Index

_

__add__() (siibra.features.anchor.AnatomicalAnchor method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) __contains__() (siibra.commons.InstanceTable method) (siibra.core.region.Region method) (siibra.core.structure.BrainStructure method) (siibra.vocabularies.InstanceTable method) __dir__() (in module siibra) (in module siibra.features) (in module siibra.features.connectivity) (siibra.commons.InstanceTable method) (siibra.features.feature.CompoundFeature method) (siibra.vocabularies.InstanceTable method) __enter__() (siibra.commons.LoggingContext method) (siibra.volumes.providers.provider.SubvolumeProvider.UseCaching method) __eq__() (siibra.BoundingBox method) (siibra.commons.MapIndex method) (siibra.core.parcellation.ParcellationVersion method) (siibra.core.region.Region method) (siibra.features.dataset.ebrains.EbrainsDataFeature method) (siibra.features.dataset.EbrainsDataFeature method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method) (siibra.locations.Location method) (siibra.locations.location.Location method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.Point method) (siibra.PointCloud method) (siibra.retrieval.datasets.EbrainsBaseDataset method) (siibra.retrieval.datasets.GenericDataset method) (siibra.retrieval.GitlabConnector method) (siibra.retrieval.LocalFileRepository method) (siibra.retrieval.repositories.GitlabConnector method) (siibra.retrieval.repositories.LocalFileRepository method) (siibra.retrieval.repositories.RepositoryConnector method) (siibra.retrieval.repositories.ZipfileConnector method) (siibra.retrieval.ZipfileConnector method) (siibra.volumes.Volume method) (siibra.volumes.volume.Volume method) __exit__() (siibra.commons.LoggingContext method) (siibra.volumes.providers.provider.SubvolumeProvider.UseCaching method) __ge__() (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) __getattr__() (in module siibra) (in module siibra.features) (siibra.commons.InstanceTable method) (siibra.features.feature.CompoundFeature method) (siibra.vocabularies.InstanceTable method) (siibra.volumes.providers.provider.SubvolumeProvider method) __getitem__() (siibra.commons.InstanceTable method) (siibra.configuration.Configuration method) (siibra.configuration.configuration.Configuration method) (siibra.core.parcellation.Parcellation method) (siibra.features.feature.CompoundFeature method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.Point method) (siibra.PointCloud method) (siibra.vocabularies.InstanceTable method) __gt__() (siibra.core.concept.AtlasConcept method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) __hash__() (siibra.BoundingBox method) (siibra.commons.MapIndex method) (siibra.core.region.Region method) (siibra.core.structure.BrainStructure method) (siibra.features.dataset.ebrains.EbrainsDataFeature method) (siibra.features.dataset.EbrainsDataFeature method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method) (siibra.locations.Location method) (siibra.locations.location.Location method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.Point method) (siibra.PointCloud method) (siibra.retrieval.datasets.EbrainsBaseDataset method) (siibra.retrieval.datasets.GenericDataset method) (siibra.volumes.Volume method) (siibra.volumes.volume.Volume method) __init_subclass__() (siibra.core.concept.AtlasConcept class method) (siibra.features.Feature class method) (siibra.features.feature.Compoundable class method) (siibra.features.feature.Feature class method) (siibra.livequeries.query.LiveQuery class method) (siibra.volumes.providers.provider.VolumeProvider class method) __iter__() (siibra.BoundingBox method) (siibra.commons.InstanceTable method) (siibra.core.parcellation.ParcellationVersion method) (siibra.core.region.Region method) (siibra.features.feature.CompoundFeature method) (siibra.livequeries.allen.AllenBrainAtlasQuery method) (siibra.livequeries.AllenBrainAtlasQuery method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.Point method) (siibra.PointCloud method) (siibra.retrieval.cache.Cache method) (siibra.vocabularies.InstanceTable method) (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method)

__le__() (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) __len__() (siibra.commons.InstanceTable method) (siibra.features.connectivity.regional_connectivity.RegionalConnectivity method) (siibra.features.feature.CompoundFeature method) (siibra.livequeries.bigbrain.WagstylProfileLoader method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.Point method) (siibra.PointCloud method) (siibra.vocabularies.InstanceTable method) (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method) __lt__() (siibra.core.assignment.AnatomicalAssignment method) (siibra.core.assignment.Qualification method) (siibra.core.concept.AtlasConcept method) (siibra.core.parcellation.Parcellation method) (siibra.core.parcellation.ParcellationVersion method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) (siibra.volumes.providers.neuroglancer.NeuroglancerScale method) __mul__() (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) __radd__() (siibra.features.anchor.AnatomicalAnchor method) __repr__() (siibra.commons.InstanceTable method) (siibra.commons.MapIndex method) (siibra.commons.Species method) (siibra.core.assignment.Qualification method) (siibra.core.concept.AtlasConcept method) (siibra.core.parcellation.ParcellationVersion method) (siibra.core.structure.BrainStructure method) (siibra.features.Feature method) (siibra.features.feature.Feature method) (siibra.features.image.BigBrain1MicronPatch method) (siibra.features.image.sections.BigBrain1MicronPatch method) (siibra.locations.Location method) (siibra.locations.location.Location method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) (siibra.vocabularies.InstanceTable method) (siibra.volumes.providers.neuroglancer.NeuroglancerScale method) (siibra.volumes.Volume method) (siibra.volumes.volume.Volume method) __setitem__() (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) __str__() (siibra.BoundingBox method) (siibra.commons.InstanceTable method) (siibra.commons.MapIndex method) (siibra.commons.Species method) (siibra.core.assignment.AnatomicalAssignment method) (siibra.core.assignment.Qualification method) (siibra.core.concept.AtlasConcept method) (siibra.core.parcellation.ParcellationVersion method) (siibra.features.anchor.AnatomicalAnchor method) (siibra.features.connectivity.regional_connectivity.RegionalConnectivity method) (siibra.features.image.image.ImageAnchor method) (siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity method) (siibra.locations.AxisAlignedPatch method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method) (siibra.locations.experimental.AxisAlignedPatch method) (siibra.locations.Location method) (siibra.locations.location.Location method) (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.PointCloud method) (siibra.retrieval.GitlabConnector method) (siibra.retrieval.LocalFileRepository method) (siibra.retrieval.repositories.GitlabConnector method) (siibra.retrieval.repositories.LocalFileRepository method) (siibra.retrieval.repositories.ZipfileConnector method) (siibra.retrieval.requests.SiibraHttpRequestError method) (siibra.retrieval.SiibraHttpRequestError method) (siibra.retrieval.ZipfileConnector method) (siibra.vocabularies.InstanceTable method) (siibra.volumes.providers.neuroglancer.NeuroglancerScale method) (siibra.volumes.Volume method) (siibra.volumes.volume.Volume method) __sub__() (siibra.commons.InstanceTable method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) (siibra.vocabularies.InstanceTable method) __truediv__() (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) __version__ (in module siibra) (in module siibra.commons)

A

add() (siibra.commons.InstanceTable method) (siibra.vocabularies.InstanceTable method) add_img() (siibra.volumes.sparsemap.SparseIndex method) affine (siibra.volumes.Map property) (siibra.volumes.parcellationmap.Map property) (siibra.volumes.providers.neuroglancer.NeuroglancerScale property) (siibra.volumes.providers.neuroglancer.NeuroglancerVolume property) (siibra.volumes.sparsemap.SparseIndex attribute) (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 (class in siibra.core.assignment) AnatomoFunctionalConnectivity (class in siibra.features.connectivity) (class in siibra.features.connectivity.functional_connectivity) 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.assignment.Qualification attribute) archive_mode (siibra.retrieval.GitlabConnector attribute) (siibra.retrieval.repositories.GithubConnector attribute) (siibra.retrieval.repositories.GitlabConnector attribute)

argmax_dim4() (in module siibra.commons) as_list() (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.PointCloud method) assert_folder() (in module siibra.retrieval.cache) assign() (siibra.core.region.Region method) (siibra.core.structure.BrainStructure method) (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.assignment.AnatomicalAssignment attribute) AssignImageResult (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) AxisAlignedPatch (class in siibra.locations) (class in siibra.locations.experimental)

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) (siibra.retrieval.repositories.RepositoryConnector attribute) bboxes (siibra.volumes.sparsemap.SparseIndex attribute) BigBrain1MicronPatch (class in siibra.features.image) (class in siibra.features.image.sections) BigBrain1MicronPatchQuery (class in siibra.livequeries.bigbrain) BIGBRAIN_ID (siibra.locations.Location attribute) (siibra.locations.location.Location attribute) bigbrain_section (siibra.features.image.BigBrain1MicronPatch property) (siibra.features.image.sections.BigBrain1MicronPatch property) 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) (siibra.features.tabular.layerwise_cell_density.LayerwiseCellDensity attribute) (siibra.features.tabular.LayerwiseCellDensity 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) (class in siibra.locations) (class in siibra.locations.boundingbox) boundingbox (siibra.locations.PointCloud property) (siibra.locations.pointcloud.PointCloud property) (siibra.PointCloud property) BrainStructure (class in siibra.core.structure) 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_boundingbox() (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_generic_tabular() (siibra.configuration.factory.Factory class 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_pointcloud() (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) build_volumeproviders() (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) cachefile (siibra.retrieval.HttpRequest attribute) (siibra.retrieval.repositories.ZipfileConnector.ZipFileLoader attribute) (siibra.retrieval.requests.FileLoader attribute) (siibra.retrieval.requests.HttpRequest attribute) (siibra.retrieval.ZipfileConnector.ZipFileLoader attribute) CALLITHRIX_JACCHUS (siibra.commons.Species attribute) category (siibra.features.Feature attribute) (siibra.features.feature.CompoundFeature attribute) (siibra.features.feature.Feature attribute) cell_reader() (in module siibra.features.tabular) (in module siibra.features.tabular.cell_density_profile) 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.BoundingBox property) (siibra.locations.BoundingBox property) (siibra.locations.boundingbox.BoundingBox property) centroid (siibra.locations.PointCloud property) (siibra.locations.pointcloud.PointCloud property) (siibra.PointCloud property) (siibra.volumes.parcellationmap.MapAssignment attribute) (siibra.volumes.volume.ComponentSpatialProperties attribute) ch (in module siibra.commons) children (siibra.core.region.Region attribute) CHLOROCEBUS_AETHIOPS_SABAEUS (siibra.commons.Species attribute) chunk_sizes (siibra.volumes.providers.neuroglancer.NeuroglancerScale attribute) cipher (in module siibra.explorer.util) citation (siibra.commons.TypePublication attribute) (siibra.retrieval.EbrainsPublicDatasetConnector property) (siibra.retrieval.repositories.EbrainsPublicDatasetConnector property) 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.BoundingBox method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method) cohort (siibra.features.connectivity.regional_connectivity.RegionalConnectivity attribute) (siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity attribute) collection (siibra.core.parcellation.ParcellationVersion attribute) color_warning_issued (siibra.volumes.providers.neuroglancer.NeuroglancerScale attribute) colorize() (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method)

COMPACT_FEATURE_LIST (siibra.livequeries.ebrains.EbrainsFeatureQuery attribute) (siibra.livequeries.EbrainsFeatureQuery attribute) compare_arrays() (in module siibra.commons) CompareMapsResult (class in siibra.commons) ComponentSpatialProperties (class in siibra.volumes.volume) Compoundable (class in siibra.features.feature) CompoundFeature (class in siibra.features.feature) 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) compute_from_image() (siibra.volumes.volume.ComponentSpatialProperties static method) compute_spatial_props() (siibra.volumes.Volume method) (siibra.volumes.volume.Volume method) CONFIG_CONNECTORS (siibra.configuration.Configuration attribute) (siibra.configuration.configuration.Configuration attribute) CONFIG_EXTENSIONS (siibra.configuration.Configuration attribute) (siibra.configuration.configuration.Configuration attribute) CONFIG_REPOS (siibra.configuration.Configuration attribute) (siibra.configuration.configuration.Configuration attribute) Configuration (class in siibra.configuration) (class in siibra.configuration.configuration) ConflictingArgumentException connected_components() (in module siibra.commons) connectors (siibra.retrieval.requests.GitlabProxyEnum property) CONTAINED (siibra.core.assignment.Qualification attribute) CONTAINS (siibra.core.assignment.Qualification attribute) Contour (class in siibra.locations) (class in siibra.locations.pointcloud) 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) coordinate (siibra.locations.Point attribute) (siibra.locations.point.Point attribute) (siibra.Point attribute) coordinates (siibra.locations.PointCloud property) (siibra.locations.pointcloud.PointCloud property) (siibra.PointCloud property) coords() (siibra.volumes.sparsemap.SparseIndex method) copy() (siibra.core.region.Region static method) corners (siibra.BoundingBox property) (siibra.locations.BoundingBox property) (siibra.locations.boundingbox.BoundingBox property) 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) crop() (siibra.locations.Contour method) (siibra.locations.pointcloud.Contour method) 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.connectivity.regional_connectivity.RegionalConnectivity property) (siibra.features.feature.CompoundFeature property) (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.regional_timeseries_activity.RegionalTimeseriesActivity property) (siibra.features.tabular.tabular.Tabular property) DATA (siibra.retrieval.cache.WarmupLevel attribute) data (siibra.retrieval.HttpRequest property) (siibra.retrieval.repositories.ZipfileConnector.ZipFileLoader property) (siibra.retrieval.requests.HttpRequest property) (siibra.retrieval.requests.MultiSourcedRequest property) (siibra.retrieval.ZipfileConnector.ZipFileLoader property) DATA (siibra.WarmupLevel attribute) dataframe (siibra.commons.InstanceTable property) (siibra.vocabularies.InstanceTable property) DATASET (siibra.features.tabular.gene_expression.GeneExpressions attribute) (siibra.features.tabular.GeneExpressions attribute) (siibra.livequeries.bigbrain.WagstylProfileLoader attribute) dataset_id (siibra.retrieval.EbrainsHdgConnector attribute) (siibra.retrieval.EbrainsPublicDatasetConnector attribute) (siibra.retrieval.repositories.EbrainsHdgConnector attribute) (siibra.retrieval.repositories.EbrainsPublicDatasetConnector attribute) DATASET_V1 (siibra.retrieval.requests.GitlabProxyEnum attribute) DATASET_V3 (siibra.retrieval.requests.GitlabProxyEnum attribute) datasets (siibra.core.concept.AtlasConcept attribute) (siibra.features.Feature attribute) (siibra.features.feature.Feature attribute) (siibra.volumes.Volume attribute) (siibra.volumes.volume.Volume 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)

deprecated (siibra.core.parcellation.ParcellationVersion attribute) depth_image (siibra.features.tabular.cell_density_profile.CellDensityProfile property) (siibra.features.tabular.CellDensityProfile property) deregister_warmup_fn() (siibra.retrieval.cache.Warmup class method) (siibra.Warmup class method) 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) 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) device_flow() (siibra.retrieval.EbrainsRequest class method) (siibra.retrieval.requests.EbrainsRequest class method) distance_from_origin (siibra.locations.experimental.Plane property) (siibra.locations.Plane property) (siibra.Plane property) DOI_TMPL (in module siibra.features.dataset.ebrains) draw_samples() (siibra.volumes.Volume method) (siibra.volumes.volume.Volume method) DTIVolumeOfInterest (class in siibra.features.image) (class in siibra.features.image.volume_of_interest) dtype (siibra.volumes.providers.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) elements (siibra.features.feature.CompoundFeature property)

embargo_status (siibra.retrieval.datasets.EbrainsDataset attribute) EmptyPointCloudError 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 encoding (siibra.volumes.providers.neuroglancer.NeuroglancerScale attribute) estimate_affine() (siibra.BoundingBox method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method) evaluate_points() (siibra.volumes.Volume method) (siibra.volumes.volume.Volume method) EXACT (siibra.core.assignment.Qualification attribute) ExcessiveArgumentException explanation (siibra.core.assignment.AnatomicalAssignment attribute) 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_volume() (siibra.locations.AxisAlignedPatch method) (siibra.locations.experimental.AxisAlignedPatch 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) feature (siibra.features.connectivity.regional_connectivity.RegionalConnectivity property) feature_type (siibra.features.feature.CompoundFeature property) fetch() (siibra.features.image.BigBrain1MicronPatch method) (siibra.features.image.sections.BigBrain1MicronPatch method) (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method) (siibra.volumes.providers.freesurfer.FreesurferAnnot method) (siibra.volumes.providers.freesurfer.ZippedFreesurferAnnot method) (siibra.volumes.providers.FreesurferAnnot method) (siibra.volumes.providers.gifti.GiftiMesh method) (siibra.volumes.providers.gifti.GiftiSurfaceLabeling method) (siibra.volumes.providers.GiftiMesh method) (siibra.volumes.providers.GiftiSurfaceLabeling method) (siibra.volumes.providers.neuroglancer.NeuroglancerMesh method) (siibra.volumes.providers.neuroglancer.NeuroglancerProvider method) (siibra.volumes.providers.neuroglancer.NeuroglancerScale method) (siibra.volumes.providers.neuroglancer.NeuroglancerSurfaceMesh method) (siibra.volumes.providers.neuroglancer.NeuroglancerVolume method) (siibra.volumes.providers.NeuroglancerMesh method) (siibra.volumes.providers.NeuroglancerProvider method) (siibra.volumes.providers.nifti.NiftiProvider method) (siibra.volumes.providers.NiftiProvider method) (siibra.volumes.providers.provider.SubvolumeProvider method) (siibra.volumes.providers.provider.VolumeProvider method) (siibra.volumes.providers.ZippedFreesurferAnnot method) (siibra.volumes.Volume method) (siibra.volumes.volume.FilteredVolume method) (siibra.volumes.volume.ReducedVolume method) (siibra.volumes.volume.Volume method) fetch_connected_components() (siibra.volumes.Volume method) (siibra.volumes.volume.Volume method) fetch_iter() (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method) (siibra.volumes.providers.gifti.GiftiMesh method) (siibra.volumes.providers.GiftiMesh method) fetch_token() (siibra.retrieval.EbrainsRequest class method) (siibra.retrieval.requests.EbrainsRequest class method) FileLoader (class in siibra.retrieval.requests) filename (siibra.retrieval.repositories.ZipfileConnector.ZipFileLoader attribute) (siibra.retrieval.requests.ZipfileRequest attribute) (siibra.retrieval.ZipfileConnector.ZipFileLoader attribute) (siibra.retrieval.ZipfileRequest attribute) filter_attributes (siibra.features.feature.Compoundable property) FilteredVolume (class in siibra.volumes.volume) find (siibra.core.region.Region attribute) find() (siibra.commons.InstanceTable method) (siibra.vocabularies.InstanceTable method) find_clusters() (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.PointCloud method) find_indices() (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method) find_peaks() (siibra.volumes.providers.nifti.NiftiProvider method) (siibra.volumes.providers.NiftiProvider method) (siibra.volumes.Volume method) (siibra.volumes.volume.Volume method)

find_regions (in module siibra) find_regions() (in module siibra.core.parcellation) (siibra.core.atlas.Atlas method) find_suitable_decoder() (in module siibra.retrieval.requests) flavour (siibra.retrieval.requests.GitlabProxy attribute) flip() (siibra.locations.AxisAlignedPatch method) (siibra.locations.experimental.AxisAlignedPatch method) fn (siibra.retrieval.cache.WarmupParam attribute) fn_eql() (siibra.retrieval.cache.Warmup static method) (siibra.Warmup static method) folder (siibra.retrieval.cache.Cache attribute) (siibra.retrieval.requests.GitlabProxy 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 property) (siibra.volumes.volume.ReducedVolume property) (siibra.volumes.volume.Volume property) formatter (in module siibra.commons) fragment (siibra.commons.MapIndex attribute) (siibra.volumes.parcellationmap.MapAssignment attribute) (siibra.volumes.volume.FilteredVolume attribute) fragments (siibra.volumes.Map property) (siibra.volumes.parcellationmap.Map property) (siibra.volumes.providers.gifti.GiftiMesh property) (siibra.volumes.providers.GiftiMesh property) (siibra.volumes.providers.neuroglancer.NeuroglancerSurfaceMesh property) (siibra.volumes.providers.nifti.NiftiProvider property) (siibra.volumes.providers.NiftiProvider property) (siibra.volumes.providers.provider.VolumeProvider property) (siibra.volumes.Volume property) (siibra.volumes.volume.Volume property) FreesurferAnnot (class in siibra.volumes.providers) (class in siibra.volumes.providers.freesurfer) from_array() (in module siibra.locations.boundingbox) (in module siibra.volumes) (in module siibra.volumes.volume) from_dict() (siibra.commons.MapIndex class method) from_file() (in module siibra.volumes) (in module siibra.volumes.volume) from_image() (siibra.locations.experimental.Plane class method) (siibra.locations.Plane class method) (siibra.Plane class method) from_json (in module siibra) from_json() (siibra.configuration.factory.Factory class method) from_nifti() (in module siibra.volumes) (in module siibra.volumes.volume) from_pointcloud() (in module siibra.volumes) (in module siibra.volumes.volume) from_points() (in module siibra.locations) (in module siibra.locations.pointcloud) from_sparsemap() (siibra.volumes.sparsemap.SparseIndex class method) from_volume() (in module siibra.volumes.parcellationmap) func (siibra.retrieval.repositories.ZipfileConnector.ZipFileLoader attribute) (siibra.retrieval.ZipfileConnector.ZipFileLoader attribute) 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) generate_uuid() (in module siibra.commons) GenericDataset (class in siibra.retrieval.datasets) get (in module siibra.features) (siibra.retrieval.requests.GitlabProxy attribute) get() (siibra.commons.InstanceTable method) (siibra.retrieval.EbrainsRequest method) (siibra.retrieval.HttpRequest method) (siibra.retrieval.repositories.RepositoryConnector method) (siibra.retrieval.requests.EbrainsRequest 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_boundingbox() (siibra.core.region.Region method) (siibra.features.image.BigBrain1MicronPatch method) (siibra.features.image.sections.BigBrain1MicronPatch method) (siibra.volumes.providers.freesurfer.FreesurferAnnot method) (siibra.volumes.providers.freesurfer.ZippedFreesurferAnnot method) (siibra.volumes.providers.FreesurferAnnot method) (siibra.volumes.providers.gifti.GiftiMesh method) (siibra.volumes.providers.gifti.GiftiSurfaceLabeling method) (siibra.volumes.providers.GiftiMesh method) (siibra.volumes.providers.GiftiSurfaceLabeling method) (siibra.volumes.providers.neuroglancer.NeuroglancerMesh method) (siibra.volumes.providers.neuroglancer.NeuroglancerProvider method) (siibra.volumes.providers.NeuroglancerMesh method) (siibra.volumes.providers.NeuroglancerProvider method) (siibra.volumes.providers.nifti.NiftiProvider method) (siibra.volumes.providers.NiftiProvider method) (siibra.volumes.providers.provider.SubvolumeProvider method) (siibra.volumes.providers.provider.VolumeProvider method) (siibra.volumes.providers.ZippedFreesurferAnnot method) (siibra.volumes.Volume method) (siibra.volumes.volume.FilteredVolume method) (siibra.volumes.volume.ReducedVolume method) (siibra.volumes.volume.Volume method) get_colormap() (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method) get_element() (siibra.features.feature.CompoundFeature method) get_enclosing_cube() (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.Point method) get_enclosing_patch() (siibra.locations.experimental.Plane method) (siibra.locations.Plane method) (siibra.Plane 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_loader() (siibra.retrieval.EbrainsHdgConnector method) (siibra.retrieval.EbrainsPublicDatasetConnector method) (siibra.retrieval.GitlabConnector method) (siibra.retrieval.LocalFileRepository method) (siibra.retrieval.repositories.EbrainsHdgConnector method) (siibra.retrieval.repositories.EbrainsPublicDatasetConnector method) (siibra.retrieval.repositories.EbrainsPublicDatasetConnectorMinds method) (siibra.retrieval.repositories.GithubConnector method) (siibra.retrieval.repositories.GitlabConnector 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_object() (siibra.core.region.RegionRelationAssessments class method) get_parcellation() (siibra.core.atlas.Atlas method) get_peid_from_region() (in module siibra.core.region) get_perspective_zoom() (in module siibra.explorer.url) get_profile() (siibra.features.connectivity.regional_connectivity.RegionalConnectivity method) get_profile_colorscale() (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_regional_map() (siibra.core.region.Region method) get_regional_mask() (siibra.core.region.Region method) get_registry() (in module siibra.core.concept) get_related_regions() (in module siibra.core.region) (siibra.core.region.Region method) get_resampled_template() (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method) get_shape() (siibra.volumes.providers.neuroglancer.NeuroglancerVolume method) (siibra.volumes.providers.nifti.NiftiProvider method) (siibra.volumes.providers.NiftiProvider method) get_snapshot_factory() (siibra.core.region.RegionRelationAssessments class method) get_space() (siibra.core.atlas.Atlas 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_volume() (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method) get_zoom() (in module siibra.explorer.url) GiftiMesh (class in siibra.volumes.providers) (class in siibra.volumes.providers.gifti) GiftiSurfaceLabeling (class in siibra.volumes.providers) (class in siibra.volumes.providers.gifti) GithubConnector (class in siibra.retrieval.repositories) 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.PointCloud property) (siibra.locations.pointcloud.PointCloud property) (siibra.PointCloud 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.PointCloud property) (siibra.locations.pointcloud.PointCloud property) (siibra.Point property) (siibra.PointCloud property)

HOMOLOGOUS (siibra.core.assignment.Qualification attribute) HttpRequest (class in siibra.retrieval) (class in siibra.retrieval.requests)

I

id (siibra.BoundingBox property) (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.CompoundFeature 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) (siibra.retrieval.EbrainsPublicDatasetConnector attribute) (siibra.retrieval.repositories.EbrainsPublicDatasetConnector attribute) Image (class in siibra.features.image.image) IMAGE_FORMATS (siibra.volumes.Volume attribute) (siibra.volumes.volume.Volume attribute) ImageAnchor (class in siibra.features.image.image) includes() (siibra.core.region.Region method) indexing_attributes (siibra.features.feature.CompoundFeature property) indices (siibra.features.feature.CompoundFeature property) init_oidc() (siibra.retrieval.EbrainsRequest class method) (siibra.retrieval.requests.EbrainsRequest class method) input_structure (siibra.volumes.parcellationmap.MapAssignment attribute) INSTANCE (siibra.retrieval.cache.WarmupLevel attribute) (siibra.WarmupLevel attribute) instance() (siibra.retrieval.cache.Cache class method) instance_id (siibra.retrieval.requests.GitlabProxy attribute) InstanceTable (class in siibra.commons) (class in siibra.vocabularies) InsufficientArgumentException intersect_line_segments() (siibra.locations.experimental.Plane method) (siibra.locations.Plane method) (siibra.Plane method)

intersect_mesh() (siibra.locations.experimental.Plane method) (siibra.locations.Plane method) (siibra.Plane method) intersection() (siibra.BoundingBox method) (siibra.core.region.Region method) (siibra.core.structure.BrainStructure method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.Point method) (siibra.PointCloud method) (siibra.volumes.Volume method) (siibra.volumes.volume.Volume method) intersection_over_first (siibra.commons.CompareMapsResult attribute) intersection_over_second (siibra.commons.CompareMapsResult attribute) intersection_over_union (siibra.commons.CompareMapsResult attribute) intersects() (siibra.core.structure.BrainStructure method) InvalidAllenAPIResponseException invert() (siibra.core.assignment.AnatomicalAssignment method) (siibra.core.assignment.Qualification method) io (siibra.volumes.providers.neuroglancer.NeuroglancerVolume property) is_allen_api_microarray_service_available() (in module siibra.livequeries.allen) is_exact (siibra.core.assignment.AnatomicalAssignment property) is_factory (siibra.retrieval.cache.WarmupParam attribute) is_float() (siibra.volumes.providers.neuroglancer.NeuroglancerVolume method) (siibra.volumes.providers.nifti.NiftiProvider method) (siibra.volumes.providers.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.BoundingBox property) (siibra.locations.BoundingBox property) (siibra.locations.boundingbox.BoundingBox property) is_registered() (siibra.retrieval.cache.Warmup class method) (siibra.Warmup class method) is_version_of (siibra.retrieval.datasets.EbrainsV3DatasetVersion property)

J

jobmemory_path (in module siibra.retrieval.cache)

K

key (siibra.core.concept.AtlasConcept property) (siibra.features.tabular.receptor_density_profile.ReceptorDensityProfile property) (siibra.features.tabular.ReceptorDensityProfile property) (siibra.volumes.Map property) (siibra.volumes.parcellationmap.Map property) (siibra.volumes.providers.neuroglancer.NeuroglancerScale attribute) 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) kwargs (siibra.retrieval.HttpRequest attribute) (siibra.retrieval.requests.HttpRequest attribute)

L

label (siibra.commons.MapIndex attribute) (siibra.locations.Point attribute) (siibra.locations.point.Point attribute) (siibra.Point attribute) (siibra.volumes.providers.neuroglancer.NeuroglancerSurfaceMesh attribute) (siibra.volumes.volume.FilteredVolume attribute) label_colors (siibra.locations.PointCloud property) (siibra.locations.pointcloud.PointCloud property) (siibra.PointCloud property) LABELLED (siibra.commons.MapType attribute) (siibra.MapType attribute) labels (siibra.locations.PointCloud attribute) (siibra.locations.pointcloud.PointCloud attribute) (siibra.PointCloud attribute) (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() (in module siibra.features.tabular) (in module siibra.features.tabular.cell_density_profile) layermap (siibra.livequeries.bigbrain.BigBrain1MicronPatchQuery attribute) 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.features.tabular.cell_density_profile.PolyLine method) lengths (siibra.features.tabular.cell_density_profile.PolyLine attribute) level (siibra.commons.LoggingContext attribute) (siibra.retrieval.cache.WarmupParam attribute) LICENSE (siibra.core.concept.AtlasConcept property) (siibra.features.Feature property) (siibra.features.feature.Feature property) (siibra.retrieval.datasets.EbrainsBaseDataset property) (siibra.retrieval.datasets.GenericDataset property) LiveQuery (class in siibra.livequeries.query) load() (siibra.volumes.sparsemap.SparseIndex class method) loader (siibra.livequeries.ebrains.EbrainsFeatureQuery attribute) (siibra.livequeries.EbrainsFeatureQuery attribute) LocalFileRepository (class in siibra.retrieval) (class in siibra.retrieval.repositories) Location (class in siibra.locations) (class in siibra.locations.location) location (siibra.features.anchor.AnatomicalAnchor property) (siibra.features.image.image.ImageAnchor property) (siibra.features.tabular.bigbrain_intensity_profile.BigBrainIntensityProfile property) (siibra.features.tabular.BigBrainIntensityProfile property) (siibra.features.tabular.cell_density_profile.CellDensityProfile property) (siibra.features.tabular.CellDensityProfile property) LOCATION_PRECISION_MM (in module siibra.livequeries.allen) logger (in module siibra) (in module siibra.commons) (in module siibra.features) (in module siibra.volumes) LoggingContext (class in siibra.commons) lower_threshold (siibra.livequeries.bigbrain.BigBrain1MicronPatchQuery attribute) 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.providers.neuroglancer.NeuroglancerVolume property) map_value (siibra.volumes.parcellationmap.MapAssignment attribute) MapAssignment (class in siibra.volumes.parcellationmap) MapIndex (class in siibra.commons) MapNotFound 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.retrieval.datasets.EbrainsBaseDataset 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.providers.neuroglancer.NeuroglancerVolume attribute) 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) maxpoint (siibra.BoundingBox attribute) (siibra.locations.BoundingBox attribute) (siibra.locations.boundingbox.BoundingBox attribute) merge() (in module siibra.volumes.volume) merge_meshes() (in module siibra.commons) MESH_FILE_LEFT (siibra.livequeries.bigbrain.WagstylProfileLoader attribute) MESH_FORMATS (siibra.volumes.Volume attribute) (siibra.volumes.volume.Volume attribute) MI() (in module siibra.commons) min_int32 (in module siibra.explorer.url) minpoint (siibra.BoundingBox attribute) (siibra.locations.BoundingBox attribute) (siibra.locations.boundingbox.BoundingBox attribute) modality (siibra.core.concept.AtlasConcept attribute) (siibra.features.Feature property) (siibra.features.feature.Feature property) module siibra siibra.commons siibra.configuration siibra.configuration.configuration siibra.configuration.factory siibra.core siibra.core.assignment siibra.core.atlas siibra.core.concept siibra.core.parcellation siibra.core.region siibra.core.space siibra.core.structure siibra.exceptions siibra.explorer siibra.explorer.url siibra.explorer.util siibra.features siibra.features.anchor siibra.features.connectivity 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 siibra.features.dataset.ebrains siibra.features.feature siibra.features.image siibra.features.image.image siibra.features.image.sections siibra.features.image.volume_of_interest siibra.features.tabular 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 siibra.livequeries.allen siibra.livequeries.bigbrain siibra.livequeries.ebrains siibra.livequeries.query siibra.locations siibra.locations.boundingbox siibra.locations.experimental siibra.locations.location siibra.locations.point siibra.locations.pointcloud siibra.retrieval siibra.retrieval.cache siibra.retrieval.datasets siibra.retrieval.exceptions siibra.retrieval.repositories siibra.retrieval.requests siibra.vocabularies siibra.volumes siibra.volumes.parcellationmap siibra.volumes.providers siibra.volumes.providers.freesurfer siibra.volumes.providers.gifti siibra.volumes.providers.neuroglancer siibra.volumes.providers.nifti siibra.volumes.providers.provider siibra.volumes.sparsemap siibra.volumes.volume

MorphometryVolumeOfInterest (class in siibra.features.image) (class in siibra.features.image.volume_of_interest) MRIVolumeOfInterest (class in siibra.features.image) (class in siibra.features.image.volume_of_interest) msg (siibra.retrieval.requests.SiibraHttpRequestError attribute) (siibra.retrieval.SiibraHttpRequestError attribute) msg_if_not_cached (siibra.retrieval.HttpRequest attribute) (siibra.retrieval.requests.HttpRequest attribute) MultiSourcedRequest (class in siibra.retrieval.requests) MultiSourceRequestException MUS_MUSCULUS (siibra.commons.Species attribute)

N

name (siibra.core.concept.AtlasConcept attribute) (siibra.core.parcellation.ParcellationVersion attribute) (siibra.features.connectivity.functional_connectivity.FunctionalConnectivity property) (siibra.features.connectivity.FunctionalConnectivity property) (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.CompoundFeature property) (siibra.features.feature.Feature property) (siibra.features.image.image.Image property) (siibra.features.tabular.cortical_profile.CorticalProfile property) (siibra.features.tabular.regional_timeseries_activity.RegionalBOLD property) (siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity property) (siibra.features.tabular.RegionalBOLD 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 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) NeuroglancerMesh (class in siibra.volumes.providers) (class in siibra.volumes.providers.neuroglancer)

NeuroglancerProvider (class in siibra.volumes.providers) (class in siibra.volumes.providers.neuroglancer) NeuroglancerScale (class in siibra.volumes.providers.neuroglancer) NeuroglancerSurfaceMesh (class in siibra.volumes.providers.neuroglancer) NeuroglancerVolume (class in siibra.volumes.providers.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) new_labels (siibra.volumes.volume.ReducedVolume attribute) next() (siibra.volumes.providers.neuroglancer.NeuroglancerScale method) next_id (siibra.core.parcellation.ParcellationVersion attribute) NiftiProvider (class in siibra.volumes.providers) (class in siibra.volumes.providers.nifti) NoMapAvailableError NoneCoordinateSuppliedError NonUniqueIndexError nonzero_coordinates() (in module siibra.commons) NoPredifinedColormapException normal (siibra.locations.experimental.Plane property) (siibra.locations.Plane property) (siibra.Plane property) NoSiibraConfigMirrorsAvailableException, [1] NotFoundException NoVolumeFound num_volumes (siibra.volumes.sparsemap.SparseIndex property) NZCACHE (in module siibra.commons)

O

OTHER_VERSION (siibra.core.assignment.Qualification attribute) OVERLAPS (siibra.core.assignment.Qualification attribute)

OwncloudConnector (class in siibra.retrieval) (class in siibra.retrieval.repositories)

P

pairwise_union() (in module siibra.locations) paradigm (siibra.features.connectivity.functional_connectivity.FunctionalConnectivity attribute) (siibra.features.connectivity.FunctionalConnectivity attribute) (siibra.features.tabular.regional_timeseries_activity.RegionalBOLD attribute) (siibra.features.tabular.RegionalBOLD attribute) params (siibra.retrieval.EbrainsRequest attribute) (siibra.retrieval.requests.EbrainsRequest attribute) Parcellation (class in siibra.core.parcellation) parcellation (siibra.core.parcellation.ParcellationVersion attribute) (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) parent (siibra.core.region.Region attribute) parse() (siibra.locations.Point static method) (siibra.locations.point.Point static method) (siibra.Point static method) parse_from_region() (siibra.core.region.RegionRelationAssessments class method) parse_gene() (in module siibra.livequeries.allen) parse_id_arg() (siibra.core.region.RegionRelationAssessments static method) parse_relation_assessment() (siibra.core.assignment.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) ParseCompoundFeatureIdException ParseLiveQueryIdException patch (siibra.features.tabular.cell_density_profile.CellDensityProfile attribute) (siibra.features.tabular.CellDensityProfile attribute) Plane (class in siibra) (class in siibra.locations) (class in siibra.locations.experimental) PLIVolumeOfInterest (class in siibra.features.image) (class in siibra.features.image.volume_of_interest) plot() (siibra.features.connectivity.regional_connectivity.RegionalConnectivity method) (siibra.features.Feature method) (siibra.features.feature.CompoundFeature 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.layerwise_cell_density.LayerwiseCellDensity method) (siibra.features.tabular.LayerwiseCellDensity 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) Point (class in siibra) (class in siibra.locations) (class in siibra.locations.point) PointCloud (class in siibra) (class in siibra.locations) (class in siibra.locations.pointcloud) polar_plot() (siibra.features.tabular.receptor_density_fingerprint.ReceptorDensityFingerprint method) (siibra.features.tabular.ReceptorDensityFingerprint method) poly_rev() (in module siibra.features.tabular.cell_density_profile) poly_srt() (in module siibra.features.tabular.cell_density_profile) PolyLine (class in siibra.features.tabular.cell_density_profile) post (siibra.retrieval.HttpRequest attribute) (siibra.retrieval.requests.HttpRequest attribute) post_process() (in module siibra.explorer.util) prev() (siibra.volumes.providers.neuroglancer.NeuroglancerScale method) prev_id (siibra.core.parcellation.ParcellationVersion attribute) probs (siibra.volumes.sparsemap.SparseIndex attribute) profile (siibra.features.image.BigBrain1MicronPatch property) (siibra.features.image.sections.BigBrain1MicronPatch property) profile_labels (siibra.livequeries.bigbrain.WagstylProfileLoader property) PROFILES_FILE_LEFT (siibra.livequeries.bigbrain.WagstylProfileLoader attribute) project_points() (siibra.locations.experimental.Plane method) (siibra.locations.Plane method) (siibra.Plane method) provider (siibra.volumes.providers.provider.SubvolumeProvider attribute) providers (siibra.volumes.Volume property) (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 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 property) (siibra.volumes.volume.Volume property) pts (siibra.features.tabular.cell_density_profile.PolyLine attribute) publications (siibra.core.concept.AtlasConcept property)

Q

Qualification (class in siibra.core.assignment) qualification (siibra.core.assignment.AnatomicalAssignment attribute) query() (siibra.livequeries.allen.AllenBrainAtlasQuery method) (siibra.livequeries.AllenBrainAtlasQuery method) (siibra.livequeries.bigbrain.BigBrain1MicronPatchQuery 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.assignment.AnatomicalAssignment attribute) QUIET (in module siibra) (in module siibra.commons)

R

RATTUS_NORVEGICUS (siibra.commons.Species attribute) read_as_bytesio() (in module siibra.retrieval.requests) reassign_union() (in module siibra.locations) receptor (siibra.features.tabular.receptor_density_profile.ReceptorDensityProfile attribute) (siibra.features.tabular.ReceptorDensityProfile attribute) receptor_fullname (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) ReducedVolume (class in siibra.volumes.volume) refresh (siibra.retrieval.HttpRequest attribute) (siibra.retrieval.requests.HttpRequest attribute) reftag (siibra.retrieval.GitlabConnector attribute) (siibra.retrieval.repositories.GithubConnector attribute) (siibra.retrieval.repositories.GitlabConnector attribute) 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.features.connectivity.regional_connectivity.RegionalConnectivity attribute) (siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity attribute) (siibra.volumes.Map property) (siibra.volumes.parcellationmap.Map property) register_cleanup() (siibra.configuration.Configuration class method) (siibra.configuration.configuration.Configuration class method) register_warmup_fn() (siibra.retrieval.cache.Warmup class method) (siibra.Warmup class method) registry() (siibra.core.concept.AtlasConcept class method) relevance (siibra.features.image.BigBrain1MicronPatch attribute) (siibra.features.image.sections.BigBrain1MicronPatch attribute) REMOVE_FROM_NAME (in module siibra.commons) render_ascii_tree() (in module siibra.features) 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.providers.neuroglancer.NeuroglancerScale property) res_nm (siibra.volumes.providers.neuroglancer.NeuroglancerScale attribute) resample_img_to_img() (in module siibra.commons) resolves() (siibra.volumes.providers.neuroglancer.NeuroglancerScale method) rgb (siibra.core.region.Region attribute) 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.features.tabular.cell_density_profile.PolyLine method) sample_locations() (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method) sanitize_id() (in module siibra.explorer.url) save() (siibra.volumes.sparsemap.SparseIndex method) scales (siibra.volumes.providers.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.GithubConnector 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) section (siibra.features.image.BigBrain1MicronPatch property) (siibra.features.image.sections.BigBrain1MicronPatch property) (siibra.features.tabular.cell_density_profile.CellDensityProfile attribute) (siibra.features.tabular.CellDensityProfile attribute) separator (in module siibra.explorer.util) set_cache_size() (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.BoundingBox property) (siibra.features.tabular.cell_density_profile.CellDensityProfile property) (siibra.features.tabular.CellDensityProfile property) (siibra.locations.BoundingBox property) (siibra.locations.boundingbox.BoundingBox property) (siibra.volumes.providers.neuroglancer.NeuroglancerVolume property) (siibra.volumes.sparsemap.SparseIndex attribute) (siibra.volumes.sparsemap.SparseMap property) shift() (siibra.BoundingBox method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method) shift_ng_transfrom() (in module siibra.volumes.providers.neuroglancer) shortname (siibra.core.concept.AtlasConcept attribute) sidedness() (siibra.locations.experimental.Plane method) (siibra.locations.Plane method) (siibra.Plane method) sigma (siibra.locations.Point attribute) (siibra.locations.point.Point attribute) (siibra.locations.PointCloud property) (siibra.locations.pointcloud.PointCloud property) (siibra.Point attribute) (siibra.PointCloud property) sigma_mm (siibra.BoundingBox attribute) (siibra.locations.BoundingBox attribute) (siibra.locations.boundingbox.BoundingBox attribute) siibra module siibra.commons module siibra.configuration module siibra.configuration.configuration module siibra.configuration.factory module siibra.core module siibra.core.assignment module siibra.core.atlas module siibra.core.concept module siibra.core.parcellation module siibra.core.region module siibra.core.space module siibra.core.structure module siibra.exceptions module siibra.explorer module siibra.explorer.url module siibra.explorer.util module siibra.features module siibra.features.anchor module siibra.features.connectivity module 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 siibra.features.dataset.ebrains module siibra.features.feature module siibra.features.image module siibra.features.image.image module siibra.features.image.sections module siibra.features.image.volume_of_interest module siibra.features.tabular module 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 siibra.livequeries.allen module siibra.livequeries.bigbrain module siibra.livequeries.ebrains module siibra.livequeries.query module siibra.locations module siibra.locations.boundingbox module siibra.locations.experimental module siibra.locations.location module siibra.locations.point module siibra.locations.pointcloud module siibra.retrieval module siibra.retrieval.cache module siibra.retrieval.datasets module siibra.retrieval.exceptions module siibra.retrieval.repositories module siibra.retrieval.requests module siibra.vocabularies module siibra.volumes module siibra.volumes.parcellationmap module siibra.volumes.providers module siibra.volumes.providers.freesurfer module siibra.volumes.providers.gifti module siibra.volumes.providers.neuroglancer module siibra.volumes.providers.nifti module siibra.volumes.providers.provider module siibra.volumes.sparsemap module siibra.volumes.volume module SIIBRA_CACHEDIR (in module siibra.commons) SIIBRA_LOG_LEVEL (in module siibra.commons) SIIBRA_MAX_FETCH_SIZE_BYTES (in module siibra.commons) siibra_tqdm() (in module siibra.commons) (in module siibra.features) SIIBRA_USE_CONFIGURATION (in module siibra.commons) SIIBRA_USE_LOCAL_SNAPSPOT (in module siibra.commons) SiibraHttpRequestError, [1] size (siibra.retrieval.cache.Cache property) (siibra.volumes.providers.neuroglancer.NeuroglancerScale attribute) SIZE_GIB (siibra.retrieval.cache.Cache attribute) SKIP_CACHEINIT_MAINTENANCE (in module siibra.commons) snake2camel() (in module siibra.commons) source_volumes (siibra.volumes.volume.ReducedVolume attribute) Space (class in siibra.core.space) space (siibra.features.anchor.AnatomicalAnchor property) (siibra.features.image.image.ImageAnchor property) (siibra.locations.experimental.Plane attribute) (siibra.locations.Location property) (siibra.locations.location.Location property) (siibra.locations.Plane attribute) (siibra.Plane attribute) (siibra.volumes.Map property) (siibra.volumes.parcellationmap.Map property) (siibra.volumes.Volume property) (siibra.volumes.volume.Volume property) spaces (siibra.core.atlas.Atlas property) (siibra.core.region.Region property) SPACEWARP_IDS (siibra.locations.Location attribute) (siibra.locations.location.Location attribute) SPACEWARP_SERVER (siibra.locations.Location attribute) (siibra.locations.location.Location attribute) SpaceWarpingFailedError 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) spec_loaders (siibra.configuration.Configuration attribute) (siibra.configuration.configuration.Configuration attribute) 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.locations.Location property) (siibra.locations.location.Location property) (siibra.volumes.Map property) (siibra.volumes.parcellationmap.Map property) (siibra.volumes.Volume property) (siibra.volumes.volume.Volume property) srctype (siibra.volumes.providers.provider.SubvolumeProvider attribute) STATISTICAL (siibra.commons.MapType attribute) (siibra.MapType attribute) status_code (siibra.retrieval.requests.SiibraHttpRequestError attribute) (siibra.retrieval.SiibraHttpRequestError 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) subject (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.providers.provider) SubvolumeProvider.UseCaching (class in siibra.volumes.providers.provider) SUPPORTED_FORMATS (siibra.volumes.Volume attribute) (siibra.volumes.volume.Volume attribute) supported_prefix (in module siibra.explorer.url) supported_spaces (siibra.core.region.Region property)

T

T (in module siibra.commons) (in module siibra.core.assignment) (in module siibra.core.concept) Tabular (class in siibra.features.tabular.tabular) TagNotFoundException, [1] TEST (siibra.retrieval.cache.WarmupLevel attribute) (siibra.WarmupLevel attribute) THICKNESSES_FILE_LEFT (siibra.livequeries.bigbrain.WagstylProfileLoader attribute) threshold (siibra.volumes.volume.FilteredVolume attribute) THRESHOLD_STATISTICAL_MAPS (in module siibra.core.region) timestep (siibra.features.tabular.regional_timeseries_activity.RegionalTimeseriesActivity attribute) to_sparse() (siibra.volumes.Map method) (siibra.volumes.parcellationmap.Map method) to_zip() (siibra.features.Feature method) (siibra.features.feature.Feature method) TracingConnectivity (class in siibra.features.connectivity) (class in siibra.features.connectivity.tracing_connectivity) transform() (siibra.BoundingBox method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method) (siibra.locations.Location method) (siibra.locations.location.Location method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.Point method) (siibra.PointCloud method)

transform_nm (siibra.volumes.providers.neuroglancer.NeuroglancerVolume property) translate_cae() (siibra.core.region.RegionRelationAssessments class method) translate_pes() (siibra.core.region.RegionRelationAssessments class method) translate_pevs() (siibra.core.region.RegionRelationAssessments class method) translation_matrix() (in module siibra.commons) 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) TypePublication (class in siibra.commons) TYPES (in module siibra.features)

U

unify_stringlist() (in module siibra.commons) union() (siibra.locations.Location static method) (siibra.locations.location.Location static method) unit (siibra.features.tabular.cortical_profile.CorticalProfile property) (siibra.features.tabular.gene_expression.GeneExpressions attribute) (siibra.features.tabular.GeneExpressions attribute) (siibra.features.tabular.layerwise_cell_density.LayerwiseCellDensity attribute) (siibra.features.tabular.LayerwiseCellDensity attribute) (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) (siibra.retrieval.HttpRequest attribute) (siibra.retrieval.repositories.ZipfileConnector attribute) (siibra.retrieval.requests.HttpRequest attribute) (siibra.retrieval.requests.SiibraHttpRequestError attribute) (siibra.retrieval.SiibraHttpRequestError attribute) (siibra.retrieval.ZipfileConnector attribute) (siibra.volumes.providers.neuroglancer.NeuroglancerVolume attribute)

urls (siibra.core.concept.AtlasConcept property) (siibra.features.Feature property) (siibra.features.feature.Feature 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) USE_CACHE (siibra.volumes.providers.neuroglancer.NeuroglancerVolume attribute) use_configuration() (siibra.configuration.Configuration class method) (siibra.configuration.configuration.Configuration class method) use_version (siibra.retrieval.EbrainsPublicDatasetConnector attribute) (siibra.retrieval.repositories.EbrainsPublicDatasetConnector attribute) USER_AGENT_HEADER (in module siibra.retrieval.requests)

V

values() (siibra.commons.InstanceTable method) (siibra.vocabularies.InstanceTable method) variant (siibra.volumes.Volume attribute) (siibra.volumes.volume.Volume attribute) variants (siibra.volumes.providers.gifti.GiftiMesh property) (siibra.volumes.providers.GiftiMesh property) verb (siibra.core.assignment.Qualification property) VERBOSE (in module siibra) (in module siibra.commons) version (siibra.core.parcellation.Parcellation attribute) (siibra.features.dataset.ebrains.EbrainsDataFeature attribute) (siibra.features.dataset.EbrainsDataFeature attribute) VERSION_BLACKLIST_WORDS (in module siibra.core.atlas) version_changelog (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) versions (siibra.retrieval.EbrainsPublicDatasetConnector attribute) (siibra.retrieval.repositories.EbrainsPublicDatasetConnector attribute) vertex (siibra.features.image.BigBrain1MicronPatch attribute) (siibra.features.image.sections.BigBrain1MicronPatch attribute)

Volume (class in siibra.volumes) (class in siibra.volumes.volume) volume (siibra.BoundingBox property) (siibra.commons.MapIndex attribute) (siibra.features.image.image.ImageAnchor attribute) (siibra.locations.BoundingBox property) (siibra.locations.boundingbox.BoundingBox property) (siibra.locations.Point property) (siibra.locations.point.Point property) (siibra.locations.PointCloud property) (siibra.locations.pointcloud.PointCloud property) (siibra.Point property) (siibra.PointCloud property) (siibra.volumes.parcellationmap.MapAssignment attribute) (siibra.volumes.providers.gifti.GiftiMesh attribute) (siibra.volumes.providers.GiftiMesh attribute) (siibra.volumes.providers.neuroglancer.NeuroglancerMesh attribute) (siibra.volumes.providers.neuroglancer.NeuroglancerScale attribute) (siibra.volumes.providers.NeuroglancerMesh attribute) (siibra.volumes.volume.ComponentSpatialProperties attribute) VolumeData (in module siibra.volumes.providers.provider) VolumeProvider (class in siibra.volumes.providers.provider) volumes (siibra.core.space.Space attribute) (siibra.volumes.Map attribute) (siibra.volumes.parcellationmap.Map attribute) voxel_offset (siibra.volumes.providers.neuroglancer.NeuroglancerScale attribute) voxels (siibra.volumes.sparsemap.SparseIndex attribute)

W

WagstylProfileLoader (class in siibra.livequeries.bigbrain) want_commit (siibra.retrieval.GitlabConnector property) (siibra.retrieval.repositories.GitlabConnector property) warm_cache() (in module siibra) Warmup (class in siibra) (class in siibra.retrieval.cache) warmup() (siibra.retrieval.cache.Warmup class method) (siibra.Warmup class method) WarmupLevel (class in siibra) (class in siibra.retrieval.cache) WarmupParam (class in siibra.retrieval.cache) WarmupRegException

warp() (siibra.BoundingBox method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method) (siibra.locations.Location method) (siibra.locations.location.Location method) (siibra.locations.Point method) (siibra.locations.point.Point method) (siibra.locations.PointCloud method) (siibra.locations.pointcloud.PointCloud method) (siibra.Point method) (siibra.PointCloud method) weighted_mean_of_first (siibra.commons.CompareMapsResult attribute) weighted_mean_of_second (siibra.commons.CompareMapsResult attribute)

X

XPCTVolumeOfInterest (class in siibra.features.image) (class in siibra.features.image.volume_of_interest)

Y

y_rotation_matrix() (in module siibra.commons)

Z

z (siibra.volumes.providers.provider.SubvolumeProvider attribute) ZeroVolumeBoundingBox ZipContainedNiftiProvider (class in siibra.volumes.providers.nifti) zipfile (siibra.retrieval.repositories.ZipfileConnector property) (siibra.retrieval.repositories.ZipfileConnector.ZipFileLoader attribute) (siibra.retrieval.ZipfileConnector property) (siibra.retrieval.ZipfileConnector.ZipFileLoader attribute) 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) ZippedFreesurferAnnot (class in siibra.volumes.providers) (class in siibra.volumes.providers.freesurfer) zoom() (siibra.BoundingBox method) (siibra.locations.BoundingBox method) (siibra.locations.boundingbox.BoundingBox method)