allensdk.core package¶
Subpackages¶
Submodules¶
- allensdk.core.auth_config module
- allensdk.core.authentication module
- allensdk.core.brain_observatory_cache module
- allensdk.core.brain_observatory_nwb_data_set module
BrainObservatoryNwbDataSet
BrainObservatoryNwbDataSet.FILE_METADATA_MAPPING
BrainObservatoryNwbDataSet.MOTION_CORRECTION_DATASETS
BrainObservatoryNwbDataSet.PIPELINE_DATASET
BrainObservatoryNwbDataSet.STIMULUS_TABLE_TYPES
BrainObservatoryNwbDataSet.SUPPORTED_PIPELINE_VERSION
BrainObservatoryNwbDataSet.get_cell_specimen_ids()
BrainObservatoryNwbDataSet.get_cell_specimen_indices()
BrainObservatoryNwbDataSet.get_corrected_fluorescence_traces()
BrainObservatoryNwbDataSet.get_demixed_traces()
BrainObservatoryNwbDataSet.get_dff_traces()
BrainObservatoryNwbDataSet.get_fluorescence_timestamps()
BrainObservatoryNwbDataSet.get_fluorescence_traces()
BrainObservatoryNwbDataSet.get_locally_sparse_noise_stimulus_template()
BrainObservatoryNwbDataSet.get_max_projection()
BrainObservatoryNwbDataSet.get_metadata()
BrainObservatoryNwbDataSet.get_motion_correction()
BrainObservatoryNwbDataSet.get_neuropil_r()
BrainObservatoryNwbDataSet.get_neuropil_traces()
BrainObservatoryNwbDataSet.get_pupil_location()
BrainObservatoryNwbDataSet.get_pupil_size()
BrainObservatoryNwbDataSet.get_roi_ids()
BrainObservatoryNwbDataSet.get_roi_mask()
BrainObservatoryNwbDataSet.get_roi_mask_array()
BrainObservatoryNwbDataSet.get_running_speed()
BrainObservatoryNwbDataSet.get_session_type()
BrainObservatoryNwbDataSet.get_stimulus()
BrainObservatoryNwbDataSet.get_stimulus_epoch_table()
BrainObservatoryNwbDataSet.get_stimulus_table()
BrainObservatoryNwbDataSet.get_stimulus_template()
BrainObservatoryNwbDataSet.list_stimuli()
BrainObservatoryNwbDataSet.number_of_cells
BrainObservatoryNwbDataSet.save_analysis_arrays()
BrainObservatoryNwbDataSet.save_analysis_dataframes()
BrainObservatoryNwbDataSet.stimulus_search
align_running_speed()
get_epoch_mask_list()
- allensdk.core.cache_method_utilities module
- allensdk.core.cell_types_cache module
CellTypesCache
CellTypesCache.CELLS_KEY
CellTypesCache.EPHYS_DATA_KEY
CellTypesCache.EPHYS_FEATURES_KEY
CellTypesCache.EPHYS_SWEEPS_KEY
CellTypesCache.MANIFEST_VERSION
CellTypesCache.MARKER_KEY
CellTypesCache.MORPHOLOGY_FEATURES_KEY
CellTypesCache.RECONSTRUCTION_KEY
CellTypesCache.build_manifest()
CellTypesCache.get_all_features()
CellTypesCache.get_cells()
CellTypesCache.get_ephys_data()
CellTypesCache.get_ephys_features()
CellTypesCache.get_ephys_sweeps()
CellTypesCache.get_morphology_features()
CellTypesCache.get_reconstruction()
CellTypesCache.get_reconstruction_markers()
ReporterStatus
- allensdk.core.dat_utilities module
- allensdk.core.dataframe_utils module
- allensdk.core.exceptions module
- allensdk.core.h5_utilities module
- allensdk.core.json_utilities module
- allensdk.core.mouse_connectivity_cache module
MouseConnectivityCache
MouseConnectivityCache.ALIGNMENT3D_KEY
MouseConnectivityCache.DATA_MASK_KEY
MouseConnectivityCache.DEFAULT_STRUCTURE_SET_IDS
MouseConnectivityCache.DEFORMATION_FIELD_HEADER_KEY
MouseConnectivityCache.DEFORMATION_FIELD_VOXEL_KEY
MouseConnectivityCache.DFMFLD_RESOLUTIONS
MouseConnectivityCache.EXPERIMENTS_KEY
MouseConnectivityCache.INJECTION_DENSITY_KEY
MouseConnectivityCache.INJECTION_FRACTION_KEY
MouseConnectivityCache.MANIFEST_VERSION
MouseConnectivityCache.PROJECTION_DENSITY_KEY
MouseConnectivityCache.STRUCTURE_UNIONIZES_KEY
MouseConnectivityCache.SUMMARY_STRUCTURE_SET_ID
MouseConnectivityCache.add_manifest_paths()
MouseConnectivityCache.default_structure_ids
MouseConnectivityCache.filter_experiments()
MouseConnectivityCache.filter_structure_unionizes()
MouseConnectivityCache.get_affine_parameters()
MouseConnectivityCache.get_data_mask()
MouseConnectivityCache.get_deformation_field()
MouseConnectivityCache.get_experiment_structure_unionizes()
MouseConnectivityCache.get_experiments()
MouseConnectivityCache.get_injection_density()
MouseConnectivityCache.get_injection_fraction()
MouseConnectivityCache.get_projection_density()
MouseConnectivityCache.get_projection_matrix()
MouseConnectivityCache.get_structure_unionizes()
MouseConnectivityCache.rank_structures()
- allensdk.core.nwb_data_set module
NwbDataSet
NwbDataSet.DEPRECATED_SPIKE_TIMES
NwbDataSet.SPIKE_TIMES
NwbDataSet.fill_sweep_responses()
NwbDataSet.get_experiment_sweep_numbers()
NwbDataSet.get_pipeline_version()
NwbDataSet.get_spike_times()
NwbDataSet.get_sweep()
NwbDataSet.get_sweep_metadata()
NwbDataSet.get_sweep_numbers()
NwbDataSet.set_spike_times()
NwbDataSet.set_sweep()
- allensdk.core.obj_utilities module
- allensdk.core.ontology module
- allensdk.core.ophys_experiment_session_id_mapping module
- allensdk.core.pickle_utils module
- allensdk.core.reference_space module
ReferenceSpace
ReferenceSpace.check_and_write()
ReferenceSpace.check_coverage()
ReferenceSpace.direct_voxel_counts()
ReferenceSpace.direct_voxel_map
ReferenceSpace.downsample()
ReferenceSpace.export_itksnap_labels()
ReferenceSpace.get_slice_image()
ReferenceSpace.make_structure_mask()
ReferenceSpace.many_structure_masks()
ReferenceSpace.remove_unassigned()
ReferenceSpace.return_mask_cb()
ReferenceSpace.total_voxel_counts()
ReferenceSpace.total_voxel_map
ReferenceSpace.validate_structures()
ReferenceSpace.write_itksnap_labels()
- allensdk.core.reference_space_cache module
ReferenceSpaceCache
ReferenceSpaceCache.ANNOTATION_KEY
ReferenceSpaceCache.MANIFEST_VERSION
ReferenceSpaceCache.REFERENCE_SPACE_VERSION_KEY
ReferenceSpaceCache.STRUCTURES_KEY
ReferenceSpaceCache.STRUCTURE_MASK_KEY
ReferenceSpaceCache.STRUCTURE_MESH_KEY
ReferenceSpaceCache.STRUCTURE_TREE_KEY
ReferenceSpaceCache.TEMPLATE_KEY
ReferenceSpaceCache.add_manifest_paths()
ReferenceSpaceCache.get_annotation_volume()
ReferenceSpaceCache.get_reference_space()
ReferenceSpaceCache.get_structure_mask()
ReferenceSpaceCache.get_structure_mesh()
ReferenceSpaceCache.get_structure_tree()
ReferenceSpaceCache.get_template_volume()
ReferenceSpaceCache.validate_structure_id()
ReferenceSpaceCache.validate_structure_ids()
- allensdk.core.simple_tree module
SimpleTree
SimpleTree.ancestor_ids()
SimpleTree.ancestors()
SimpleTree.child_ids()
SimpleTree.children()
SimpleTree.descendant_ids()
SimpleTree.descendants()
SimpleTree.filter_nodes()
SimpleTree.node()
SimpleTree.node_ids()
SimpleTree.nodes()
SimpleTree.nodes_by_property()
SimpleTree.parent()
SimpleTree.parent_id()
SimpleTree.parent_ids()
SimpleTree.parents()
SimpleTree.value_map()
- allensdk.core.sitk_utilities module
- allensdk.core.structure_tree module
StructureTree
StructureTree.clean_structures()
StructureTree.collect_sets()
StructureTree.data_transforms()
StructureTree.export_label_description()
StructureTree.get_ancestor_id_map()
StructureTree.get_colormap()
StructureTree.get_id_acronym_map()
StructureTree.get_name_map()
StructureTree.get_structure_sets()
StructureTree.get_structures_by_acronym()
StructureTree.get_structures_by_id()
StructureTree.get_structures_by_name()
StructureTree.get_structures_by_set_id()
StructureTree.has_overlaps()
StructureTree.hex_to_rgb()
StructureTree.path_to_list()
StructureTree.renames()
StructureTree.structure_descends_from()
StructureTree.whitelist()
- allensdk.core.swc module
Compartment
Marker
Morphology
Morphology.APICAL_DENDRITE
Morphology.AXON
Morphology.BASAL_DENDRITE
Morphology.DENDRITE
Morphology.NODE_TYPES
Morphology.SOMA
Morphology.append()
Morphology.apply_affine()
Morphology.change_parent()
Morphology.children_of()
Morphology.compartment_index
Morphology.compartment_index_by_type()
Morphology.compartment_list
Morphology.compartment_list_by_type()
Morphology.convert_type()
Morphology.delete_tree()
Morphology.find()
Morphology.node()
Morphology.num_nodes
Morphology.num_trees
Morphology.parent_of()
Morphology.root
Morphology.save()
Morphology.soma
Morphology.sparsify()
Morphology.strip_all_other_types()
Morphology.strip_type()
Morphology.stumpify_axon()
Morphology.tree()
Morphology.write()
read_marker_file()
read_swc()
- allensdk.core.typing module
- allensdk.core.utilities module