Index _ | A | C | D | E | F | L | M | O | P | Q | S | U _ __init__() (skeleton_keys.cmds.calc_histogram_loadings.CalcHistogramLoadingsParameters method) (skeleton_keys.cmds.depth_profiles_from_aligned_coords.ProfilesFromAlignedCoordsParameters method) (skeleton_keys.cmds.depth_profiles_from_aligned_swcs.ProfilesFromAlignedSwcsParameters method) (skeleton_keys.cmds.layer_aligned_coords.LayerAlignedCoordsSchema method) (skeleton_keys.cmds.layer_aligned_swc.LayerAlignedSwcSchema method) (skeleton_keys.cmds.postprocess_features.PostprocessFeaturesParameters method) (skeleton_keys.cmds.process_morphology_features.ProcessMorphologyFeaturesParameters method) (skeleton_keys.cmds.upright_corrected_swc.UprightCorrectedSwcSchema method) A analyze_depth_profiles() (in module skeleton_keys.cmds.process_morphology_features) apply_loadings_to_profiles() (in module skeleton_keys.depth_profile) C CalcHistogramLoadingsParameters (class in skeleton_keys.cmds.calc_histogram_loadings) calculate_length_of_path_list() (in module skeleton_keys.layer_alignment) calculate_pca_transforms_and_loadings() (in module skeleton_keys.depth_profile) convert_and_translate_snapped_to_microns() (in module skeleton_keys.drawings) corrected_without_uprighting_morph() (in module skeleton_keys.upright) cortex_thickness_aligned_y_values() (in module skeleton_keys.layer_alignment) cortex_thickness_aligned_y_values_for_morph() (in module skeleton_keys.layer_alignment) D default_features() (in module skeleton_keys.feature_definition) default_query_engine() (in module skeleton_keys.database_queries) determine_flip_switch() (in module skeleton_keys.database_queries) E earthmover_distance_between_compartments() (in module skeleton_keys.depth_profile) F fractions_within_layer() (in module skeleton_keys.layer_alignment) L layer_aligned_y_values() (in module skeleton_keys.layer_alignment) layer_aligned_y_values_for_morph() (in module skeleton_keys.layer_alignment) layer_locations() (in module skeleton_keys.layer_alignment) layer_polygons_from_database() (in module skeleton_keys.database_queries) layer_side_depths() (in module skeleton_keys.layer_alignment) LayerAlignedCoordsSchema (class in skeleton_keys.cmds.layer_aligned_coords) LayerAlignedSwcSchema (class in skeleton_keys.cmds.layer_aligned_swc) load_default_layer_template() (in module skeleton_keys.io) load_swc_as_dataframe() (in module skeleton_keys.io) M module skeleton_keys.cmds skeleton_keys.database_queries skeleton_keys.depth_profile skeleton_keys.drawings skeleton_keys.feature_definition skeleton_keys.io skeleton_keys.layer_alignment skeleton_keys.plotting skeleton_keys.slice_angle skeleton_keys.upright O overlap_between_compartments() (in module skeleton_keys.depth_profile) P path_dist_from_node() (in module skeleton_keys.layer_alignment) pia_wm_soma_from_database() (in module skeleton_keys.database_queries) plot_cortical_cell() (in module skeleton_keys.plotting) plot_layer_polygon() (in module skeleton_keys.plotting) PostprocessFeaturesParameters (class in skeleton_keys.cmds.postprocess_features) ProcessMorphologyFeaturesParameters (class in skeleton_keys.cmds.process_morphology_features) ProfilesFromAlignedCoordsParameters (class in skeleton_keys.cmds.depth_profiles_from_aligned_coords) ProfilesFromAlignedSwcsParameters (class in skeleton_keys.cmds.depth_profiles_from_aligned_swcs) Q query_cell_depth() (in module skeleton_keys.database_queries) query_for_cortical_surfaces() (in module skeleton_keys.database_queries) query_for_image_series_id() (in module skeleton_keys.database_queries) query_for_layer_polygons() (in module skeleton_keys.database_queries) query_for_soma_center() (in module skeleton_keys.database_queries) query_for_swc_file() (in module skeleton_keys.database_queries) query_marker_file() (in module skeleton_keys.database_queries) query_pinning_info() (in module skeleton_keys.database_queries) S save_lims_surface_and_layers_to_json() (in module skeleton_keys.io) select_and_convert_depth_columns() (in module skeleton_keys.cmds.process_morphology_features) setup_interpolator_without_nan() (in module skeleton_keys.layer_alignment) shrinkage_factor_from_database() (in module skeleton_keys.database_queries) skeleton_keys.cmds module skeleton_keys.database_queries module skeleton_keys.depth_profile module skeleton_keys.drawings module skeleton_keys.feature_definition module skeleton_keys.io module skeleton_keys.layer_alignment module skeleton_keys.plotting module skeleton_keys.slice_angle module skeleton_keys.upright module slice_angle_tilt() (in module skeleton_keys.slice_angle) snap_hand_drawn_polygons() (in module skeleton_keys.drawings) soma_distance_from_pia() (in module skeleton_keys.cmds.upright_corrected_swc) soma_locations() (in module skeleton_keys.cmds.process_morphology_features) specimen_morph_features() (in module skeleton_keys.cmds.process_morphology_features) step_all_nodes() (in module skeleton_keys.layer_alignment) swc_paths_from_database() (in module skeleton_keys.database_queries) U upright_corrected_morph() (in module skeleton_keys.upright) UprightCorrectedSwcSchema (class in skeleton_keys.cmds.upright_corrected_swc)