v0.4EOL
Getting started
Step-by-step guide
API Documentation
Guide for adding new data
Developer documentation
How to contribute
Acknowledgements
How to cite
siibra-python
»
Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Z
A
add() (siibra.commons.InstanceTable method)
(siibra.vocabularies.InstanceTable method)
add_img() (siibra.volumes.sparsemap.SparseIndex method)
affine (siibra.volumes.Map property)
(siibra.volumes.neuroglancer.NeuroglancerScale property)
(siibra.volumes.neuroglancer.NeuroglancerVolume property)
(siibra.volumes.parcellationmap.Map property)
(siibra.volumes.sparsemap.SparseMap property)
affine_scaling() (in module siibra.commons)
ALLEN_ATLAS_NOTIFICATION (siibra.features.tabular.gene_expression.GeneExpressions attribute)
(siibra.features.tabular.GeneExpressions attribute)
AllenBrainAtlasQuery (class in siibra.livequeries)
(class in siibra.livequeries.allen)
AnatomicalAnchor (class in siibra.features.anchor)
AnatomicalAssignment (in module siibra.features.anchor)
anchor (siibra.features.Feature property)
(siibra.features.feature.Feature property)
anony_client (siibra.core.region.RegionRelationAssessments attribute)
api_version (siibra.retrieval.EbrainsHdgConnector attribute)
(siibra.retrieval.repositories.EbrainsHdgConnector attribute)
append_query_params() (in module siibra.explorer.url)
APPROXIMATE (siibra.core.relation_qualification.Qualification attribute)
argmax_dim4() (in module siibra.commons)
as_list() (siibra.locations.PointSet method)
(siibra.locations.pointset.PointSet method)
(siibra.PointSet method)
assert_folder() (in module siibra.retrieval.cache)
assign() (siibra.features.anchor.AnatomicalAnchor method)
(siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
assign_layer() (siibra.features.tabular.cortical_profile.CorticalProfile method)
assigned_structure (siibra.core.relation_qualification.RelationAssignment attribute)
AssignImageResult (class in siibra.volumes.parcellationmap)
Assignment (class in siibra.volumes.parcellationmap)
Atlas (class in siibra.core.atlas)
AtlasConcept (class in siibra.core.concept)
auth_headers (siibra.retrieval.EbrainsRequest property)
(siibra.retrieval.requests.EbrainsRequest property)
authors (siibra.core.concept.AtlasConcept property)
(siibra.features.Feature property)
(siibra.features.feature.Feature property)
(siibra.retrieval.EbrainsPublicDatasetConnector property)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnector property)
B
BASE_URL (in module siibra.livequeries.allen)
base_url (siibra.retrieval.EbrainsHdgConnector attribute)
(siibra.retrieval.EbrainsPublicDatasetConnector attribute)
(siibra.retrieval.repositories.EbrainsHdgConnector attribute)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnector attribute)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnectorMinds attribute)
BIGBRAIN_ID (siibra.locations.location.Location attribute)
bigbrain_section() (siibra.locations.Point method)
(siibra.locations.point.Point method)
(siibra.Point method)
BIGBRAIN_VOLUMETRIC_SHRINKAGE_FACTOR (siibra.features.tabular.cell_density_profile.CellDensityProfile attribute)
(siibra.features.tabular.CellDensityProfile attribute)
BigBrainIntensityProfile (class in siibra.features.tabular)
(class in siibra.features.tabular.bigbrain_intensity_profile)
BigBrainProfileQuery (class in siibra.livequeries)
(class in siibra.livequeries.bigbrain)
BlockfaceVolumeOfInterest (class in siibra.features.image)
(class in siibra.features.image.volume_of_interest)
BOUNDARIES (siibra.features.tabular.cortical_profile.CorticalProfile attribute)
boundaries_mapped (siibra.features.tabular.cortical_profile.CorticalProfile property)
boundary_annotation() (siibra.features.tabular.cell_density_profile.CellDensityProfile method)
(siibra.features.tabular.CellDensityProfile method)
boundary_positions (siibra.features.tabular.cell_density_profile.CellDensityProfile property)
(siibra.features.tabular.CellDensityProfile property)
(siibra.features.tabular.cortical_profile.CorticalProfile property)
bounding_box (siibra.explorer.url.DecodedUrl attribute)
BoundingBox (class in siibra.locations)
(class in siibra.locations.boundingbox)
boundingbox (siibra.locations.Point property)
(siibra.locations.point.Point property)
(siibra.locations.PointSet property)
(siibra.locations.pointset.PointSet property)
(siibra.Point property)
(siibra.PointSet property)
(siibra.volumes.gifti.GiftiMesh property)
(siibra.volumes.gifti.GiftiSurfaceLabeling property)
(siibra.volumes.GiftiMesh property)
(siibra.volumes.GiftiSurfaceLabeling property)
(siibra.volumes.neuroglancer.NeuroglancerMesh property)
(siibra.volumes.neuroglancer.NeuroglancerProvider property)
(siibra.volumes.NeuroglancerMesh property)
(siibra.volumes.NeuroglancerProvider property)
(siibra.volumes.nifti.NiftiProvider property)
(siibra.volumes.NiftiProvider property)
(siibra.volumes.volume.SubvolumeProvider property)
(siibra.volumes.volume.Volume property)
(siibra.volumes.volume.VolumeProvider property)
branches (siibra.retrieval.GitlabConnector property)
(siibra.retrieval.repositories.GitlabConnector property)
build_activity_timeseries() (siibra.configuration.factory.Factory class method)
build_atlas() (siibra.configuration.factory.Factory class method)
build_cell_density_fingerprint() (siibra.configuration.factory.Factory class method)
build_cell_density_profile() (siibra.configuration.factory.Factory class method)
build_connectivity_matrix() (siibra.configuration.factory.Factory class method)
build_ebrains_dataset() (siibra.configuration.factory.Factory class method)
build_filename() (siibra.retrieval.cache.Cache method)
build_map() (siibra.configuration.factory.Factory class method)
build_objects() (siibra.configuration.Configuration method)
(siibra.configuration.configuration.Configuration method)
build_parcellation() (siibra.configuration.factory.Factory class method)
build_point() (siibra.configuration.factory.Factory class method)
build_pointset() (siibra.configuration.factory.Factory class method)
build_receptor_density_fingerprint() (siibra.configuration.factory.Factory class method)
build_receptor_density_profile() (siibra.configuration.factory.Factory class method)
build_region() (siibra.configuration.factory.Factory class method)
build_section() (siibra.configuration.factory.Factory class method)
build_space() (siibra.configuration.factory.Factory class method)
build_type() (in module siibra.configuration.factory)
build_volume() (siibra.configuration.factory.Factory class method)
build_volume_of_interest() (siibra.configuration.factory.Factory class method)
C
Cache (class in siibra.retrieval.cache)
cache (in module siibra)
CACHE (in module siibra.retrieval)
(in module siibra.retrieval.cache)
cached (siibra.retrieval.HttpRequest property)
(siibra.retrieval.repositories.ZipfileConnector.ZipFileLoader property)
(siibra.retrieval.requests.HttpRequest property)
(siibra.retrieval.ZipfileConnector.ZipFileLoader property)
CATEGORIZED (siibra.features.Feature attribute)
(siibra.features.feature.Feature attribute)
category (siibra.features.Feature attribute)
(siibra.features.feature.Feature attribute)
CELL_READER() (siibra.features.tabular.cell_density_profile.CellDensityProfile class method)
(siibra.features.tabular.CellDensityProfile class method)
(siibra.features.tabular.layerwise_cell_density.LayerwiseCellDensity class method)
(siibra.features.tabular.LayerwiseCellDensity class method)
CellbodyStainedSection (class in siibra.features.image)
(class in siibra.features.image.sections)
CellBodyStainedVolumeOfInterest (class in siibra.features.image)
(class in siibra.features.image.volume_of_interest)
CellDensityProfile (class in siibra.features.tabular)
(class in siibra.features.tabular.cell_density_profile)
cells (siibra.features.tabular.cell_density_profile.CellDensityProfile property)
(siibra.features.tabular.CellDensityProfile property)
center (siibra.locations.BoundingBox property)
(siibra.locations.boundingbox.BoundingBox property)
centroid (siibra.core.region.SpatialPropCmpt attribute)
(siibra.locations.PointSet property)
(siibra.locations.pointset.PointSet property)
(siibra.PointSet property)
(siibra.volumes.parcellationmap.Assignment attribute)
ch (in module siibra.commons)
CHLOROCEBUS_AETHIOPS_SABAEUS (siibra.commons.Species attribute)
cipher (in module siibra.explorer.util)
citation (siibra.commons.TypePublication attribute)
(siibra.retrieval.EbrainsPublicDatasetConnector property)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnector property)
clean_instances() (siibra.features.Feature class method)
(siibra.features.feature.Feature class method)
clear() (siibra.retrieval.cache.Cache method)
clear_cache() (siibra.retrieval.repositories.ZipfileConnector method)
(siibra.retrieval.ZipfileConnector method)
clear_name() (in module siibra.commons)
clear_registry() (siibra.core.concept.AtlasConcept class method)
clip() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
cog (siibra.core.region.SpatialProp attribute)
color_warning_issued (siibra.volumes.neuroglancer.NeuroglancerScale attribute)
colorize() (siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
ColorVolumeNotSupported
COMPACT_FEATURE_LIST (siibra.livequeries.ebrains.EbrainsFeatureQuery attribute)
(siibra.livequeries.EbrainsFeatureQuery attribute)
compare_maps() (in module siibra.commons)
CompareMapsResult (class in siibra.commons)
components (siibra.core.region.SpatialProp attribute)
compress() (siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
compute_centroids() (siibra.core.region.Region method)
(siibra.features.connectivity.regional_connectivity.RegionalConnectivity method)
(siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity method)
(siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
CONFIG_REPOS (siibra.configuration.Configuration attribute)
(siibra.configuration.configuration.Configuration attribute)
Configuration (class in siibra.configuration)
(class in siibra.configuration.configuration)
CONFIGURATION_EXTENSIONS (siibra.configuration.Configuration attribute)
(siibra.configuration.configuration.Configuration attribute)
CONFIGURATIONS (siibra.configuration.Configuration attribute)
(siibra.configuration.configuration.Configuration attribute)
ConflictingArgumentException
connectors (siibra.retrieval.requests.GitlabProxyEnum property)
CONTAINED (siibra.core.relation_qualification.Qualification attribute)
contained_in() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
(siibra.locations.Point method)
(siibra.locations.point.Point method)
(siibra.Point method)
CONTAINS (siibra.core.relation_qualification.Qualification attribute)
contains() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
(siibra.locations.Point method)
(siibra.locations.point.Point method)
(siibra.Point method)
contributors (siibra.retrieval.datasets.EbrainsBaseDataset property)
(siibra.retrieval.datasets.EbrainsDataset property)
(siibra.retrieval.datasets.EbrainsV3Dataset property)
(siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
(siibra.retrieval.datasets.GenericDataset property)
coords() (siibra.volumes.sparsemap.SparseIndex method)
copy() (siibra.core.region.Region static method)
correlation (siibra.commons.CompareMapsResult attribute)
CorticalProfile (class in siibra.features.tabular.cortical_profile)
create_gaussian_kernel() (in module siibra.commons)
create_key() (in module siibra.commons)
custodians (siibra.retrieval.datasets.EbrainsBaseDataset property)
(siibra.retrieval.datasets.EbrainsDataset property)
(siibra.retrieval.datasets.EbrainsV3Dataset property)
(siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
D
data (siibra.features.tabular.cortical_profile.CorticalProfile property)
(siibra.features.tabular.layerwise_cell_density.LayerwiseCellDensity property)
(siibra.features.tabular.LayerwiseCellDensity property)
(siibra.features.tabular.receptor_density_fingerprint.ReceptorDensityFingerprint property)
(siibra.features.tabular.ReceptorDensityFingerprint property)
(siibra.features.tabular.tabular.Tabular property)
(siibra.retrieval.HttpRequest property)
(siibra.retrieval.LocalFileRepository.FileLoader property)
(siibra.retrieval.repositories.LocalFileRepository.FileLoader property)
(siibra.retrieval.repositories.ZipfileConnector.ZipFileLoader property)
(siibra.retrieval.requests.HttpRequest property)
(siibra.retrieval.requests.MultiSourcedRequest property)
(siibra.retrieval.ZipfileConnector.ZipFileLoader property)
dataframe (siibra.commons.InstanceTable property)
(siibra.vocabularies.InstanceTable property)
DATASET_V1 (siibra.retrieval.requests.GitlabProxyEnum attribute)
DATASET_V3 (siibra.retrieval.requests.GitlabProxyEnum attribute)
DATASETVERSION_V3 (siibra.retrieval.requests.GitlabProxyEnum attribute)
decode() (siibra.commons.Species class method)
decode_int() (in module siibra.explorer.util)
decode_number() (in module siibra.explorer.util)
decode_url() (in module siibra.explorer)
(in module siibra.explorer.url)
DecodedUrl (class in siibra.explorer.url)
DecodeNavigationException
DECODERS (in module siibra.retrieval.requests)
default_root_url (in module siibra.explorer.url)
density_image (siibra.features.tabular.cell_density_profile.CellDensityProfile property)
(siibra.features.tabular.CellDensityProfile property)
depth_image (siibra.features.tabular.cell_density_profile.CellDensityProfile property)
(siibra.features.tabular.CellDensityProfile property)
description (siibra.core.concept.AtlasConcept property)
(siibra.features.dataset.ebrains.EbrainsDataFeature property)
(siibra.features.dataset.EbrainsDataFeature property)
(siibra.features.Feature property)
(siibra.features.feature.Feature property)
(siibra.features.image.image.Image property)
DESCRIPTION (siibra.features.tabular.bigbrain_intensity_profile.BigBrainIntensityProfile attribute)
(siibra.features.tabular.BigBrainIntensityProfile attribute)
(siibra.features.tabular.cell_density_profile.CellDensityProfile attribute)
(siibra.features.tabular.CellDensityProfile attribute)
(siibra.features.tabular.gene_expression.GeneExpressions attribute)
(siibra.features.tabular.GeneExpressions attribute)
(siibra.features.tabular.layerwise_bigbrain_intensities.LayerwiseBigBrainIntensities attribute)
(siibra.features.tabular.layerwise_cell_density.LayerwiseCellDensity attribute)
(siibra.features.tabular.LayerwiseBigBrainIntensities attribute)
(siibra.features.tabular.LayerwiseCellDensity attribute)
(siibra.features.tabular.receptor_density_fingerprint.ReceptorDensityFingerprint attribute)
(siibra.features.tabular.receptor_density_profile.ReceptorDensityProfile attribute)
(siibra.features.tabular.ReceptorDensityFingerprint attribute)
(siibra.features.tabular.ReceptorDensityProfile attribute)
(siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity attribute)
description (siibra.retrieval.datasets.EbrainsBaseDataset property)
(siibra.retrieval.datasets.EbrainsDataset property)
(siibra.retrieval.datasets.EbrainsV3Dataset property)
(siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
(siibra.retrieval.datasets.GenericDataset property)
(siibra.retrieval.EbrainsPublicDatasetConnector property)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnector property)
deserialize_query_context() (siibra.features.Feature class method)
(siibra.features.feature.Feature class method)
detail (siibra.retrieval.datasets.EbrainsDataset property)
(siibra.retrieval.datasets.EbrainsV3Dataset property)
(siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
device_flow() (siibra.retrieval.EbrainsRequest class method)
(siibra.retrieval.requests.EbrainsRequest class method)
doi_or_url (siibra.core.concept.AtlasConcept property)
(siibra.features.Feature property)
(siibra.features.feature.Feature property)
DOI_TMPL (in module siibra.features.dataset.ebrains)
DTIVolumeOfInterest (class in siibra.features.image)
(class in siibra.features.image.volume_of_interest)
dtype (siibra.volumes.neuroglancer.NeuroglancerVolume property)
E
ebrains_page (siibra.retrieval.datasets.EbrainsBaseDataset property)
(siibra.retrieval.datasets.EbrainsDataset property)
(siibra.retrieval.datasets.EbrainsV3Dataset property)
(siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
EbrainsAuthenticationError
EbrainsBaseDataset (class in siibra.retrieval.datasets)
EbrainsDataFeature (class in siibra.features.dataset)
(class in siibra.features.dataset.ebrains)
EbrainsDataset (class in siibra.retrieval.datasets)
EbrainsDatasetEmbargoStatus (in module siibra.retrieval.datasets)
EbrainsDatasetPerson (in module siibra.retrieval.datasets)
EbrainsDatasetUrl (class in siibra.retrieval.datasets)
EbrainsFeatureQuery (class in siibra.livequeries)
(class in siibra.livequeries.ebrains)
EbrainsHdgConnector (class in siibra.retrieval)
(class in siibra.retrieval.repositories)
EbrainsPublicDatasetConnector (class in siibra.retrieval)
(class in siibra.retrieval.repositories)
EbrainsPublicDatasetConnectorMinds (class in siibra.retrieval.repositories)
EbrainsRequest (class in siibra.retrieval)
(class in siibra.retrieval.requests)
EbrainsV3Dataset (class in siibra.retrieval.datasets)
EbrainsV3DatasetVersion (class in siibra.retrieval.datasets)
encode_int() (in module siibra.explorer.util)
encode_number() (in module siibra.explorer.util)
encode_url() (in module siibra.explorer)
(in module siibra.explorer.url)
EncodeLiveQueryIdException
estimate_affine() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
EXACT (siibra.core.relation_qualification.Qualification attribute)
ExcessiveArgumentException
explanation (siibra.core.relation_qualification.RelationAssignment attribute)
export() (siibra.features.Feature method)
(siibra.features.feature.Feature method)
extend_configuration() (siibra.configuration.Configuration class method)
(siibra.configuration.configuration.Configuration class method)
extract_anchor() (siibra.configuration.factory.Factory class method)
extract_connector() (siibra.configuration.factory.Factory class method)
extract_datasets() (siibra.configuration.factory.Factory class method)
extract_decoder() (siibra.configuration.factory.Factory class method)
extract_volumes() (siibra.configuration.factory.Factory class method)
F
factors (siibra.livequeries.allen.AllenBrainAtlasQuery attribute)
(siibra.livequeries.AllenBrainAtlasQuery attribute)
Factory (class in siibra.configuration.factory)
Feature (class in siibra.features)
(class in siibra.features.feature)
fetch() (siibra.volumes.gifti.GiftiMesh method)
(siibra.volumes.gifti.GiftiSurfaceLabeling method)
(siibra.volumes.GiftiMesh method)
(siibra.volumes.GiftiSurfaceLabeling method)
(siibra.volumes.Map method)
(siibra.volumes.neuroglancer.NeuroglancerMesh method)
(siibra.volumes.neuroglancer.NeuroglancerProvider method)
(siibra.volumes.neuroglancer.NeuroglancerScale method)
(siibra.volumes.neuroglancer.NeuroglancerSurfaceMesh method)
(siibra.volumes.neuroglancer.NeuroglancerVolume method)
(siibra.volumes.NeuroglancerMesh method)
(siibra.volumes.NeuroglancerProvider method)
(siibra.volumes.nifti.NiftiProvider method)
(siibra.volumes.NiftiProvider method)
(siibra.volumes.parcellationmap.Map method)
(siibra.volumes.sparsemap.SparseMap method)
(siibra.volumes.volume.SubvolumeProvider method)
(siibra.volumes.volume.Volume method)
(siibra.volumes.volume.VolumeProvider method)
fetch_ebrains_token (in module siibra)
fetch_iter() (siibra.volumes.gifti.GiftiMesh method)
(siibra.volumes.GiftiMesh method)
(siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
fetch_regional_map() (siibra.core.region.Region method)
(siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
fetch_token() (siibra.retrieval.EbrainsRequest class method)
(siibra.retrieval.requests.EbrainsRequest class method)
find() (siibra.commons.InstanceTable method)
(siibra.core.region.Region method)
(siibra.vocabularies.InstanceTable method)
find_indices() (siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
find_peaks() (siibra.volumes.nifti.NiftiProvider method)
(siibra.volumes.NiftiProvider method)
find_regions (in module siibra)
find_regions() (siibra.core.atlas.Atlas method)
(siibra.core.parcellation.Parcellation static method)
find_suitiable_decoder() (in module siibra.retrieval.requests)
folder (siibra.retrieval.cache.Cache attribute)
folder_dict (siibra.retrieval.requests.GitlabProxy attribute)
folders (siibra.configuration.Configuration property)
(siibra.configuration.configuration.Configuration property)
formats (siibra.volumes.Map property)
(siibra.volumes.parcellationmap.Map property)
(siibra.volumes.volume.Volume property)
formatter (in module siibra.commons)
fragment (siibra.volumes.parcellationmap.Assignment attribute)
fragments (siibra.volumes.gifti.GiftiMesh property)
(siibra.volumes.GiftiMesh property)
(siibra.volumes.Map property)
(siibra.volumes.neuroglancer.NeuroglancerSurfaceMesh property)
(siibra.volumes.nifti.NiftiProvider property)
(siibra.volumes.NiftiProvider property)
(siibra.volumes.parcellationmap.Map property)
(siibra.volumes.volume.Volume property)
(siibra.volumes.volume.VolumeProvider property)
from_dict() (siibra.commons.MapIndex class method)
(siibra.MapIndex class method)
from_image() (siibra.locations.BoundingBox class method)
(siibra.locations.boundingbox.BoundingBox class method)
from_json (in module siibra)
from_json() (siibra.configuration.factory.Factory class method)
FunctionalConnectivity (class in siibra.features.connectivity)
(class in siibra.features.connectivity.functional_connectivity)
G
GeneExpressions (class in siibra.features.tabular)
(class in siibra.features.tabular.gene_expression)
GenericDataset (class in siibra.retrieval.datasets)
get (in module siibra.features)
get() (siibra.commons.InstanceTable method)
(siibra.retrieval.EbrainsRequest method)
(siibra.retrieval.GitlabConnector method)
(siibra.retrieval.HttpRequest method)
(siibra.retrieval.repositories.GitlabConnector method)
(siibra.retrieval.repositories.RepositoryConnector method)
(siibra.retrieval.requests.EbrainsRequest method)
(siibra.retrieval.requests.GitlabProxy method)
(siibra.retrieval.requests.GitlabProxyEnum method)
(siibra.retrieval.requests.HttpRequest method)
(siibra.retrieval.requests.MultiSourcedRequest method)
(siibra.retrieval.requests.ZipfileRequest method)
(siibra.retrieval.ZipfileRequest method)
(siibra.vocabularies.InstanceTable method)
get_ascii_tree() (siibra.features.Feature class method)
(siibra.features.feature.Feature class method)
get_bounding_box() (siibra.core.region.Region method)
(siibra.core.space.Space method)
get_colormap() (siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
get_enclosing_cube() (siibra.locations.Point method)
(siibra.locations.point.Point method)
(siibra.Point method)
get_folders() (siibra.configuration.Configuration static method)
(siibra.configuration.configuration.Configuration static method)
get_hash() (in module siibra.explorer.url)
get_index() (siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
get_instance() (siibra.core.concept.AtlasConcept class method)
get_instance_by_id() (siibra.features.Feature class method)
(siibra.features.feature.Feature class method)
get_instances() (siibra.features.Feature class method)
(siibra.features.feature.Feature class method)
get_loader() (siibra.retrieval.EbrainsHdgConnector method)
(siibra.retrieval.EbrainsPublicDatasetConnector method)
(siibra.retrieval.LocalFileRepository method)
(siibra.retrieval.repositories.EbrainsHdgConnector method)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnector method)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnectorMinds method)
(siibra.retrieval.repositories.LocalFileRepository method)
(siibra.retrieval.repositories.RepositoryConnector method)
(siibra.retrieval.repositories.ZipfileConnector method)
(siibra.retrieval.ZipfileConnector method)
get_loaders() (siibra.retrieval.repositories.RepositoryConnector method)
get_map() (in module siibra)
(siibra.core.atlas.Atlas method)
(siibra.core.parcellation.Parcellation method)
get_matrix() (siibra.features.connectivity.regional_connectivity.RegionalConnectivity method)
get_object() (siibra.core.region.RegionRelationAssessments class method)
get_parcellation() (siibra.core.atlas.Atlas method)
get_perspective_zoom() (in module siibra.explorer.url)
get_profile() (siibra.features.connectivity.regional_connectivity.RegionalConnectivity method)
get_region() (in module siibra)
(siibra.core.atlas.Atlas method)
(siibra.core.parcellation.Parcellation method)
(siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
get_related_regions() (siibra.core.region.Region method)
get_resampled_template() (siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
get_shape() (siibra.volumes.neuroglancer.NeuroglancerVolume method)
(siibra.volumes.nifti.NiftiProvider method)
(siibra.volumes.NiftiProvider method)
get_snapshot_factory() (siibra.core.region.RegionRelationAssessments class method)
get_space() (siibra.core.atlas.Atlas method)
get_table() (siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity method)
get_template() (in module siibra)
(siibra.core.atlas.Atlas method)
(siibra.core.space.Space method)
get_uuid() (siibra.core.region.RegionRelationAssessments static method)
get_voi() (siibra.core.atlas.Atlas method)
get_zoom() (in module siibra.explorer.url)
GiftiMesh (class in siibra.volumes)
(class in siibra.volumes.gifti)
GiftiSurfaceLabeling (class in siibra.volumes)
(class in siibra.volumes.gifti)
GitlabConnector (class in siibra.retrieval)
(class in siibra.retrieval.repositories)
GitlabProxy (class in siibra.retrieval.requests)
GitlabProxyEnum (class in siibra.retrieval.requests)
H
has_constant_sigma (siibra.locations.PointSet property)
(siibra.locations.pointset.PointSet property)
(siibra.PointSet property)
has_parent() (siibra.core.region.Region method)
has_region_aliases (siibra.features.anchor.AnatomicalAnchor property)
HBP_AUTH_TOKEN (in module siibra.commons)
HOMO_SAPIENS (siibra.commons.Species attribute)
homogeneous (siibra.locations.Point property)
(siibra.locations.point.Point property)
(siibra.locations.PointSet property)
(siibra.locations.pointset.PointSet property)
(siibra.Point property)
(siibra.PointSet property)
HOMOLOGOUS (siibra.core.relation_qualification.Qualification attribute)
HttpRequest (class in siibra.retrieval)
(class in siibra.retrieval.requests)
I
id (siibra.core.concept.AtlasConcept property)
(siibra.core.parcellation.Parcellation property)
(siibra.core.region.Region property)
(siibra.features.connectivity.functional_connectivity.FunctionalConnectivity property)
(siibra.features.connectivity.FunctionalConnectivity property)
(siibra.features.dataset.ebrains.EbrainsDataFeature property)
(siibra.features.dataset.EbrainsDataFeature property)
(siibra.features.Feature property)
(siibra.features.feature.Feature property)
(siibra.locations.BoundingBox property)
(siibra.locations.boundingbox.BoundingBox property)
(siibra.locations.Point property)
(siibra.locations.point.Point property)
(siibra.Point property)
(siibra.retrieval.datasets.EbrainsBaseDataset property)
(siibra.retrieval.datasets.EbrainsDataset property)
(siibra.retrieval.datasets.EbrainsV3Dataset property)
(siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
(siibra.retrieval.datasets.GenericDataset property)
Image (class in siibra.features.image.image)
IMAGE_FORMATS (siibra.volumes.volume.Volume attribute)
ImageAnchor (class in siibra.features.image.image)
includes() (siibra.core.region.Region method)
init_oidc() (siibra.retrieval.EbrainsRequest class method)
(siibra.retrieval.requests.EbrainsRequest class method)
input_structure (siibra.volumes.parcellationmap.Assignment attribute)
instance() (siibra.retrieval.cache.Cache class method)
InstanceTable (class in siibra.commons)
(class in siibra.vocabularies)
InsufficientArgumentException
intersection() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
(siibra.locations.location.Location method)
(siibra.locations.location.WholeBrain method)
(siibra.locations.Point method)
(siibra.locations.point.Point method)
(siibra.locations.PointSet method)
(siibra.locations.pointset.PointSet method)
(siibra.locations.WholeBrain method)
(siibra.Point method)
(siibra.PointSet method)
intersection_over_first (siibra.commons.CompareMapsResult attribute)
intersection_over_second (siibra.commons.CompareMapsResult attribute)
intersection_over_union (siibra.commons.CompareMapsResult attribute)
intersects() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
(siibra.locations.location.Location method)
(siibra.locations.location.WholeBrain method)
(siibra.locations.Point method)
(siibra.locations.point.Point method)
(siibra.locations.PointSet method)
(siibra.locations.pointset.PointSet method)
(siibra.locations.WholeBrain method)
(siibra.Point method)
(siibra.PointSet method)
invert() (siibra.core.relation_qualification.Qualification method)
(siibra.core.relation_qualification.RelationAssignment method)
is_exact (siibra.core.relation_qualification.RelationAssignment property)
is_float() (siibra.volumes.neuroglancer.NeuroglancerVolume method)
(siibra.volumes.nifti.NiftiProvider method)
(siibra.volumes.NiftiProvider method)
is_labelled (siibra.volumes.Map property)
(siibra.volumes.parcellationmap.Map property)
is_mesh() (in module siibra.commons)
is_newest_version (siibra.core.parcellation.Parcellation property)
is_planar (siibra.locations.BoundingBox property)
(siibra.locations.boundingbox.BoundingBox property)
is_version_of (siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
iterate_connected_components() (in module siibra.commons)
K
key (siibra.core.concept.AtlasConcept property)
(siibra.features.tabular.cell_density_profile.CellDensityProfile property)
(siibra.features.tabular.CellDensityProfile property)
(siibra.features.tabular.layerwise_cell_density.LayerwiseCellDensity property)
(siibra.features.tabular.LayerwiseCellDensity property)
(siibra.features.tabular.receptor_density_profile.ReceptorDensityProfile property)
(siibra.features.tabular.ReceptorDensityProfile property)
key_to_name() (siibra.commons.Species static method)
KEYCLOAK_CLIENT_ID (in module siibra.commons)
KEYCLOAK_CLIENT_SECRET (in module siibra.commons)
keycloak_endpoint (siibra.retrieval.EbrainsRequest attribute)
(siibra.retrieval.requests.EbrainsRequest attribute)
kg_token (siibra.retrieval.EbrainsRequest property)
(siibra.retrieval.requests.EbrainsRequest property)
L
LABELLED (siibra.commons.MapType attribute)
(siibra.MapType attribute)
labels (siibra.volumes.Map property)
(siibra.volumes.parcellationmap.Map property)
last_match_description (siibra.features.anchor.AnatomicalAnchor property)
(siibra.features.Feature property)
(siibra.features.feature.Feature property)
last_match_result (siibra.features.anchor.AnatomicalAnchor property)
(siibra.features.Feature property)
(siibra.features.feature.Feature property)
layer_annotation() (siibra.features.tabular.cell_density_profile.CellDensityProfile method)
(siibra.features.tabular.CellDensityProfile method)
layer_mask (siibra.features.tabular.cell_density_profile.CellDensityProfile property)
(siibra.features.tabular.CellDensityProfile property)
LAYER_READER() (siibra.features.tabular.cell_density_profile.CellDensityProfile class method)
(siibra.features.tabular.CellDensityProfile class method)
(siibra.features.tabular.layerwise_cell_density.LayerwiseCellDensity class method)
(siibra.features.tabular.LayerwiseCellDensity class method)
layers (siibra.features.tabular.cell_density_profile.CellDensityProfile property)
(siibra.features.tabular.CellDensityProfile property)
LAYERS (siibra.features.tabular.cortical_profile.CorticalProfile attribute)
LayerwiseBigBrainIntensities (class in siibra.features.tabular)
(class in siibra.features.tabular.layerwise_bigbrain_intensities)
LayerwiseBigBrainIntensityQuery (class in siibra.livequeries)
(class in siibra.livequeries.bigbrain)
LayerwiseCellDensity (class in siibra.features.tabular)
(class in siibra.features.tabular.layerwise_cell_density)
length() (siibra.commons.PolyLine method)
LICENSE (siibra.core.concept.AtlasConcept property)
(siibra.features.Feature property)
(siibra.features.feature.Feature property)
(siibra.retrieval.datasets.EbrainsDataset property)
(siibra.retrieval.datasets.EbrainsV3Dataset property)
(siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
(siibra.retrieval.datasets.GenericDataset property)
LiveQuery (class in siibra.livequeries.query)
livequery() (siibra.features.Feature class method)
(siibra.features.feature.Feature class method)
load_zipped_sparseindex() (siibra.volumes.sparsemap.SparseMap method)
loader (siibra.livequeries.ebrains.EbrainsFeatureQuery attribute)
(siibra.livequeries.EbrainsFeatureQuery attribute)
LocalFileRepository (class in siibra.retrieval)
(class in siibra.retrieval.repositories)
LocalFileRepository.FileLoader (class in siibra.retrieval)
(class in siibra.retrieval.repositories)
Location (class in siibra.locations.location)
location (siibra.features.anchor.AnatomicalAnchor property)
(siibra.features.image.image.ImageAnchor property)
logger (in module siibra)
(in module siibra.commons)
LoggingContext (class in siibra.commons)
LSFMVolumeOfInterest (class in siibra.features.image)
(class in siibra.features.image.volume_of_interest)
M
MACACA_FASCICULARIS (siibra.commons.Species attribute)
MACACA_FUSCATA (siibra.commons.Species attribute)
MACACA_MULATTA (siibra.commons.Species attribute)
Map (class in siibra.volumes)
(class in siibra.volumes.parcellationmap)
map_type (siibra.volumes.neuroglancer.NeuroglancerVolume property)
map_value (siibra.volumes.parcellationmap.Assignment attribute)
MapIndex (class in siibra)
(class in siibra.commons)
mapped_in_space() (siibra.core.region.Region method)
mapped_voxels() (siibra.volumes.sparsemap.SparseIndex method)
MapType (class in siibra)
(class in siibra.commons)
maptype (siibra.volumes.Map property)
(siibra.volumes.parcellationmap.Map property)
match() (siibra.core.concept.AtlasConcept class method)
(siibra.features.Feature class method)
(siibra.features.feature.Feature class method)
(siibra.livequeries.bigbrain.WagstylProfileLoader method)
(siibra.retrieval.datasets.EbrainsBaseDataset method)
match_location_to_region() (siibra.features.anchor.AnatomicalAnchor class method)
match_locations() (siibra.features.anchor.AnatomicalAnchor class method)
match_regions() (siibra.features.anchor.AnatomicalAnchor class method)
matches() (siibra.core.concept.AtlasConcept method)
(siibra.core.parcellation.Parcellation method)
(siibra.core.region.Region method)
(siibra.features.anchor.AnatomicalAnchor method)
(siibra.features.Feature method)
(siibra.features.feature.Feature method)
max() (siibra.volumes.sparsemap.SparseIndex method)
MAX_BYTES (siibra.volumes.neuroglancer.NeuroglancerVolume property)
max_int32 (in module siibra.explorer.url)
maxentries (siibra.retrieval.EbrainsHdgConnector attribute)
(siibra.retrieval.EbrainsPublicDatasetConnector attribute)
(siibra.retrieval.repositories.EbrainsHdgConnector attribute)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnector attribute)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnectorMinds attribute)
merge_meshes() (in module siibra.commons)
MESH_FILE_LEFT (siibra.livequeries.bigbrain.WagstylProfileLoader attribute)
MESH_FORMATS (siibra.volumes.volume.Volume attribute)
MI() (in module siibra.commons)
min_int32 (in module siibra.explorer.url)
modality (siibra.features.Feature property)
(siibra.features.feature.Feature property)
module
siibra
siibra.commons
,
[1]
siibra.configuration
,
[1]
siibra.configuration.configuration
siibra.configuration.factory
siibra.core
,
[1]
siibra.core.atlas
,
[1]
siibra.core.concept
,
[1]
siibra.core.parcellation
,
[1]
siibra.core.region
,
[1]
siibra.core.relation_qualification
,
[1]
siibra.core.space
,
[1]
siibra.explorer
,
[1]
siibra.explorer.url
siibra.explorer.util
siibra.features
,
[1]
siibra.features.anchor
,
[1]
siibra.features.connectivity
,
[1]
siibra.features.connectivity.functional_connectivity
siibra.features.connectivity.regional_connectivity
siibra.features.connectivity.streamline_counts
siibra.features.connectivity.streamline_lengths
siibra.features.connectivity.tracing_connectivity
siibra.features.dataset
,
[1]
siibra.features.dataset.ebrains
siibra.features.feature
,
[1]
siibra.features.image
,
[1]
siibra.features.image.image
siibra.features.image.sections
siibra.features.image.volume_of_interest
siibra.features.tabular
,
[1]
siibra.features.tabular.bigbrain_intensity_profile
siibra.features.tabular.cell_density_profile
siibra.features.tabular.cortical_profile
siibra.features.tabular.gene_expression
siibra.features.tabular.layerwise_bigbrain_intensities
siibra.features.tabular.layerwise_cell_density
siibra.features.tabular.receptor_density_fingerprint
siibra.features.tabular.receptor_density_profile
siibra.features.tabular.regional_timeseries_activity
siibra.features.tabular.tabular
siibra.livequeries
,
[1]
siibra.livequeries.allen
,
[1]
siibra.livequeries.bigbrain
,
[1]
siibra.livequeries.ebrains
,
[1]
siibra.livequeries.query
,
[1]
siibra.locations
,
[1]
siibra.locations.boundingbox
,
[1]
siibra.locations.location
,
[1]
siibra.locations.point
,
[1]
siibra.locations.pointset
,
[1]
siibra.retrieval
,
[1]
siibra.retrieval.cache
,
[1]
siibra.retrieval.datasets
,
[1]
siibra.retrieval.exceptions
,
[1]
siibra.retrieval.repositories
,
[1]
siibra.retrieval.requests
,
[1]
siibra.vocabularies
,
[1]
siibra.volumes
,
[1]
siibra.volumes.gifti
,
[1]
siibra.volumes.neuroglancer
,
[1]
siibra.volumes.nifti
,
[1]
siibra.volumes.parcellationmap
,
[1]
siibra.volumes.sparsemap
,
[1]
siibra.volumes.volume
,
[1]
MRIVolumeOfInterest (class in siibra.features.image)
(class in siibra.features.image.volume_of_interest)
MultiSourcedRequest (class in siibra.retrieval.requests)
MultiSourceRequestException
MUS_MUSCULUS (siibra.commons.Species attribute)
N
name (siibra.features.connectivity.regional_connectivity.RegionalConnectivity property)
(siibra.features.dataset.ebrains.EbrainsDataFeature property)
(siibra.features.dataset.EbrainsDataFeature property)
(siibra.features.Feature property)
(siibra.features.feature.Feature property)
(siibra.features.image.image.Image property)
(siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity property)
(siibra.retrieval.datasets.EbrainsBaseDataset property)
(siibra.retrieval.datasets.EbrainsDataset property)
(siibra.retrieval.datasets.EbrainsV3Dataset property)
(siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
(siibra.retrieval.datasets.GenericDataset property)
(siibra.retrieval.EbrainsPublicDatasetConnector property)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnector property)
(siibra.volumes.volume.Volume property)
name_to_key() (siibra.commons.Species static method)
names (siibra.core.region.Region property)
neg (in module siibra.explorer.util)
NEUROGLANCER_MAX_GIB (in module siibra.commons)
NeuroglancerMesh (class in siibra.volumes)
(class in siibra.volumes.neuroglancer)
NeuroglancerProvider (class in siibra.volumes)
(class in siibra.volumes.neuroglancer)
NeuroglancerScale (class in siibra.volumes.neuroglancer)
NeuroglancerSurfaceMesh (class in siibra.volumes.neuroglancer)
NeuroglancerVolume (class in siibra.volumes.neuroglancer)
neurotransmitter (siibra.features.tabular.receptor_density_profile.ReceptorDensityProfile property)
(siibra.features.tabular.ReceptorDensityProfile property)
neurotransmitters (siibra.features.tabular.receptor_density_fingerprint.ReceptorDensityFingerprint property)
(siibra.features.tabular.ReceptorDensityFingerprint property)
next() (siibra.volumes.neuroglancer.NeuroglancerScale method)
NiftiProvider (class in siibra.volumes)
(class in siibra.volumes.nifti)
NonUniqueIndexError
nonzero_coordinates() (in module siibra.commons)
NoSiibraConfigMirrorsAvailableException
,
[1]
NotFoundException
NoVolumeFound
num_volumes (siibra.volumes.sparsemap.SparseIndex property)
NZCACHE (in module siibra.commons)
O
OTHER_VERSION (siibra.core.relation_qualification.Qualification attribute)
OVERLAPS (siibra.core.relation_qualification.Qualification attribute)
OwncloudConnector (class in siibra.retrieval)
(class in siibra.retrieval.repositories)
P
Parcellation (class in siibra.core.parcellation)
parcellation (siibra.core.region.Region property)
(siibra.volumes.Map property)
(siibra.volumes.parcellationmap.Map property)
parcellation_ids (siibra.livequeries.ebrains.EbrainsFeatureQuery attribute)
(siibra.livequeries.EbrainsFeatureQuery attribute)
PARCELLATIONREGION_V1 (siibra.retrieval.requests.GitlabProxyEnum attribute)
parcellations (siibra.core.atlas.Atlas property)
(siibra.features.anchor.AnatomicalAnchor property)
ParcellationVersion (class in siibra.core.parcellation)
parse() (siibra.locations.Point static method)
(siibra.locations.point.Point static method)
(siibra.Point static method)
parse_featuretype() (siibra.features.Feature class method)
(siibra.features.feature.Feature class method)
parse_from_region() (siibra.core.region.RegionRelationAssessments class method)
parse_id_arg() (siibra.core.region.RegionRelationAssessments static method)
parse_person() (siibra.retrieval.datasets.EbrainsV3DatasetVersion static method)
parse_relation_assessment() (siibra.core.relation_qualification.Qualification static method)
parse_relationship_assessment() (siibra.core.region.RegionRelationAssessments class method)
parse_tsv_data() (siibra.features.tabular.receptor_density_fingerprint.ReceptorDensityFingerprint class method)
(siibra.features.tabular.receptor_density_profile.ReceptorDensityProfile class method)
(siibra.features.tabular.ReceptorDensityFingerprint class method)
(siibra.features.tabular.ReceptorDensityProfile class method)
ParseLiveQueryIdException
PLIVolumeOfInterest (class in siibra.features.image)
(class in siibra.features.image.volume_of_interest)
plot() (siibra.features.Feature method)
(siibra.features.feature.Feature method)
(siibra.features.tabular.cortical_profile.CorticalProfile method)
(siibra.features.tabular.gene_expression.GeneExpressions method)
(siibra.features.tabular.GeneExpressions method)
(siibra.features.tabular.receptor_density_fingerprint.ReceptorDensityFingerprint method)
(siibra.features.tabular.ReceptorDensityFingerprint method)
(siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity method)
(siibra.features.tabular.tabular.Tabular method)
plot_carpet() (siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity method)
plot_matrix() (siibra.features.connectivity.regional_connectivity.RegionalConnectivity method)
plot_profile() (siibra.features.connectivity.regional_connectivity.RegionalConnectivity method)
Point (class in siibra)
(class in siibra.locations)
(class in siibra.locations.point)
PointSet (class in siibra)
(class in siibra.locations)
(class in siibra.locations.pointset)
polar_plot() (siibra.features.tabular.receptor_density_fingerprint.ReceptorDensityFingerprint method)
(siibra.features.tabular.ReceptorDensityFingerprint method)
poly_rev() (siibra.features.tabular.cell_density_profile.CellDensityProfile static method)
(siibra.features.tabular.CellDensityProfile static method)
poly_srt() (siibra.features.tabular.cell_density_profile.CellDensityProfile static method)
(siibra.features.tabular.CellDensityProfile static method)
PolyLine (class in siibra.commons)
post_process() (in module siibra.explorer.util)
prev() (siibra.volumes.neuroglancer.NeuroglancerScale method)
profile_labels (siibra.livequeries.bigbrain.WagstylProfileLoader property)
PROFILES_FILE_LEFT (siibra.livequeries.bigbrain.WagstylProfileLoader attribute)
providers (siibra.volumes.volume.Volume property)
provides() (siibra.commons.InstanceTable method)
(siibra.vocabularies.InstanceTable method)
provides_image (siibra.core.space.Space property)
(siibra.volumes.Map property)
(siibra.volumes.parcellationmap.Map property)
(siibra.volumes.volume.Volume property)
provides_mesh (siibra.core.space.Space property)
(siibra.volumes.Map property)
(siibra.volumes.parcellationmap.Map property)
(siibra.volumes.volume.Volume property)
publications (siibra.core.concept.AtlasConcept property)
Q
Qualification (class in siibra.core.relation_qualification)
qualification (siibra.core.relation_qualification.RelationAssignment attribute)
query() (siibra.livequeries.allen.AllenBrainAtlasQuery method)
(siibra.livequeries.AllenBrainAtlasQuery method)
(siibra.livequeries.bigbrain.BigBrainProfileQuery method)
(siibra.livequeries.bigbrain.LayerwiseBigBrainIntensityQuery method)
(siibra.livequeries.BigBrainProfileQuery method)
(siibra.livequeries.ebrains.EbrainsFeatureQuery method)
(siibra.livequeries.EbrainsFeatureQuery method)
(siibra.livequeries.LayerwiseBigBrainIntensityQuery method)
(siibra.livequeries.query.LiveQuery method)
QUERY_ID (siibra.retrieval.EbrainsPublicDatasetConnector attribute)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnector attribute)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnectorMinds attribute)
query_structure (siibra.core.relation_qualification.RelationAssignment attribute)
QUIET (in module siibra)
(in module siibra.commons)
R
RATTUS_NORVEGICUS (siibra.commons.Species attribute)
receptor (siibra.features.tabular.receptor_density_profile.ReceptorDensityProfile property)
(siibra.features.tabular.ReceptorDensityProfile property)
RECEPTOR_SYMBOLS (in module siibra.vocabularies)
ReceptorDensityFingerprint (class in siibra.features.tabular)
(class in siibra.features.tabular.receptor_density_fingerprint)
ReceptorDensityProfile (class in siibra.features.tabular)
(class in siibra.features.tabular.receptor_density_profile)
receptors (siibra.features.tabular.receptor_density_fingerprint.ReceptorDensityFingerprint property)
(siibra.features.tabular.ReceptorDensityFingerprint property)
REGEX_TYPE (in module siibra.core.region)
Region (class in siibra.core.region)
REGION_ALIASES (in module siibra.vocabularies)
region_aliases (siibra.features.anchor.AnatomicalAnchor property)
RegionalBOLD (class in siibra.features.tabular)
(class in siibra.features.tabular.regional_timeseries_activity)
RegionalConnectivity (class in siibra.features.connectivity.regional_connectivity)
RegionalTimeseriesActivity (class in siibra.features.tabular.regional_timeseries_activity)
RegionRelationAssessments (class in siibra.core.region)
regions (siibra.features.anchor.AnatomicalAnchor property)
(siibra.volumes.Map property)
(siibra.volumes.parcellationmap.Map property)
register_cleanup() (siibra.configuration.Configuration class method)
(siibra.configuration.configuration.Configuration class method)
registry() (siibra.core.concept.AtlasConcept class method)
RelationAssignment (class in siibra.core.relation_qualification)
REMOVE_FROM_NAME (in module siibra.commons)
render_tree() (siibra.core.region.Region method)
REPLACE_IN_NAME (in module siibra.commons)
REPO (siibra.livequeries.bigbrain.WagstylProfileLoader attribute)
RepositoryConnector (class in siibra.retrieval.repositories)
represented_parcellations() (siibra.features.anchor.AnatomicalAnchor method)
requests (siibra.retrieval.requests.MultiSourcedRequest attribute)
res_mm (siibra.volumes.neuroglancer.NeuroglancerScale property)
resolves() (siibra.volumes.neuroglancer.NeuroglancerScale method)
ROOT_DIR (in module siibra.commons)
RT_DIR (in module siibra.vocabularies)
run_maintenance() (siibra.retrieval.cache.Cache method)
runtime_path() (in module siibra.vocabularies)
S
sample() (siibra.commons.PolyLine method)
sample_locations() (siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
sanitize_id() (in module siibra.explorer.url)
save_sparseindex() (siibra.volumes.sparsemap.SparseMap method)
scales (siibra.volumes.neuroglancer.NeuroglancerVolume property)
search_files() (siibra.retrieval.EbrainsHdgConnector method)
(siibra.retrieval.EbrainsPublicDatasetConnector method)
(siibra.retrieval.GitlabConnector method)
(siibra.retrieval.LocalFileRepository method)
(siibra.retrieval.OwncloudConnector method)
(siibra.retrieval.repositories.EbrainsHdgConnector method)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnector method)
(siibra.retrieval.repositories.EbrainsPublicDatasetConnectorMinds method)
(siibra.retrieval.repositories.GitlabConnector method)
(siibra.retrieval.repositories.LocalFileRepository method)
(siibra.retrieval.repositories.OwncloudConnector method)
(siibra.retrieval.repositories.RepositoryConnector method)
(siibra.retrieval.repositories.ZipfileConnector method)
(siibra.retrieval.requests.GitlabProxyEnum method)
(siibra.retrieval.ZipfileConnector method)
separator (in module siibra.explorer.util)
serialize_query_context() (siibra.features.Feature static method)
(siibra.features.feature.Feature static method)
set_cache_size() (in module siibra)
set_ebrains_token (in module siibra)
set_feasible_download_size() (in module siibra)
set_log_level() (in module siibra)
(in module siibra.commons)
set_token() (siibra.retrieval.EbrainsRequest class method)
(siibra.retrieval.requests.EbrainsRequest class method)
shape (siibra.features.tabular.cell_density_profile.CellDensityProfile property)
(siibra.features.tabular.CellDensityProfile property)
(siibra.locations.BoundingBox property)
(siibra.locations.boundingbox.BoundingBox property)
(siibra.volumes.neuroglancer.NeuroglancerVolume property)
(siibra.volumes.sparsemap.SparseMap property)
shift() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
sigma (siibra.locations.PointSet property)
(siibra.locations.pointset.PointSet property)
(siibra.PointSet property)
siibra
module
siibra.commons
module
,
[1]
siibra.configuration
module
,
[1]
siibra.configuration.configuration
module
siibra.configuration.factory
module
siibra.core
module
,
[1]
siibra.core.atlas
module
,
[1]
siibra.core.concept
module
,
[1]
siibra.core.parcellation
module
,
[1]
siibra.core.region
module
,
[1]
siibra.core.relation_qualification
module
,
[1]
siibra.core.space
module
,
[1]
siibra.explorer
module
,
[1]
siibra.explorer.url
module
siibra.explorer.util
module
siibra.features
module
,
[1]
siibra.features.anchor
module
,
[1]
siibra.features.connectivity
module
,
[1]
siibra.features.connectivity.functional_connectivity
module
siibra.features.connectivity.regional_connectivity
module
siibra.features.connectivity.streamline_counts
module
siibra.features.connectivity.streamline_lengths
module
siibra.features.connectivity.tracing_connectivity
module
siibra.features.dataset
module
,
[1]
siibra.features.dataset.ebrains
module
siibra.features.feature
module
,
[1]
siibra.features.image
module
,
[1]
siibra.features.image.image
module
siibra.features.image.sections
module
siibra.features.image.volume_of_interest
module
siibra.features.tabular
module
,
[1]
siibra.features.tabular.bigbrain_intensity_profile
module
siibra.features.tabular.cell_density_profile
module
siibra.features.tabular.cortical_profile
module
siibra.features.tabular.gene_expression
module
siibra.features.tabular.layerwise_bigbrain_intensities
module
siibra.features.tabular.layerwise_cell_density
module
siibra.features.tabular.receptor_density_fingerprint
module
siibra.features.tabular.receptor_density_profile
module
siibra.features.tabular.regional_timeseries_activity
module
siibra.features.tabular.tabular
module
siibra.livequeries
module
,
[1]
siibra.livequeries.allen
module
,
[1]
siibra.livequeries.bigbrain
module
,
[1]
siibra.livequeries.ebrains
module
,
[1]
siibra.livequeries.query
module
,
[1]
siibra.locations
module
,
[1]
siibra.locations.boundingbox
module
,
[1]
siibra.locations.location
module
,
[1]
siibra.locations.point
module
,
[1]
siibra.locations.pointset
module
,
[1]
siibra.retrieval
module
,
[1]
siibra.retrieval.cache
module
,
[1]
siibra.retrieval.datasets
module
,
[1]
siibra.retrieval.exceptions
module
,
[1]
siibra.retrieval.repositories
module
,
[1]
siibra.retrieval.requests
module
,
[1]
siibra.vocabularies
module
,
[1]
siibra.volumes
module
,
[1]
siibra.volumes.gifti
module
,
[1]
siibra.volumes.neuroglancer
module
,
[1]
siibra.volumes.nifti
module
,
[1]
siibra.volumes.parcellationmap
module
,
[1]
siibra.volumes.sparsemap
module
,
[1]
siibra.volumes.volume
module
,
[1]
SIIBRA_CACHEDIR (in module siibra.commons)
SIIBRA_DEFAULT_MAP_THRESHOLD (in module siibra.commons)
SIIBRA_DEFAULT_MAPTYPE (in module siibra.commons)
SIIBRA_LOG_LEVEL (in module siibra.commons)
siibra_tqdm() (in module siibra.commons)
SIIBRA_USE_CONFIGURATION (in module siibra.commons)
SIIBRA_USE_LOCAL_SNAPSPOT (in module siibra.commons)
SiibraHttpRequestError
,
[1]
size (siibra.retrieval.cache.Cache property)
SIZE_GIB (siibra.retrieval.cache.Cache attribute)
SKIP_CACHEINIT_MAINTENANCE (in module siibra.commons)
snake2camel() (in module siibra.commons)
Space (class in siibra.core.space)
space (siibra.core.region.SpatialProp attribute)
(siibra.features.anchor.AnatomicalAnchor property)
(siibra.features.image.image.ImageAnchor property)
(siibra.volumes.Map property)
(siibra.volumes.parcellationmap.Map property)
(siibra.volumes.volume.Volume property)
spaces (siibra.core.atlas.Atlas property)
(siibra.core.region.Region property)
SPACEWARP_IDS (siibra.locations.location.Location attribute)
SPACEWARP_SERVER (siibra.locations.location.Location attribute)
sparse_index (siibra.volumes.sparsemap.SparseMap property)
SparseIndex (class in siibra.volumes.sparsemap)
SparseMap (class in siibra.volumes.sparsemap)
spatial_props() (siibra.core.region.Region method)
SpatialProp (class in siibra.core.region)
SpatialPropCmpt (class in siibra.core.region)
Species (class in siibra.commons)
species (siibra.core.concept.AtlasConcept property)
(siibra.core.region.Region property)
(siibra.livequeries.allen.AllenBrainAtlasQuery attribute)
(siibra.livequeries.AllenBrainAtlasQuery attribute)
(siibra.volumes.Map property)
(siibra.volumes.parcellationmap.Map property)
STATISTICAL (siibra.commons.MapType attribute)
(siibra.MapType attribute)
StreamlineCounts (class in siibra.features.connectivity)
(class in siibra.features.connectivity.streamline_counts)
StreamlineLengths (class in siibra.features.connectivity)
(class in siibra.features.connectivity.streamline_lengths)
SUBCLASSES (siibra.features.Feature attribute)
(siibra.features.feature.Feature attribute)
subjects (siibra.features.connectivity.regional_connectivity.RegionalConnectivity property)
(siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity property)
Subvolume (class in siibra.volumes.volume)
SubvolumeProvider (class in siibra.volumes.volume)
SubvolumeProvider.UseCaching (class in siibra.volumes.volume)
SUPPORTED_FORMATS (siibra.volumes.volume.Volume attribute)
supported_prefix (in module siibra.explorer.url)
supported_spaces (siibra.core.region.Region property)
supports_space() (siibra.core.region.Region method)
T
T (in module siibra.commons)
(in module siibra.core.concept)
(in module siibra.core.relation_qualification)
Tabular (class in siibra.features.tabular.tabular)
TagNotFoundException
,
[1]
THICKNESSES_FILE_LEFT (siibra.livequeries.bigbrain.WagstylProfileLoader attribute)
THRESHOLD_STATISTICAL_MAPS (in module siibra.core.region)
to_sparse() (siibra.volumes.Map method)
(siibra.volumes.parcellationmap.Map method)
TracingConnectivity (class in siibra.features.connectivity)
(class in siibra.features.connectivity.tracing_connectivity)
transform() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
(siibra.locations.location.Location method)
(siibra.locations.location.WholeBrain method)
(siibra.locations.Point method)
(siibra.locations.point.Point method)
(siibra.locations.PointSet method)
(siibra.locations.pointset.PointSet method)
(siibra.locations.WholeBrain method)
(siibra.Point method)
(siibra.PointSet method)
transform_nm (siibra.volumes.neuroglancer.NeuroglancerVolume property)
translate_cae() (siibra.core.region.RegionRelationAssessments class method)
translate_pevs() (siibra.core.region.RegionRelationAssessments class method)
tree2str() (siibra.core.region.Region method)
try_all_connectors() (in module siibra.retrieval.requests)
TypeDataset (in module siibra.core.concept)
(in module siibra.features.feature)
(in module siibra.volumes.volume)
TypePublication (class in siibra.commons)
TYPES (in module siibra.features)
U
unify_stringlist() (in module siibra.commons)
union() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
unit (siibra.features.tabular.cortical_profile.CorticalProfile property)
(siibra.features.tabular.receptor_density_fingerprint.ReceptorDensityFingerprint property)
(siibra.features.tabular.receptor_density_profile.ReceptorDensityProfile property)
(siibra.features.tabular.ReceptorDensityFingerprint property)
(siibra.features.tabular.ReceptorDensityProfile property)
UNSPECIFIED_SPECIES (siibra.commons.Species attribute)
url (siibra.commons.TypePublication attribute)
(siibra.features.dataset.ebrains.EbrainsDataFeature property)
(siibra.features.dataset.EbrainsDataFeature property)
(siibra.retrieval.datasets.EbrainsDatasetUrl attribute)
urls (siibra.retrieval.datasets.EbrainsBaseDataset property)
(siibra.retrieval.datasets.EbrainsDataset property)
(siibra.retrieval.datasets.EbrainsV3Dataset property)
(siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
(siibra.retrieval.datasets.GenericDataset property)
USE_CACHE (siibra.volumes.neuroglancer.NeuroglancerVolume attribute)
use_configuration() (siibra.configuration.Configuration class method)
(siibra.configuration.configuration.Configuration class method)
USER_AGENT_HEADER (in module siibra.retrieval.requests)
V
values() (siibra.commons.InstanceTable method)
(siibra.vocabularies.InstanceTable method)
variants (siibra.volumes.gifti.GiftiMesh property)
(siibra.volumes.GiftiMesh property)
verb (siibra.core.relation_qualification.Qualification property)
VERBOSE (in module siibra)
(in module siibra.commons)
VERSION_BLACKLIST_WORDS (in module siibra.core.atlas)
version_changes (siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
version_history (siibra.features.dataset.ebrains.EbrainsDataFeature property)
(siibra.features.dataset.EbrainsDataFeature property)
version_identifier (siibra.features.dataset.ebrains.EbrainsDataFeature property)
(siibra.features.dataset.EbrainsDataFeature property)
(siibra.retrieval.datasets.EbrainsV3DatasetVersion property)
version_ids (siibra.retrieval.datasets.EbrainsV3Dataset property)
VERSION_PATTERN (siibra.livequeries.ebrains.EbrainsFeatureQuery attribute)
(siibra.livequeries.EbrainsFeatureQuery attribute)
Volume (class in siibra.volumes.volume)
volume (siibra.core.region.SpatialPropCmpt attribute)
(siibra.locations.BoundingBox property)
(siibra.locations.boundingbox.BoundingBox property)
(siibra.locations.Point property)
(siibra.locations.point.Point property)
(siibra.locations.PointSet property)
(siibra.locations.pointset.PointSet property)
(siibra.Point property)
(siibra.PointSet property)
(siibra.volumes.parcellationmap.Assignment attribute)
VolumeData (in module siibra.volumes.volume)
VolumeProvider (class in siibra.volumes.volume)
W
WagstylProfileLoader (class in siibra.livequeries.bigbrain)
want_commit (siibra.retrieval.GitlabConnector property)
(siibra.retrieval.repositories.GitlabConnector property)
warm_cache() (in module siibra)
(in module siibra.core)
(in module siibra.features)
(in module siibra.livequeries)
(in module siibra.volumes)
warp() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
(siibra.locations.location.Location method)
(siibra.locations.location.WholeBrain method)
(siibra.locations.Point method)
(siibra.locations.point.Point method)
(siibra.locations.PointSet method)
(siibra.locations.pointset.PointSet method)
(siibra.locations.WholeBrain method)
(siibra.Point method)
(siibra.PointSet method)
weighted_mean_of_first (siibra.commons.CompareMapsResult attribute)
weighted_mean_of_second (siibra.commons.CompareMapsResult attribute)
WholeBrain (class in siibra.locations)
(class in siibra.locations.location)
wrap_livequery_feature() (siibra.features.Feature static method)
(siibra.features.feature.Feature static method)
X
XPCTVolumeOfInterest (class in siibra.features.image)
(class in siibra.features.image.volume_of_interest)
Z
ZipContainedNiftiProvider (class in siibra.volumes.nifti)
zipfile (siibra.retrieval.repositories.ZipfileConnector property)
(siibra.retrieval.ZipfileConnector property)
ZipfileConnector (class in siibra.retrieval)
(class in siibra.retrieval.repositories)
ZipfileConnector.ZipFileLoader (class in siibra.retrieval)
(class in siibra.retrieval.repositories)
ZipfileRequest (class in siibra.retrieval)
(class in siibra.retrieval.requests)
zoom() (siibra.locations.BoundingBox method)
(siibra.locations.boundingbox.BoundingBox method)
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