapi.atlas_generation.structure_json_to_csv) get_plane() (brainrender.atlas.Atlas method) get_region() (brainrender.atlas.Atlas method) get_streamlines_data() (in module brainrender.atlas_specific.allen_brain_atlas.streamlines) get_streamlines_for_region() (in module brainrender.atlas_specific.allen_brain_atlas.streamlines) get_structure_ancestors() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) (brainrender.atlas.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) (brainrender.atlas.Atlas method) get_structure_mask() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) (brainrender.atlas.Atlas method) get_structure_terminal_nodes() (in module brainglobe_atlasapi.atlas_generation.structures) get_structures_at_hierarchy_level() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) (brainrender.atlas.Atlas method) get_structures_tree() (in module brainglobe_atlasapi.structure_tree_util) griddata_to_volume() (brainrender.atlas_specific.allen_brain_atlas.gene_expression.api.GeneExpressionAPI method)

H

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

hemispheres_stack (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) hierarchy (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property) (brainrender.atlas.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

KeyframeCallback (class in brainrender.video) keypress() (brainrender.render.Render method) (brainrender.scene.Scene method)

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

L

Line (class in brainrender.actors.line) load_cached_gene() (in module brainrender.atlas_specific.allen_brain_atlas.gene_expression.ge_utils) load_structures_from_csv() (in module brainglobe_atlasapi.utils) local_full_name (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainrender.atlas.Atlas property)

local_version (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainrender.atlas.Atlas property) lookup_df (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property) (brainrender.atlas.Atlas property)

M

make_actor() (brainrender.actor.Actor class method) (brainrender.actors.cylinder.Cylinder class method) (brainrender.actors.line.Line class method) (brainrender.actors.neurons.Neuron class method) (brainrender.actors.points.Point class method) (brainrender.actors.points.Points class method) (brainrender.actors.points.PointsDensity class method) (brainrender.actors.streamlines.Streamlines class method) (brainrender.actors.volume.Volume class method) make_actor_label() (in module brainrender.actor) make_label() (brainrender.actor.Actor method) (brainrender.actors.cylinder.Cylinder method) (brainrender.actors.line.Line method) (brainrender.actors.neurons.Neuron method) (brainrender.actors.points.Point method) (brainrender.actors.points.Points method) (brainrender.actors.points.PointsDensity method) (brainrender.actors.streamlines.Streamlines method) (brainrender.actors.volume.Volume method) make_neurons() (in module brainrender.actors.neurons) make_silhouette() (brainrender.actor.Actor method) (brainrender.actors.cylinder.Cylinder method) (brainrender.actors.line.Line method) (brainrender.actors.neurons.Neuron method) (brainrender.actors.points.Point method) (brainrender.actors.points.Points method) (brainrender.actors.points.PointsDensity method) (brainrender.actors.streamlines.Streamlines method) (brainrender.actors.volume.Volume method) make_streamlines() (in module brainrender.actors.streamlines) mesh_from_structure() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) (brainrender.atlas.Atlas method) meshes_dict (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) meshfile_from_structure() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) (brainrender.atlas.Atlas method) metadata (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo attribute) mirror() (brainrender.actor.Actor method) (brainrender.actors.cylinder.Cylinder method) (brainrender.actors.line.Line method) (brainrender.actors.neurons.Neuron method) (brainrender.actors.points.Point method) (brainrender.actors.points.Points method) (brainrender.actors.points.PointsDensity method) (brainrender.actors.streamlines.Streamlines method) (brainrender.actors.volume.Volume method)

modal_filter_ignore_zeros() (in module brainglobe_atlasapi.atlas_generation.annotation_utils) module brainglobe_atlasapi.atlas_generation.annotation_utils brainglobe_atlasapi.atlas_generation.atlas_packaging_data brainglobe_atlasapi.atlas_generation.mesh_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.atlas_name 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 brainrender.actor brainrender.actors.cylinder brainrender.actors.line brainrender.actors.neurons brainrender.actors.points brainrender.actors.streamlines brainrender.actors.volume brainrender.atlas brainrender.atlas_specific.allen_brain_atlas.gene_expression.api brainrender.atlas_specific.allen_brain_atlas.gene_expression.ge_utils brainrender.atlas_specific.allen_brain_atlas.streamlines brainrender.camera brainrender.cameras brainrender.render brainrender.scene brainrender.settings brainrender.video

N

name (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo attribute)

Neuron (class in brainrender.actors.neurons)

O

open_for_visual_check() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) orientation (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property) (brainrender.atlas.Atlas property)

P

Point (class in brainrender.actors.points) Points (class in brainrender.actors.points) PointsBase (class in brainrender.actors.points) PointsDensity (class in brainrender.actors.points) 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) postorder_depth_first_search() (in module brainglobe_atlasapi.structure_tree_util) preorder_breadth_first_search() (in module brainglobe_atlasapi.structure_tree_util) preorder_depth_first_search() (in module brainglobe_atlasapi.structure_tree_util)

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) (brainrender.atlas.Atlas property) reference_stack (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) Region (class in brainglobe_atlasapi.atlas_generation.mesh_utils) remote_version (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainrender.atlas.Atlas property) remove() (brainrender.scene.Scene method) Render (class in brainrender.render) render() (brainrender.render.Render method) (brainrender.scene.Scene method) renderables (brainrender.scene.Scene property) report_validation_results() (in module brainglobe_atlasapi.atlas_generation.validate_atlases)

resolution (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property) (brainrender.atlas.Atlas property) retrieve_over_http() (in module brainglobe_atlasapi.utils) root_dir (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AnnotationInfo attribute) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo attribute) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.CoordinateSpaceInfo attribute) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.TemplateInfo attribute) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.TerminologyInfo attribute) root_id (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) root_mesh() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) (brainrender.atlas.Atlas method) root_meshfile() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) (brainrender.atlas.Atlas method) ruler() (in module brainrender.actors)

S

save_annotation() (in module brainglobe_atlasapi.atlas_generation.stacks) save_annotation_masks() (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_template() (in module brainglobe_atlasapi.atlas_generation.stacks) Scene (class in brainrender.scene) screenshot() (brainrender.render.Render method) (brainrender.scene.Scene method) set_camera() (in module brainrender.camera) set_camera_params() (in module brainrender.camera) 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) (brainrender.atlas.Atlas property) shape_um (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property) (brainrender.atlas.Atlas property)

show_atlases() (in module brainglobe_atlasapi.list_atlases) sigma() (in module brainrender.video) slice() (brainrender.scene.Scene method) species (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) split_label_text() (in module brainglobe_atlasapi.atlas_generation.annotation_utils) Streamlines (class in brainrender.actors.streamlines) Structure (class in brainglobe_atlasapi.structure_class) structure_from_coords() (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas method) (brainglobe_atlasapi.core.Atlas method) (brainrender.atlas.Atlas method) structure_id_path_to_string() (in module brainglobe_atlasapi.atlas_generation.structure_json_to_csv) structures_list (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute) StructuresDict (class in brainglobe_atlasapi.structure_class) stub (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo attribute) symmetric (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AtlasPackagingData attribute)

T

template (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AnnotationInfo attribute) (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.CoordinateSpaceInfo attribute) (brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas property) (brainglobe_atlasapi.core.Atlas property) (brainrender.atlas.Atlas property)

TemplateInfo (class in brainglobe_atlasapi.atlas_generation.atlas_packaging_data) terminology (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.AnnotationInfo attribute) TerminologyInfo (class in brainglobe_atlasapi.atlas_generation.atlas_packaging_data)

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) update_existing (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo attribute) use_existing (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo attribute)

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_atlas_name_listed() (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_template_image_pixels() (in module brainglobe_atlasapi.atlas_generation.validate_atlases) validate_unique_acronyms() (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) version (brainglobe_atlasapi.atlas_generation.atlas_packaging_data.ComponentInfo attribute) VideoMaker (class in brainrender.video) Volume (class in brainrender.actors.volume)

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_mesh() (in module brainglobe_atlasapi.atlas_generation.mesh_utils) write_mesh_info() (in module brainglobe_atlasapi.atlas_generation.mesh_utils) write_multiscale_ome_zarr() (in module brainglobe_atlasapi.atlas_generation.stacks) write_stack() (in module brainglobe_atlasapi.atlas_generation.stacks)

Z

zoom (brainrender.atlas.Atlas property)