Index

_

__init__() (neurd.h01_volume_utils.DataInterface method) (neurd.microns_volume_utils.DataInterface method) (neurd.neuron.Branch method) (neurd.neuron.Limb method) (neurd.neuron.Neuron method) (neurd.neuron.Soma method) (neurd.neuron_searching.run_options method) (neurd.parameter_utils.PackageParameters method) (neurd.parameter_utils.Parameters method) (neurd.spine_utils.Spine method) (neurd.synapse_utils.Synapse method) (neurd.vdi_default.DataInterfaceBoilerplate method) (neurd.vdi_default.DataInterfaceDefault method) (neurd.vdi_h01.DataInterfaceH01 method) (neurd.vdi_microns.DataInterfaceMicrons method) (neurd.vdi_microns_cave.DataInterfaceMicrons method) (neurd.volume_utils.DataInterface method)

A

A_prox_from_G_prox() (in module neurd.proximity_utils) A_syn_from_G_prox() (in module neurd.proximity_utils) accuracy_df_by_cell_type_fine() (in module neurd.cell_type_utils) add_axes_subset_soma_to_syn_euclidean_dist_to_edge_df() (in module neurd.connectome_utils) add_branch_label() (in module neurd.neuron_utils) add_compartment_coarse_fine_to_df() (in module neurd.apical_utils) add_compartment_syn_flag_columns_to_edge_df() (in module neurd.connectome_utils) add_delta_ori_edge_features() (in module neurd.connectome_utils) add_error_synapses_to_neuron_obj() (in module neurd.synapse_utils) add_euclidean_dist_to_prox_df() (in module neurd.proximity_analysis_utils) add_global_name_to_dict() (in module neurd.parameter_utils) add_head_neck_shaft_spine_objs() (in module neurd.spine_utils) add_jitter_to_endpoint() (in module neurd.branch_utils) add_limb_branch_combined_name_to_df() (in module neurd.neuron_utils) add_nm_to_synapse_df() (in module neurd.synapse_utils) (neurd.vdi_default.DataInterfaceBoilerplate method) add_node_attributes_to_proofread_graph() (in module neurd.microns_volume_utils) add_on_delta_to_df() (in module neurd.functional_tuning_utils) add_presyn_postsyn_syn_dist_signed_to_edge_df() (in module neurd.connectome_utils) add_scatter_to_current_plot() (in module neurd.neuron_visualizations) add_spine_densities_to_spine_stats_df() (in module neurd.spine_utils) add_spine_syn_flag_columns_to_edge_df() (in module neurd.connectome_utils) add_synapse_densities_to_spine_synapse_stats_df() (in module neurd.spine_utils) add_synapse_xyz_to_edge_df() (in module neurd.connectome_utils) add_synapses_to_neuron_obj() (in module neurd.synapse_utils) add_valid_soma_synapses_to_neuron_obj() (in module neurd.synapse_utils) add_valid_synapses_to_neuron_obj() (in module neurd.synapse_utils) add_xz_angles_to_df() (in module neurd.neuron_geometry_utils) adjust_obj_with_face_offset() (in module neurd.spine_utils) (in module neurd.synapse_utils) after_auto_proof_stats() (in module neurd.neuron_pipeline_utils) ais_count_bins_dict() (in module neurd.ais_utils) align_and_restrict_branch() (in module neurd.neuron_utils) align_array() (in module neurd.h01_volume_utils) (in module neurd.microns_volume_utils) (in module neurd.neuron_utils) (neurd.h01_volume_utils.DataInterface method) (neurd.microns_volume_utils.DataInterface method) (neurd.vdi_default.DataInterfaceBoilerplate method) (neurd.volume_utils.DataInterface method) align_attribute() (in module neurd.h01_volume_utils) (in module neurd.neuron_utils) align_matrix_from_rotation() (in module neurd.h01_volume_utils) align_matrix_from_soma_coordinate() (in module neurd.h01_volume_utils) align_mesh() (in module neurd.h01_volume_utils) (in module neurd.microns_volume_utils) (in module neurd.neuron_utils) (neurd.h01_volume_utils.DataInterface method) (neurd.microns_volume_utils.DataInterface method) (neurd.vdi_default.DataInterfaceBoilerplate method) (neurd.volume_utils.DataInterface method) align_mesh_from_rotation() (in module neurd.h01_volume_utils) align_neuron_obj() (in module neurd.h01_volume_utils) (in module neurd.microns_volume_utils) (neurd.h01_volume_utils.DataInterface method) (neurd.microns_volume_utils.DataInterface method) (neurd.vdi_default.DataInterfaceBoilerplate method) (neurd.volume_utils.DataInterface method) align_neuron_obj_from_align_matrix() (in module neurd.h01_volume_utils) (in module neurd.neuron_utils) (neurd.vdi_default.DataInterfaceBoilerplate method) align_neuron_objs_at_soma() (in module neurd.neuron_utils) align_skeleton() (in module neurd.h01_volume_utils) (in module neurd.microns_volume_utils) (in module neurd.neuron_utils) (neurd.h01_volume_utils.DataInterface method) (neurd.microns_volume_utils.DataInterface method) (neurd.vdi_default.DataInterfaceBoilerplate method) (neurd.volume_utils.DataInterface method) aligning_matrix_3D() (in module neurd.h01_volume_utils) all_concept_network_data_to_dict() (in module neurd.neuron_utils) all_concept_network_data_to_limb_network_stating_info() (in module neurd.neuron_utils) all_concept_network_data_updated() (in module neurd.neuron_simplification) all_donwstream_branches_from_limb_branch() (in module neurd.neuron_utils) all_downstream_branches() (in module neurd.neuron_utils) all_downstream_branches_from_branches() (in module neurd.concept_network_utils) all_downstream_branches_from_candidate() (in module neurd.neuron_utils) all_downstream_branches_from_multiple_branhes() (in module neurd.neuron_utils) all_downstream_nodes() (in module neurd.concept_network_utils) all_downtream_branches() (in module neurd.concept_network_utils) all_downtream_branches_including_branch() (in module neurd.concept_network_utils) all_medain_mesh_center_widths() (in module neurd.neuron_utils) all_no_spine_median_mesh_center_widths() (in module neurd.neuron_utils) all_paths_to_leaf_nodes() (in module neurd.limb_utils) all_skeletal_lengths() (in module neurd.neuron_utils) all_soma_connnecting_endpionts_from_starting_info() (in module neurd.neuron_utils) all_soma_meshes_from_limb() (in module neurd.neuron_utils) all_soma_names_from_limb() (in module neurd.neuron_utils) all_soma_soma_connections_from_limb() (in module neurd.neuron_utils) all_starting_attr_by_limb_and_soma() (in module neurd.neuron_utils) all_starting_coordinates (neurd.neuron.Limb property) all_starting_dicts_by_soma() (in module neurd.neuron_utils) all_starting_nodes (neurd.neuron.Limb property) all_training_df() (in module neurd.cell_type_utils) all_upstream_branches() (in module neurd.concept_network_utils) all_upstream_branches_from_branches() (in module neurd.concept_network_utils) all_upstream_branches_including_branch() (in module neurd.concept_network_utils) angle_from_top() (in module neurd.neuron_statistics) annotate_synapse_df() (in module neurd.synapse_utils) annotated_motif_df() (in module neurd.motif_utils) apical_branch_candidates_on_limb() (in module neurd.classification_utils) apical_classification() (in module neurd.apical_utils) (in module neurd.classification_utils)

apical_classification_high_soma_center() (in module neurd.apical_utils) apical_limb_branch_dict (neurd.neuron.Neuron property) apical_limb_branch_dict() (in module neurd.apical_utils) apical_shaft_classification_old() (in module neurd.apical_utils) apical_shaft_direct_downstream() (in module neurd.apical_utils) apical_shaft_like_limb_branch() (in module neurd.apical_utils) apical_shaft_limb_branch_dict (neurd.neuron.Neuron property) apical_shaft_limb_branch_dict() (in module neurd.apical_utils) apical_total_limb_branch_dict() (in module neurd.apical_utils) apical_tuft_classification() (in module neurd.apical_utils) apical_tuft_limb_branch_dict (neurd.neuron.Neuron property) apical_tuft_limb_branch_dict() (in module neurd.apical_utils) append_synapses_to_plot() (in module neurd.synapse_utils) apply_adaptive_mesh_correspondence_to_neuron() (in module neurd.neuron_utils) apply_function_to_neuron() (in module neurd.neuron_searching) apply_proofreading_filters_to_neuron() (in module neurd.proofreading_utils) apply_sdf_filter() (in module neurd.spine_utils) area (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) (neurd.neuron.Soma property) (neurd.spine_utils.Spine property) area() (in module neurd.neuron_searching) area_from_compartment() (in module neurd.spine_utils) area_of_border_verts (neurd.spine_utils.Spine property) area_of_border_verts() (in module neurd.spine_utils) area_over_limb_branch() (in module neurd.neuron_utils) area_with_somas (neurd.neuron.Neuron property) array_shape_from_radius() (in module neurd.neuron_graph_lite_utils) attach_floating_pieces_to_limb_correspondence() (in module neurd.preprocess_neuron) attempt_width_matching_for_fork_divergence() (in module neurd.error_detection) attr_activation_map() (in module neurd.neuron_graph_lite_utils) attr_map() (neurd.parameter_utils.Parameters method) attr_value_by_node() (in module neurd.neuron_graph_lite_utils) attr_value_soma() (in module neurd.neuron_graph_lite_utils) attribute_from_edge_dict() (in module neurd.connectome_utils) attribute_upstream_downstream() (in module neurd.concept_network_utils) auto_proof_stage() (in module neurd.neuron_pipeline_utils) average_branch_length() (in module neurd.neuron_searching) axes_limits_coordinates() (in module neurd.neuron_graph_lite_utils) axes_limits_from_df() (in module neurd.neuron_graph_lite_utils) axon_ais_synapses() (in module neurd.synapse_utils) axon_angles() (in module neurd.axon_utils) axon_angles_from_neuron() (in module neurd.axon_utils) axon_area (neurd.neuron.Neuron property) axon_area() (in module neurd.neuron_utils) axon_branching_attributes() (in module neurd.axon_utils) axon_candidates() (in module neurd.classification_utils) axon_classification() (in module neurd.classification_utils) (neurd.neuron.Neuron method) axon_classification_excitatory() (in module neurd.axon_utils) axon_classification_inhibitory() (in module neurd.axon_utils) axon_classification_using_synapses() (in module neurd.axon_utils) axon_classification_without_synapses() (in module neurd.axon_utils) axon_compartment (neurd.neuron.Branch property) axon_compartment_extract() (in module neurd.neuron_graph_lite_utils) axon_double_back_filter() (in module neurd.graph_filters) axon_double_back_inh_filter() (in module neurd.graph_filters) axon_faces_from_labels_on_original_mesh() (in module neurd.classification_utils) axon_features_from_neuron_obj() (in module neurd.axon_utils) axon_fork_divergence_errors_limb_branch_dict() (in module neurd.error_detection) axon_label() (in module neurd.neuron_searching) axon_length (neurd.neuron.Neuron property) axon_length() (in module neurd.neuron_utils) axon_like_limb_branch_dict() (in module neurd.classification_utils) axon_like_segments() (in module neurd.axon_utils) axon_limb (neurd.neuron.Neuron property) axon_limb_branch_dict (neurd.neuron.Neuron property) axon_limb_branch_dict() (in module neurd.apical_utils) (in module neurd.axon_utils) (in module neurd.classification_utils) axon_limb_idx (neurd.neuron.Neuron property) axon_limb_name (neurd.neuron.Neuron property) axon_merge_error_width_like_query() (in module neurd.neuron_searching) axon_mesh (neurd.neuron.Neuron property) axon_mesh() (in module neurd.neuron_utils) axon_mesh_from_labels() (in module neurd.classification_utils) axon_on_dendrite_limb_branch_dict (neurd.neuron.Neuron property) axon_on_dendrite_limb_branch_dict() (in module neurd.axon_utils) axon_on_dendrite_plus_downstream() (in module neurd.proofreading_utils) axon_on_dendrite_synapses() (in module neurd.synapse_utils) axon_only_group() (in module neurd.neuron_utils) axon_segment() (in module neurd.neuron_searching) axon_segment_clean_false_positives() (in module neurd.neuron_searching) axon_segment_downstream_dendrites() (in module neurd.neuron_searching) axon_segments_after_checks() (in module neurd.neuron_searching) axon_skeleton (neurd.neuron.Neuron property) axon_skeleton() (in module neurd.neuron_utils) axon_spine_at_intersection_filter() (in module neurd.graph_filters) axon_spines_limb_branch_dict() (in module neurd.axon_utils) axon_start_distance_from_soma() (in module neurd.axon_utils) axon_starting_branch (neurd.neuron.Neuron property) axon_starting_branch() (in module neurd.classification_utils) axon_starting_coordinate (neurd.neuron.Neuron property) axon_starting_coordinate() (in module neurd.classification_utils) axon_synapses() (in module neurd.synapse_utils) axon_webbing_filter() (in module neurd.graph_filters) axon_width() (in module neurd.axon_utils) (in module neurd.neuron_searching) axon_width_like_query() (in module neurd.neuron_searching) axon_width_like_query_revised() (in module neurd.classification_utils) axon_width_like_segments() (in module neurd.classification_utils) axon_width_like_segments_old() (in module neurd.neuron_searching)

B

basal_classfication() (in module neurd.apical_utils) basal_limb_branch_dict (neurd.neuron.Neuron property) basal_limb_branch_dict() (in module neurd.apical_utils) base_coordinate (neurd.spine_utils.Spine property) base_coordinate_x_nm (neurd.spine_utils.Spine property) base_coordinate_y_nm (neurd.spine_utils.Spine property) base_coordinate_z_nm (neurd.spine_utils.Spine property) basic_connectivity_axon_dendrite_stats_from_G() (in module neurd.connectome_utils) bbox_max_x_nm_from_compartment() (in module neurd.spine_utils) bbox_max_y_nm_from_compartment() (in module neurd.spine_utils) bbox_max_z_nm_from_compartment() (in module neurd.spine_utils) bbox_min_x_nm_from_compartment() (in module neurd.spine_utils) bbox_min_y_nm_from_compartment() (in module neurd.spine_utils) bbox_min_z_nm_from_compartment() (in module neurd.spine_utils) bbox_oriented_side_lengths (neurd.spine_utils.Spine attribute) (neurd.spine_utils.Spine property) bbox_oriented_side_max (neurd.spine_utils.Spine property) bbox_oriented_side_middle (neurd.spine_utils.Spine property) bbox_oriented_side_min (neurd.spine_utils.Spine property) best_feature_match_in_descendents() (in module neurd.limb_utils) border_area (neurd.spine_utils.Spine property) border_training_df() (in module neurd.cell_type_utils) bouton_meshes() (in module neurd.axon_utils) bouton_non_bouton_idx_from_branch() (in module neurd.spine_utils) boutons (neurd.neuron.Limb property) (neurd.neuron.Neuron property) boutons_above_thresholds() (in module neurd.neuron_utils) boutons_cdfs_extract() (in module neurd.neuron_graph_lite_utils) boutons_volume (neurd.neuron.Limb property) (neurd.neuron.Neuron property) boutons_volume_extract() (in module neurd.neuron_graph_lite_utils) Branch (class in neurd.neuron)

branch_attr_dict_from_node() (in module neurd.neuron_utils) branch_boundary_transition() (in module neurd.neuron_utils) branch_boundary_transition_old() (in module neurd.neuron_utils) branch_dynamics_attr_dict_dynamics_from_node() (in module neurd.branch_utils) branch_idx (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute) branch_idx_map_from_branches_to_delete_on_limb() (in module neurd.neuron_simplification) branch_mesh_no_spines() (in module neurd.neuron_utils) branch_neighbors() (in module neurd.neuron_utils) branch_neighbors_attribute() (in module neurd.neuron_utils) branch_neighbors_mesh() (in module neurd.neuron_utils) branch_objects (neurd.neuron.Limb property) branch_path_to_node() (in module neurd.neuron_utils) branch_path_to_soma() (in module neurd.neuron_utils) branch_path_to_start_node() (in module neurd.neuron_utils) branch_skeletal_distance_from_soma() (in module neurd.neuron_utils) branch_skeletal_length (neurd.spine_utils.Spine attribute) branch_stats_dict_from_df() (in module neurd.neuron_statistics) branch_stats_over_limb_branch() (in module neurd.neuron_statistics) branch_width_at_base (neurd.spine_utils.Spine attribute) branch_width_overall (neurd.spine_utils.Spine attribute) branches (neurd.neuron.Limb property) branches_at_high_degree_coordinates() (in module neurd.neuron_utils) branches_combined_mesh() (in module neurd.neuron_utils) branches_on_limb_after_edges_deleted_and_created() (in module neurd.neuron_utils) branches_to_concept_network() (in module neurd.neuron_utils) branches_with_parent_branching() (in module neurd.concept_network_utils) branches_with_parent_non_branching() (in module neurd.concept_network_utils) branches_within_distance() (in module neurd.concept_network_utils) branches_within_distance_downstream() (in module neurd.concept_network_utils) branches_within_distance_upstream() (in module neurd.concept_network_utils) branches_within_skeletal_distance() (in module neurd.neuron_utils) branching_simplification() (in module neurd.neuron_simplification)

C

calculate_axon_webbing() (in module neurd.axon_utils) calculate_axon_webbing_on_branch() (in module neurd.axon_utils) calculate_boutons() (in module neurd.axon_utils) calculate_boutons_over_limb_branch_dict() (in module neurd.axon_utils) calculate_branch_attr_soma_distances_on_limb() (in module neurd.branch_attr_utils) calculate_branch_overall_features() (in module neurd.spine_utils) calculate_branch_width_at_base() (in module neurd.spine_utils) calculate_closest_mesh_sk_coordinates() (neurd.spine_utils.Spine method) calculate_decomposition_products() (in module neurd.neuron_utils) (neurd.neuron.Neuron method) calculate_endpoints() (neurd.neuron.Branch method) calculate_endpoints_dist() (in module neurd.branch_attr_utils) (in module neurd.spine_utils) (in module neurd.synapse_utils) calculate_error_rate() (in module neurd.proofreading_utils) calculate_face_idx() (in module neurd.spine_utils) (neurd.spine_utils.Spine method) calculate_head_neck() (neurd.spine_utils.Spine method) calculate_limb_concept_networks() (in module neurd.preprocess_neuron) calculate_limb_synapse_soma_distances() (in module neurd.synapse_utils) calculate_multi_soma_split_suggestions() (in module neurd.soma_splitting_utils) (neurd.neuron.Neuron method) calculate_neuron_soma_distance() (in module neurd.branch_attr_utils) (in module neurd.synapse_utils) calculate_neuron_soma_distance_euclidean() (in module neurd.branch_attr_utils) (in module neurd.synapse_utils) calculate_new_width() (in module neurd.width_utils) (neurd.neuron.Neuron method) calculate_new_width_for_neuron_obj() (in module neurd.width_utils) calculate_skeleton() (neurd.spine_utils.Spine method) calculate_skip_distance() (in module neurd.error_detection) calculate_skip_distance_poly() (in module neurd.error_detection) calculate_soma_distance_euclidean() (in module neurd.spine_utils) calculate_soma_distance_skeletal() (in module neurd.spine_utils) calculate_spine_attributes() (in module neurd.spine_utils) (neurd.spine_utils.Spine method) calculate_spine_attributes_for_list() (in module neurd.spine_utils) calculate_spine_obj_attr_for_neuron() (in module neurd.spine_utils) calculate_spine_obj_mesh_skeleton_coordinates() (in module neurd.spine_utils) calculate_spine_obj_mesh_skeleton_coordinates_for_branch() (in module neurd.spine_utils) calculate_spines_old() (neurd.neuron.Neuron method) calculate_spines_on_branch() (in module neurd.spine_utils) calculate_spines_on_neuron() (in module neurd.spine_utils) calculate_spines_skeletal_length() (in module neurd.neuron_utils) calculate_upstream_downstream_dist() (in module neurd.branch_attr_utils) (in module neurd.synapse_utils) calculate_upstream_downstream_dist_from_down_idx() (in module neurd.branch_attr_utils) (in module neurd.synapse_utils) calculate_upstream_downstream_dist_from_up_idx() (in module neurd.branch_attr_utils) (in module neurd.spine_utils) (in module neurd.synapse_utils) calculate_volume() (neurd.spine_utils.Spine method) candidate_from_branches() (in module neurd.neuron_utils) candidate_groups_from_limb_branch() (in module neurd.neuron_utils) candidate_limb_branch_dict_branch_intersection() (in module neurd.neuron_utils) candidate_starting_skeletal_angle() (in module neurd.classification_utils) candidates_from_limb_branch_candidates() (in module neurd.neuron_utils) category_param_from_module() (in module neurd.parameter_utils) CaveInterface (class in neurd.cave_client_utils) cdiff() (in module neurd.functional_tuning_utils) cdist() (in module neurd.functional_tuning_utils) cell_count() (in module neurd.connectome_analysis_utils) cell_type() (neurd.vdi_default.DataInterfaceBoilerplate method) cell_type_ax_dendr_stage() (in module neurd.neuron_pipeline_utils) cell_type_fine_classifier_map_derived() (in module neurd.cell_type_utils) cell_type_fine_for_clustering_inh (in module neurd.cell_type_utils) cell_type_fine_mapping_publishable() (in module neurd.cell_type_utils) cell_type_fine_name_cleaner() (in module neurd.cell_type_utils) cell_type_from_feature_df() (in module neurd.cell_type_utils) cell_type_high_probability_df_from_df() (in module neurd.cell_type_utils) cell_type_names_str() (in module neurd.cell_type_utils) centroid_stats_from_neuron_obj() (in module neurd.neuron_statistics) check_concept_network() (in module neurd.neuron_utils) check_points_inside_soma_bbox() (in module neurd.neuron_utils) check_skeletonization_and_decomp() (in module neurd.preprocess_neuron) child_angles() (in module neurd.neuron_statistics) children_axon_width() (in module neurd.neuron_statistics) children_axon_width_max() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) children_feature() (in module neurd.neuron_statistics) children_nodes() (in module neurd.neuron_utils) children_skeletal_angle() (in module neurd.limb_utils) children_skeletal_angle_max() (in module neurd.limb_utils) children_skeletal_angle_min() (in module neurd.limb_utils) children_skeletal_lengths() (in module neurd.neuron_statistics) children_skeletal_lengths_min() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) classes_from_cell_type_name() (in module neurd.cell_type_utils) classify_endpoint_error_branches_from_limb_concept_network() (in module neurd.neuron_utils) classify_error_branch() (in module neurd.neuron_utils) classify_upstream_downsream() (in module neurd.neuron_utils) clean_all_concept_network_data() (in module neurd.neuron_utils) clean_cell_type_fine() (in module neurd.cell_type_utils) clean_modules_dict() (in module neurd.parameter_utils) clean_neuron_all_concept_network_data() (in module neurd.neuron_utils) clear_all_branch_labels() (in module neurd.neuron_utils) clear_axon_labels_from_dendritic_paths_to_starter_node() (in module neurd.classification_utils) clear_certain_branch_labels() (in module neurd.neuron_utils) closest_branch_endpoint_to_limb_starting_coordinate() (in module neurd.neuron_utils) closest_branch_face_idx (neurd.spine_utils.Spine attribute) closest_branch_to_coordinates() (in module neurd.neuron_utils) closest_dist_from_floating_mesh_to_skeleton() (in module neurd.preprocess_neuron) closest_face_coordinate (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute) closest_face_dist (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute) closest_mesh_skeleton_dist() (in module neurd.branch_utils) (in module neurd.neuron_searching) closest_node_idx_to_sample_idx() (in module neurd.neuron_graph_lite_utils) closest_sk_coordinate (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute) coarse_cell_type_from_coarse() (in module neurd.cell_type_utils) coarse_cell_type_from_fine() (in module neurd.cell_type_utils)

coarse_fine_compartment_from_label() (in module neurd.apical_utils) collapse_branches_on_limb() (in module neurd.proofreading_utils) colors_from_compartments() (in module neurd.apical_utils) colors_from_spine_bouton_labels() (in module neurd.spine_utils) combine_attr_lists() (in module neurd.branch_utils) combine_branches() (in module neurd.branch_utils) combine_path_branches() (in module neurd.neuron_simplification) combine_path_branches_on_limb() (in module neurd.neuron_simplification) combine_synapse_dict_into_presyn_postsyn_valid_error_dict() (in module neurd.synapse_utils) combined_somas_neuron_obj() (in module neurd.neuron_utils) compartment (neurd.neuron.Branch property) (neurd.neuron.Soma property) (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute) compartment_classification_by_cell_type() (in module neurd.apical_utils) compartment_feature_over_limb_branch_dict() (in module neurd.apical_utils) compartment_features_from_skeleton_and_soma_center() (in module neurd.apical_utils) compartment_from_branch() (in module neurd.apical_utils) compartment_from_face_overlap_with_comp_faces_dict() (in module neurd.apical_utils) compartment_groups_from_synapses_obj() (in module neurd.synapse_utils) compartment_idx_for_mesh_face_idx_of_spine() (in module neurd.spine_utils) compartment_index_from_id() (in module neurd.spine_utils) compartment_label_from_branch_obj() (in module neurd.apical_utils) compartment_label_to_all_labels() (in module neurd.apical_utils) compartment_labels_for_externals() (in module neurd.apical_utils) compartment_labels_for_stats() (in module neurd.apical_utils) compartment_labels_for_synapses_stats() (in module neurd.apical_utils) compartment_limb_branch_dict() (in module neurd.apical_utils) compartment_mesh() (in module neurd.apical_utils) compartment_root_skeleton_angle_max() (in module neurd.neuron_utils) compartment_root_skeleton_angle_min() (in module neurd.neuron_utils) compartment_root_width_max() (in module neurd.neuron_utils) compartment_root_width_min() (in module neurd.neuron_utils) compartment_roots_stat() (in module neurd.neuron_utils) compartment_roots_stat_extrema() (in module neurd.neuron_utils) compartment_roots_stat_max() (in module neurd.neuron_utils) compartment_roots_stat_min() (in module neurd.neuron_utils) compartment_skeleton() (in module neurd.apical_utils) compartments_feature_over_limb_branch_dict() (in module neurd.apical_utils) compartments_from_cell_type() (in module neurd.apical_utils) compartments_mesh() (in module neurd.apical_utils) compartments_skeleton() (in module neurd.apical_utils) compartments_stats() (in module neurd.apical_utils) compartments_to_plot() (in module neurd.apical_utils) complete_axon_processing() (in module neurd.axon_utils) complete_axon_processing_old() (in module neurd.axon_utils) complete_n_synapses_analysis() (in module neurd.synapse_utils) complete_spine_processing() (in module neurd.spine_utils) compute_all_concept_network_data_from_limb() (in module neurd.neuron_utils) compute_axon_on_dendrite_limb_branch_dict() (in module neurd.axon_utils) compute_boutons_volume() (neurd.neuron.Branch method) (neurd.neuron.Limb method) (neurd.neuron.Neuron method) compute_dendrite_on_axon_limb_branch_dict() (in module neurd.axon_utils) compute_dendrite_on_axon_limb_branch_dict_excitatory() (in module neurd.axon_utils) compute_dendrite_on_axon_limb_branch_dict_inhibitory() (in module neurd.axon_utils) compute_edge_attributes_around_node() (in module neurd.neuron_statistics) compute_edge_attributes_globally() (in module neurd.neuron_statistics) compute_edge_attributes_locally() (in module neurd.neuron_statistics) compute_edge_attributes_locally_upstream_downstream() (in module neurd.neuron_statistics) compute_edge_statistic() (in module neurd.connectome_utils) compute_feature_over_object() (in module neurd.neuron_utils) compute_mesh_attribute_volume() (in module neurd.neuron_utils) compute_node_attributes() (in module neurd.neuron_statistics) compute_node_attributes_upstream_downstream() (in module neurd.neuron_statistics) compute_presyn_postsyn_walk_euclidean_skeletal_dist() (in module neurd.connectome_utils) compute_presyn_soma_postsyn_soma_euclid_dist_axis() (in module neurd.connectome_utils) compute_spines_volume() (neurd.neuron.Branch method) (neurd.neuron.Limb method) (neurd.neuron.Neuron method) computed_presyn_postsyn_soma_relative_synapse_coordinate() (in module neurd.connectome_utils) concatenate_feature_over_limb_branch_dict() (in module neurd.neuron_utils) concept_network_data_by_soma (neurd.neuron.Limb property) concept_network_data_by_starting_node (neurd.neuron.Limb property) concept_network_data_from_soma() (in module neurd.neuron_utils) config_directory() (in module neurd.parameter_utils) connected_components_from_branches() (in module neurd.neuron_utils) connectivity (in module neurd.spine_utils) contains_excitatory_apical() (in module neurd.classification_utils) contains_excitatory_axon() (in module neurd.classification_utils) conversion_df() (in module neurd.proximity_analysis_utils) conversion_df_from_proximity_df() (in module neurd.proximity_analysis_utils) conversion_rate() (in module neurd.proximity_analysis_utils) conversion_rate_by_attribute_and_cell_type_pairs() (in module neurd.proximity_analysis_utils) convert_concept_network_to_directional() (in module neurd.neuron_utils) (neurd.neuron.Limb method) convert_concept_network_to_skeleton() (in module neurd.neuron_utils) convert_concept_network_to_undirectional() (in module neurd.neuron_utils) convert_int_names_to_string_names() (in module neurd.neuron_utils) convert_limb_concept_network_to_neuron_skeleton() (in module neurd.neuron_utils) convert_limb_function_return_to_dict() (in module neurd.neuron_searching) convert_limb_function_return_to_limb_branch_dict() (in module neurd.neuron_searching) convert_neuron_to_branches_dataframe() (in module neurd.neuron_searching) convert_number_of_columns_to_dtype() (in module neurd.spine_utils) convert_soma_to_piece_connectivity_to_graph() (in module neurd.neuron) convert_string_names_to_int_names() (in module neurd.neuron_utils) coordinate (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute) coordinate_border_verts (neurd.spine_utils.Spine attribute) coordinate_border_verts_area (neurd.spine_utils.Spine property) coordinate_to_offset_skeletons() (in module neurd.neuron_utils) coordinates_function_list() (in module neurd.neuron_statistics) coordinates_stats_df() (in module neurd.neuron_statistics) coordinates_to_closest_limb_branch() (in module neurd.neuron_utils) coordinates_to_layer_height() (in module neurd.microns_volume_utils) copy_concept_network() (in module neurd.neuron) copy_neuron() (in module neurd.neuron_utils) correspondence_1_to_1() (in module neurd.preprocess_neuron) counts_df_from_motif_df() (in module neurd.motif_utils) crossover_elimination_limb_branch_dict() (in module neurd.proofreading_utils) current_starting_soma_vertices (neurd.neuron.Limb property) cut_kissing_graph_edges() (in module neurd.error_detection) cut_limb_network_by_edges() (in module neurd.proofreading_utils) cut_limb_network_by_suggestions() (in module neurd.proofreading_utils)

D

DataInterface (class in neurd.h01_volume_utils) (class in neurd.microns_volume_utils) (class in neurd.volume_utils) DataInterfaceBoilerplate (class in neurd.vdi_default) DataInterfaceDefault (class in neurd.vdi_default) DataInterfaceH01 (class in neurd.vdi_h01) DataInterfaceMicrons (class in neurd.vdi_microns) (class in neurd.vdi_microns_cave) dc_check() (in module neurd.neuron) debug_branches_high_degree() (in module neurd.error_detection) debug_branches_low_degree() (in module neurd.error_detection) decode_head_neck_shaft_idx() (in module neurd.spine_utils) decompress_neuron() (in module neurd.neuron_utils) default_low_degree_graph_filters (neurd.vdi_default.DataInterfaceDefault property) (neurd.vdi_h01.DataInterfaceH01 property) delete_branches_from_limb() (in module neurd.neuron_simplification) (in module neurd.proofreading_utils) delete_branches_from_neuron() (in module neurd.neuron_simplification) (in module neurd.proofreading_utils) dendrite_branch_restriction() (in module neurd.error_detection) dendrite_branch_stats_near_soma() (in module neurd.cell_type_utils) dendrite_branches_on_limb() (in module neurd.classification_utils) dendrite_compartment_labels() (in module neurd.apical_utils) dendrite_limb_branch_dict (neurd.neuron.Neuron property) dendrite_limb_branch_dict() (in module neurd.apical_utils) (in module neurd.axon_utils) (in module neurd.classification_utils) dendrite_mesh (neurd.neuron.Neuron property) dendrite_mesh() (in module neurd.neuron_utils) dendrite_on_axon_limb_branch_dict (neurd.neuron.Neuron property) dendrite_on_axon_limb_branch_dict() (in module neurd.axon_utils) dendrite_skeleton (neurd.neuron.Neuron property) dendrite_skeleton() (in module neurd.neuron_utils) df_cell_type_fine() (in module neurd.cell_type_utils) df_from_spine_objs() (in module neurd.spine_utils) dict (neurd.parameter_utils.PackageParameters property) (neurd.parameter_utils.Parameters property)

distance_between_nodes_di() (in module neurd.concept_network_utils) distance_between_nodes_di_downstream() (in module neurd.concept_network_utils) distance_between_nodes_di_upstream() (in module neurd.concept_network_utils) distance_errored_synapses_post (neurd.neuron.Neuron property) distance_errored_synapses_pre (neurd.neuron.Neuron property) distance_from_microns_volume_bbox_midpoint() (in module neurd.microns_volume_utils) distance_from_soma() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) distance_from_soma_candidate() (in module neurd.neuron_statistics) distance_from_soma_euclidean() (in module neurd.neuron_statistics) distance_to_soma_from_coordinate_close_to_branch() (in module neurd.neuron_utils) divided_skeletons (neurd.neuron.Limb property) dotmotif_str_from_G_motif() (in module neurd.motif_utils) double_back_axon_thick() (in module neurd.error_detection) double_back_axon_thin() (in module neurd.error_detection) double_back_dendrite() (in module neurd.error_detection) double_back_edges() (in module neurd.error_detection) double_back_edges_path() (in module neurd.error_detection) double_back_error_limb_branch_dict() (in module neurd.error_detection) double_back_threshold_axon_by_width() (in module neurd.error_detection) doubling_back_and_width_elimination_limb_branch_dict() (in module neurd.proofreading_utils) downstream_dist (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute) downstream_dist_match_ref_vector_over_candidate() (in module neurd.neuron_statistics) downstream_dist_max_over_syn() (in module neurd.synapse_utils) downstream_dist_min_over_syn() (in module neurd.synapse_utils) downstream_endpoint() (in module neurd.neuron_utils) downstream_labels() (in module neurd.neuron_utils) downstream_nodes() (in module neurd.concept_network_utils) (in module neurd.neuron_utils) downstream_nodes_from_G() (in module neurd.error_detection) downstream_nodes_mesh_connected() (in module neurd.concept_network_utils) (in module neurd.neuron_searching) downstream_nodes_without_branching() (in module neurd.concept_network_utils) downstream_upstream_diff_of_most_downstream_syn() (in module neurd.neuron_searching) (in module neurd.neuron_statistics)

E

e_i_classification_from_neuron_obj() (in module neurd.cell_type_utils) e_i_classification_from_neuron_obj_old() (in module neurd.cell_type_utils) e_i_classification_single() (in module neurd.cell_type_utils) e_i_color_dict() (in module neurd.cell_type_utils) e_i_label_from_cell_type_fine() (in module neurd.cell_type_utils) e_i_model_as_logistic_reg_on_border_df() (in module neurd.cell_type_utils) edges_from_motif_dict() (in module neurd.motif_utils) edges_from_str() (in module neurd.motif_utils) edges_to_create_and_delete_by_doubling_back_and_width() (in module neurd.proofreading_utils) edges_to_create_and_delete_crossover() (in module neurd.proofreading_utils) edges_to_create_and_delete_high_degree_coordinates() (in module neurd.proofreading_utils) edges_to_cut_by_doubling_back_and_width_change() (in module neurd.proofreading_utils) edges_to_delete_from_threshold_and_buffer() (in module neurd.neuron_statistics) edges_to_delete_on_node_above_threshold_if_one_below() (in module neurd.neuron_statistics) em_alignment_coordinates_info() (in module neurd.microns_volume_utils) em_alignment_data_raw() (in module neurd.microns_volume_utils) EM_coordinates_to_layer() (in module neurd.microns_volume_utils) EM_coordinates_to_visual_areas() (in module neurd.microns_volume_utils) em_voxels_to_nm() (in module neurd.microns_volume_utils) empty_limb_object() (in module neurd.neuron_utils) endnode_branches_of_branches_within_distance_downtream() (in module neurd.concept_network_utils) endpoint_dist_0 (neurd.spine_utils.Spine property) endpoint_dist_1 (neurd.spine_utils.Spine property) endpoint_dist_extrema_over_syn() (in module neurd.synapse_utils) endpoint_downstream (neurd.neuron.Branch property) endpoint_downstream_idx() (in module neurd.branch_utils) endpoint_downstream_with_offset (neurd.neuron.Branch property) endpoint_downstream_with_offset() (in module neurd.branch_utils) endpoint_downstream_x (neurd.neuron.Branch property) endpoint_downstream_y (neurd.neuron.Branch property) endpoint_downstream_z (neurd.neuron.Branch property) endpoint_type_with_offset() (in module neurd.branch_utils) endpoint_upstream (neurd.neuron.Branch property) endpoint_upstream_idx() (in module neurd.branch_utils) endpoint_upstream_with_offset (neurd.neuron.Branch property) endpoint_upstream_with_offset() (in module neurd.branch_utils) endpoint_upstream_x (neurd.neuron.Branch property) endpoint_upstream_y (neurd.neuron.Branch property) endpoint_upstream_z (neurd.neuron.Branch property) endpoints_dist (neurd.spine_utils.Spine attribute) endpoints_nodes (neurd.neuron.Branch property) error_branches_by_axons() (in module neurd.error_detection) error_faces_by_axons() (in module neurd.error_detection) error_limb_indexes() (in module neurd.neuron_utils) error_limbs() (in module neurd.neuron_utils)

error_query() (in module neurd.synapse_utils) error_synapses_to_scatter_info() (in module neurd.synapse_utils) euclidean_distance_close_to_soma_limb_branch() (in module neurd.neuron_statistics) euclidean_distance_farther_than_soma_limb_branch() (in module neurd.neuron_statistics) euclidean_distance_from_soma_limb_branch() (in module neurd.neuron_statistics) examle_plot_spines_from_spine_df_query() (in module neurd.spine_utils) example_basal_conversion_rate() (in module neurd.proximity_analysis_utils) example_comparing_mesh_segmentation_vs_spine_head_segmentation() (in module neurd.spine_utils) example_histogram_nice() (in module neurd.nature_paper_plotting) example_kde_plot() (in module neurd.nature_paper_plotting) example_nwb_file() (in module neurd.nwb_utils) example_pairwise_postsyn_analysis() (in module neurd.proximity_analysis_utils) example_plot_coordinates_from_spine_df_idx() (in module neurd.spine_utils) example_plot_small_volume_spines_from_spine_df() (in module neurd.spine_utils) example_proximity() (in module neurd.proximity_utils) example_syn_df_spine_correlations() (in module neurd.spine_utils) example_trying_to_skeletonize_spine() (in module neurd.spine_utils) exc_axon_on_dendrite_merges_filter() (in module neurd.proofreading_utils) exc_double_back_dendrite_filter() (in module neurd.proofreading_utils) exc_filters_auto_proof() (neurd.vdi_default.DataInterfaceDefault method) exc_high_degree_branching_dendrite_filter() (in module neurd.proofreading_utils) exc_high_degree_branching_filter() (in module neurd.proofreading_utils) exc_low_degree_branching_filter() (in module neurd.proofreading_utils) exc_to_exc_edge_df() (in module neurd.connectome_utils) exc_width_jump_up_axon_filter() (in module neurd.proofreading_utils) exc_width_jump_up_dendrite_filter() (in module neurd.proofreading_utils) excitatory_cells_node_df() (in module neurd.connectome_query_utils) (in module neurd.microns_graph_query_utils) excitatory_high_probability_df_from_df() (in module neurd.cell_type_utils) excitatory_nodes() (in module neurd.connectome_utils) expand_candidate_branches_to_soma() (in module neurd.apical_utils) export() (in module neurd.spine_utils) (in module neurd.synapse_utils) (neurd.spine_utils.Spine method) (neurd.synapse_utils.Synapse method) export_cell_type_abbreviations_csv() (in module neurd.cell_type_utils) export_csv() (in module neurd.parameter_utils) export_df() (in module neurd.parameter_utils) export_mesh_labels() (in module neurd.neuron) export_package_param_dict_to_file() (in module neurd.parameter_utils) export_skeleton() (in module neurd.neuron) exports_to_synapses() (in module neurd.synapse_utils) extract_blue_red_points_from_limb_branch_dict_to_cancel() (in module neurd.proofreading_utils) extract_from_filter_info() (in module neurd.proofreading_utils) extract_soma_center() (in module neurd.soma_extraction_utils)

F

face_idx_map_from_spine_objs() (in module neurd.spine_utils) false_positive_queries() (in module neurd.spine_utils) farthest_dendrite_branch_from_soma() (in module neurd.neuron_statistics) farthest_distance_from_skeleton_to_mesh() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) feature_list_over_object() (in module neurd.neuron_utils) feature_map_df() (in module neurd.neuron_graph_lite_utils) feature_over_branches() (in module neurd.concept_network_utils) (in module neurd.neuron_utils) feature_over_limb_branch_dict() (in module neurd.neuron_utils) feature_summed_over_compartments() (in module neurd.spine_utils) features_from_neuron_skeleton_and_soma_center() (in module neurd.neuron_statistics) features_from_skeleton_and_soma_center() (in module neurd.neuron_statistics) features_to_export_for_db() (in module neurd.spine_utils) fetch_proofread_mesh() (neurd.vdi_default.DataInterfaceDefault method) fetch_segment_id_mesh() (neurd.vdi_default.DataInterfaceDefault method) (neurd.vdi_microns_cave.DataInterfaceMicrons method) fetch_soma_mesh() (neurd.vdi_default.DataInterfaceDefault method) fetch_synapse_dict_by_mesh_labels() (in module neurd.synapse_utils) fetch_undecimated_segment_id_mesh() (neurd.vdi_default.DataInterfaceDefault method) filter_ais_df_cell_type_splits_by_n_ais_perc() (in module neurd.ais_utils) filter_and_scale_spine_syn_df() (in module neurd.spine_utils) filter_apical_candidates() (in module neurd.apical_utils) filter_apical_candidates_to_one() (in module neurd.apical_utils) filter_away_axon_on_dendrite_merges() (in module neurd.proofreading_utils) filter_away_axon_on_dendrite_merges_old() (in module neurd.proofreading_utils) filter_away_crossovers() (in module neurd.proofreading_utils) filter_away_dendrite_on_axon_merges() (in module neurd.proofreading_utils) filter_away_dendrite_on_axon_merges_old() (in module neurd.proofreading_utils) filter_away_double_back_axon_thick() (in module neurd.proofreading_utils) filter_away_double_back_axon_thin() (in module neurd.proofreading_utils) filter_away_double_back_dendrite() (in module neurd.proofreading_utils) filter_away_fp_from_df() (in module neurd.spine_utils) filter_away_high_degree_branching() (in module neurd.proofreading_utils) filter_away_high_degree_branching_dendrite() (in module neurd.proofreading_utils) filter_away_high_degree_coordinates() (in module neurd.proofreading_utils) filter_away_inside_soma_pieces() (in module neurd.soma_extraction_utils) filter_away_large_double_back_or_width_changes() (in module neurd.proofreading_utils) filter_away_limb_branch_dict() (in module neurd.proofreading_utils) filter_away_limb_branch_dict_with_function() (in module neurd.proofreading_utils) filter_away_low_branch_length_clusters() (in module neurd.proofreading_utils) filter_away_low_branch_length_clusters_axon() (in module neurd.proofreading_utils) filter_away_low_branch_length_clusters_dendrite() (in module neurd.proofreading_utils) filter_away_low_degree_branching() (in module neurd.proofreading_utils) filter_away_neuron_limbs() (in module neurd.neuron_utils) filter_away_neuron_limbs_by_min_skeletal_length() (in module neurd.neuron_utils) filter_away_presyns_with_soma_postsyns() (in module neurd.connectome_utils) filter_away_small_axon_fork_divergence() (in module neurd.proofreading_utils) filter_away_thick_t_merge() (in module neurd.proofreading_utils) filter_away_webbing_t_merges() (in module neurd.proofreading_utils) filter_away_width_jump_up_axon() (in module neurd.proofreading_utils)

filter_away_width_jump_up_dendrite() (in module neurd.proofreading_utils) filter_axon_candiates() (in module neurd.classification_utils) filter_axon_candiates_old() (in module neurd.classification_utils) filter_axon_limb_false_positive_end_nodes() (in module neurd.axon_utils) filter_axon_neuron_false_positive_end_nodes() (in module neurd.axon_utils) filter_branches_by_restriction_mesh() (in module neurd.neuron_utils) filter_candidate_branches_by_downstream_postsyn() (in module neurd.axon_utils) filter_candidates_away_with_downstream_high_postsyn_branches_NOT_USED() (in module neurd.axon_utils) filter_cell_type_df_for_most_complete_duplicates() (in module neurd.cell_type_utils) filter_df_by_axon_dendrite() (in module neurd.neuron_graph_lite_utils) filter_df_by_skeletal_length() (in module neurd.neuron_graph_lite_utils) filter_df_by_soma_distance() (in module neurd.neuron_graph_lite_utils) filter_df_by_xyz_window() (in module neurd.neuron_graph_lite_utils) filter_for_high_confidence_df() (in module neurd.spine_utils) filter_G_attributes() (in module neurd.motif_utils) filter_limb_branch_dict_by_limb() (in module neurd.neuron_utils) filter_limb_correspondence_for_end_nodes() (in module neurd.preprocess_neuron) filter_limbs_below_soma_percentile() (in module neurd.neuron_utils) filter_limbs_by_soma_starting_angle() (in module neurd.neuron_statistics) filter_motif_df() (in module neurd.motif_utils) filter_out_border_spines() (in module neurd.spine_utils) filter_out_soma_touching_spines() (in module neurd.spine_utils) filter_soma_touching_vertices_dict_by_mesh() (in module neurd.preprocess_neuron) filter_spine_df_samples() (in module neurd.spine_utils) filter_spine_meshes() (in module neurd.spine_utils) filter_spine_objs_by_size_bare_minimum() (in module neurd.spine_utils) filter_spine_objs_from_restrictions() (in module neurd.spine_utils) filter_spines_by_size() (in module neurd.spine_utils) filter_spines_by_size_branch() (in module neurd.spine_utils) find_branch_by_skeleton_coordinate() (neurd.neuron.Limb method) find_branch_with_specific_coordinate() (in module neurd.neuron_utils) find_branch_with_specific_endpoint() (in module neurd.neuron_utils) find_face_idx_and_check_recovery() (in module neurd.neuron_utils) find_high_degree_coordinates_on_path() (in module neurd.proofreading_utils) find_if_stitch_point_on_end_or_branch() (in module neurd.preprocess_neuron) find_mesh_width_array_border() (in module neurd.width_utils) find_parent_child_skeleton_angle() (in module neurd.neuron_utils) find_parent_child_skeleton_angle_upstream_downstream() (in module neurd.neuron_statistics) find_sibling_child_skeleton_angle() (in module neurd.neuron_utils) find_soma_centroid_containing_meshes() (in module neurd.soma_extraction_utils) find_soma_centroids() (in module neurd.soma_extraction_utils) flip_dendrite_to_axon() (in module neurd.neuron_searching) floating_end_nodes_limb_branch() (in module neurd.neuron_simplification) fork_divergence() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) fork_divergence_filter() (in module neurd.graph_filters) fork_divergence_from_branch() (in module neurd.neuron_statistics) fork_divergence_from_skeletons() (in module neurd.neuron_statistics) fork_min_skeletal_distance() (in module neurd.neuron_statistics) fork_min_skeletal_distance_filter() (in module neurd.graph_filters) fork_min_skeletal_distance_from_skeletons() (in module neurd.neuron_statistics) functions_list_from_query() (in module neurd.neuron_searching)

G

G_weighted_from_limb() (in module neurd.concept_network_utils) G_with_attrs_from_neuron_obj() (in module neurd.neuron_graph_lite_utils) generate_limb_concept_networks_from_global_connectivity() (in module neurd.neuron_utils) generate_neuron_dataframe() (in module neurd.neuron_searching) get_align_matrix() (neurd.vdi_default.DataInterfaceDefault method) (neurd.vdi_h01.DataInterfaceH01 method) (neurd.vdi_microns.DataInterfaceMicrons method) (neurd.vdi_microns_cave.DataInterfaceMicrons method) get_all_coordinate_suggestions() (in module neurd.proofreading_utils) get_all_cut_and_not_cut_path_coordinates() (in module neurd.proofreading_utils) get_attribute_dict() (neurd.neuron.Limb method) (neurd.neuron.Neuron method) get_attribute_from_suggestion() (in module neurd.proofreading_utils) get_best_cut_edge() (in module neurd.proofreading_utils) get_branch_names() (neurd.neuron.Limb method) get_branch_node_names() (neurd.neuron.Neuron method) get_computed_attribute_data() (neurd.neuron.Limb method) (neurd.neuron.Neuron method) get_concept_network_data_by_soma() (neurd.neuron.Limb method) get_concept_network_data_by_soma_and_idx() (neurd.neuron.Limb method) get_edges_to_create_from_suggestion() (in module neurd.proofreading_utils) get_edges_to_delete_from_suggestion() (in module neurd.proofreading_utils) get_errored_synapses_names() (in module neurd.synapse_utils) get_exc_filters() (in module neurd.proofreading_utils) get_exc_filters_high_fidelity_axon_postprocessing_old() (in module neurd.proofreading_utils) get_exc_filters_high_fidelity_axon_preprocessing() (in module neurd.proofreading_utils) get_exc_filters_high_fidelity_axon_preprocessing_old() (in module neurd.proofreading_utils) get_inh_filters() (in module neurd.proofreading_utils) get_limb_int_name() (in module neurd.neuron_utils) get_limb_names() (neurd.neuron.Neuron method) get_limb_names_from_concept_network() (in module neurd.neuron_utils) get_limb_node_names() (neurd.neuron.Neuron method) get_limb_starting_angle_dict() (in module neurd.neuron_utils) get_limb_string_name() (in module neurd.neuron_utils) get_limb_to_soma_border_vertices() (in module neurd.neuron_utils) get_limbs_touching_soma() (neurd.neuron.Neuron method) get_matching_concept_network_data() (in module neurd.neuron_utils)

get_n_paths_cut() (in module neurd.proofreading_utils) get_n_paths_not_cut() (in module neurd.proofreading_utils) get_removed_branches_from_suggestion() (in module neurd.proofreading_utils) get_run_type() (in module neurd.neuron_searching) get_skeleton() (neurd.neuron.Limb method) (neurd.neuron.Neuron method) get_skeleton_soma_starting_node() (neurd.neuron.Limb method) get_soma_by_starting_node() (neurd.neuron.Limb method) get_soma_group_by_starting_node() (neurd.neuron.Limb method) get_soma_indexes() (neurd.neuron.Neuron method) get_soma_int_name() (in module neurd.neuron_utils) get_soma_meshes() (in module neurd.neuron_utils) (neurd.neuron.Neuron method) get_soma_names_from_concept_network() (in module neurd.neuron_utils) get_soma_node_names() (neurd.neuron.Neuron method) get_soma_skeleton() (in module neurd.neuron_utils) get_soma_string_name() (in module neurd.neuron_utils) get_somas() (neurd.neuron.Neuron method) get_somas_touching_limbs() (neurd.neuron.Neuron method) get_spine_meshes_unfiltered() (in module neurd.spine_utils) get_spine_meshes_unfiltered_from_mesh() (in module neurd.spine_utils) get_starting_branch_by_soma() (neurd.neuron.Limb method) get_starting_info_from_concept_network() (in module neurd.neuron_utils) get_starting_node_from_limb_concept_network() (in module neurd.neuron_utils) get_stat() (in module neurd.neuron_statistics) get_synapse_types() (in module neurd.synapse_utils) get_synapses_compartment() (in module neurd.synapse_utils) get_table() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) get_tables() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) get_total_n_branches() (neurd.neuron.Neuron method) get_whole_neuron_skeleton() (in module neurd.neuron_utils) glia_nuclei_faces_from_mesh() (in module neurd.soma_extraction_utils) global_param_and_attributes_dict_to_separate_mode_jsons() (in module neurd.parameter_utils) graph_filter_adapter() (in module neurd.graph_filters) graph_obj_from_proof_stage() (neurd.vdi_default.DataInterfaceDefault method) grouping_containing_mesh_indices() (in module neurd.soma_extraction_utils)

H

head_area (neurd.spine_utils.Spine property) head_bbox_max_x_nm (neurd.spine_utils.Spine property) head_bbox_max_y_nm (neurd.spine_utils.Spine property) head_bbox_max_z_nm (neurd.spine_utils.Spine property) head_bbox_min_x_nm (neurd.spine_utils.Spine property) head_bbox_min_y_nm (neurd.spine_utils.Spine property) head_bbox_min_z_nm (neurd.spine_utils.Spine property) head_bbox_oriented_side_lengths (neurd.spine_utils.Spine attribute) (neurd.spine_utils.Spine property) head_bbox_oriented_side_max (neurd.spine_utils.Spine property) head_bbox_oriented_side_middle (neurd.spine_utils.Spine property) head_bbox_oriented_side_min (neurd.spine_utils.Spine property) head_exist (neurd.spine_utils.Spine property) head_exist() (in module neurd.spine_utils) head_face_idx (neurd.spine_utils.Spine attribute) head_mesh (neurd.spine_utils.Spine property) head_mesh() (in module neurd.spine_utils) head_mesh_splits (neurd.spine_utils.Spine attribute) (neurd.spine_utils.Spine property) head_mesh_splits_face_idx (neurd.spine_utils.Spine attribute) (neurd.spine_utils.Spine property) head_mesh_splits_face_idx_by_index() (in module neurd.spine_utils)

head_mesh_splits_from_index() (in module neurd.spine_utils) (neurd.spine_utils.Spine method) head_mesh_splits_max (neurd.spine_utils.Spine property) head_mesh_splits_min (neurd.spine_utils.Spine property) head_n_faces (neurd.spine_utils.Spine property) head_neck_shaft (neurd.synapse_utils.Synapse attribute) head_neck_shaft_idx_from_branch() (in module neurd.spine_utils) head_sdf (neurd.spine_utils.Spine attribute) head_skeletal_length (neurd.spine_utils.Spine property) head_volume (neurd.spine_utils.Spine property) head_width (neurd.spine_utils.Spine attribute) head_width_ray (neurd.spine_utils.Spine property) head_width_ray_80_perc (neurd.spine_utils.Spine property) high_degree_branch_errors_dendrite_limb_branch_dict() (in module neurd.error_detection) high_degree_branch_errors_limb_branch_dict() (in module neurd.error_detection) high_degree_branching_coordinates_on_limb() (in module neurd.neuron_utils) high_degree_branching_coordinates_on_neuron() (in module neurd.neuron_utils) high_degree_coordinates_elimination_limb_branch_dict() (in module neurd.proofreading_utils) high_degree_false_positive_low_sibling_filter() (in module neurd.error_detection) high_degree_upstream_match() (in module neurd.error_detection) high_fidelity_axon_decomposition() (in module neurd.preprocess_neuron) high_low_degree_upstream_match_preprocessing() (in module neurd.error_detection)

I

id_from_compartment_index() (in module neurd.spine_utils) id_from_idx() (in module neurd.spine_utils) idx_for_col() (in module neurd.neuron_graph_lite_utils) idx_xyz_to_df() (in module neurd.neuron_graph_lite_utils) in_limb_branch_dict() (in module neurd.neuron_utils) inh_double_back_dendrite_filter() (in module neurd.proofreading_utils) inh_filters_auto_proof() (neurd.vdi_default.DataInterfaceDefault method) inh_high_degree_branching_dendrite_filter() (in module neurd.proofreading_utils) inh_high_degree_branching_filter() (in module neurd.proofreading_utils) inh_low_degree_branching_filter() (in module neurd.proofreading_utils) inhibitory_cells_node_df() (in module neurd.connectome_query_utils) (in module neurd.microns_graph_query_utils) inhibitory_excitatory_classifier() (in module neurd.classification_utils) inhibitory_nodes() (in module neurd.connectome_utils) init_cave_client() (in module neurd.cave_client_utils)

injest_nested_dict() (in module neurd.parameter_utils) is_apical_shaft_in_downstream_branches() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) is_axon() (in module neurd.neuron_searching) is_axon_in_downstream_branches() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) is_axon_like() (in module neurd.neuron_searching) is_branch_mesh_connected_to_neighborhood() (in module neurd.neuron_searching) (in module neurd.neuron_utils) is_branch_obj() (in module neurd.neuron_utils) is_label_in_downstream_branches() (in module neurd.neuron_statistics) is_limb_obj() (in module neurd.neuron_utils) is_neuron_obj() (in module neurd.neuron_utils) is_skeleton_upstream_to_downstream() (in module neurd.branch_utils) is_spine_obj() (in module neurd.spine_utils)

J

json_dict() (neurd.parameter_utils.Parameters method)

jsonable_dict() (in module neurd.parameter_utils)

L

label_limb_branch_dict() (in module neurd.neuron_utils) (neurd.neuron.Neuron method) labels() (in module neurd.neuron_searching) labels_extract() (in module neurd.neuron_graph_lite_utils) labels_restriction() (in module neurd.neuron_searching) largest_mesh_piece() (in module neurd.soma_extraction_utils) layer_from_em_centroid_xyz() (in module neurd.microns_volume_utils) Limb (class in neurd.neuron) limb_area (neurd.neuron.Neuron property) limb_branch_after_limb_branch_removal() (in module neurd.neuron_utils) limb_branch_after_limb_edge_removal() (in module neurd.neuron_utils) limb_branch_combining() (in module neurd.neuron_utils) limb_branch_compartment_dict_from_limb_branch_face_and_compartment_faces_dict() (in module neurd.apical_utils) limb_branch_dict (neurd.neuron.Neuron property) limb_branch_dict_to_cancel_to_red_blue_groups() (in module neurd.proofreading_utils) limb_branch_dict_to_connected_components() (in module neurd.neuron_utils) limb_branch_dict_to_faces() (in module neurd.neuron_utils) limb_branch_dict_to_limb_true_false_dict() (in module neurd.neuron_utils) limb_branch_dict_to_search_for_spines() (in module neurd.spine_utils) limb_branch_dict_to_skeleton() (in module neurd.neuron_utils) limb_branch_dict_valid() (in module neurd.neuron_utils) limb_branch_dicts_to_combined_color_dict() (in module neurd.neuron_visualizations) limb_branch_face_idx_dict_from_neuron_obj_overlap_with_face_idx_on_reference_mesh() (in module neurd.neuron_utils) limb_branch_from_candidate() (in module neurd.neuron_utils) limb_branch_from_edge_function() (in module neurd.neuron_utils) limb_branch_from_keywords() (in module neurd.neuron_utils) limb_branch_from_limbs() (in module neurd.neuron_utils) limb_branch_from_stats_df() (in module neurd.neuron_statistics) limb_branch_get() (in module neurd.neuron_utils) limb_branch_intersection() (in module neurd.neuron_utils) limb_branch_invert() (in module neurd.neuron_utils) limb_branch_list_to_limb_branch_dict() (in module neurd.neuron_utils) limb_branch_removed_after_limb_branch_removal() (in module neurd.neuron_utils) limb_branch_setdiff() (in module neurd.neuron_utils) limb_branch_str_names_from_limb_branch_dict() (in module neurd.neuron_utils) limb_branch_synapses_to_scatter_info() (in module neurd.synapse_utils)

limb_branch_union() (in module neurd.neuron_utils) limb_branch_with_synapses() (in module neurd.synapse_utils) limb_correspondence (neurd.neuron.Limb property) limb_correspondence_on_limb() (in module neurd.neuron_utils) limb_correspondence_on_neuron() (in module neurd.neuron_utils) limb_correspondence_plottable() (in module neurd.neuron_visualizations) limb_edge_dict_with_function() (in module neurd.neuron_utils) limb_error_branches() (in module neurd.neuron_searching) limb_errors_to_cancel_to_red_blue_group() (in module neurd.proofreading_utils) limb_features_from_compartment() (in module neurd.apical_utils) limb_features_from_compartment_over_neuron() (in module neurd.apical_utils) limb_idx (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute) limb_idx() (in module neurd.neuron_utils) limb_label() (in module neurd.neuron_utils) limb_mesh_from_branches() (in module neurd.neuron_utils) limb_mesh_volume (neurd.neuron.Neuron property) limb_meshes_expansion() (in module neurd.preprocess_neuron) limb_red_blue_dict_from_red_blue_splits() (in module neurd.soma_splitting_utils) limb_to_soma_mapping() (in module neurd.neuron_utils) limb_true_false_dict_to_limb_branch_dict() (in module neurd.neuron_utils) limbs (neurd.neuron.Neuron property) load_border_exc_inh_df() (in module neurd.cell_type_utils) load_cave_token() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) load_edge_df() (in module neurd.microns_graph_query_utils) load_G_with_attrs() (in module neurd.neuron_graph_lite_utils) load_manual_exc_inh_df() (in module neurd.cell_type_utils) load_neuron_obj() (neurd.vdi_default.DataInterfaceBoilerplate method) load_neuron_obj_auto_proof() (neurd.vdi_default.DataInterfaceDefault method) load_node_df() (in module neurd.microns_graph_query_utils) low_branch_length_clusters() (in module neurd.neuron_utils) low_branch_length_large_clusters() (in module neurd.proofreading_utils) low_branch_length_large_clusters_axon() (in module neurd.proofreading_utils) low_branch_length_large_clusters_dendrite() (in module neurd.proofreading_utils) low_degree_branch_errors_limb_branch_dict() (in module neurd.error_detection) low_degree_upstream_match() (in module neurd.error_detection)

M

make_filter_dict() (in module neurd.proofreading_utils) map_cell_type_fine_publishable() (in module neurd.cell_type_utils) map_new_limb_node_value() (in module neurd.neuron_searching) matched_branches_by_angle() (in module neurd.error_detection) matched_branches_by_angle_at_coordinate() (in module neurd.error_detection) matching_label() (in module neurd.neuron_searching) max_height_for_multi_soma() (in module neurd.apical_utils) max_layer_distance_above_soma_over_candidate() (in module neurd.neuron_statistics) max_layer_height_over_candidate() (in module neurd.neuron_statistics) max_limb_n_branches (neurd.neuron.Neuron property) max_limb_n_branches() (in module neurd.neuron_utils) max_limb_skeletal_length (neurd.neuron.Neuron property) max_limb_skeletal_length() (in module neurd.neuron_utils) max_soma_area (neurd.neuron.Neuron property) max_soma_area() (in module neurd.neuron_utils) max_soma_n_faces (neurd.neuron.Neuron property) max_soma_n_faces() (in module neurd.neuron_utils) max_soma_volume (neurd.neuron.Neuron property) max_soma_volume() (in module neurd.neuron_utils) mean_axon_skeletal_length() (in module neurd.connectome_utils) mean_dendrite_skeletal_length() (in module neurd.connectome_utils) mean_mesh_center() (in module neurd.neuron_searching) median_branch_length (neurd.neuron.Neuron property) median_branch_length() (in module neurd.neuron_utils) median_mesh_center() (in module neurd.neuron_searching) merge_error_red_blue_suggestions_clean() (in module neurd.proofreading_utils) merge_filter_locations (neurd.neuron.Neuron property) merge_filter_suggestions (neurd.neuron.Neuron property) merge_floating_end_nodes_to_parent() (in module neurd.neuron_simplification) merge_limbs() (in module neurd.neuron_searching) merge_type_to_color() (in module neurd.proofreading_utils) mesh (neurd.spine_utils.Spine attribute) mesh_attribute_from_compartment() (in module neurd.spine_utils) mesh_center (neurd.spine_utils.Spine property) mesh_center_x (neurd.neuron.Branch property) mesh_center_x_nm (neurd.spine_utils.Spine property) mesh_center_xyz() (in module neurd.neuron_graph_lite_utils) mesh_center_y (neurd.neuron.Branch property) mesh_center_y_nm (neurd.spine_utils.Spine property) mesh_center_z (neurd.neuron.Branch property) mesh_center_z_nm (neurd.spine_utils.Spine property) mesh_correspondence_first_pass() (in module neurd.preprocess_neuron) mesh_errored_synapses_post (neurd.neuron.Neuron property) mesh_errored_synapses_pre (neurd.neuron.Neuron property) mesh_face_idx (neurd.spine_utils.Spine attribute) mesh_from_branches (neurd.neuron.Neuron property) mesh_from_compartment() (in module neurd.spine_utils) mesh_from_name_or_idx() (in module neurd.spine_utils) mesh_from_seg_id() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) mesh_kdtree (neurd.neuron.Neuron property) mesh_minus_spine_objs() (in module neurd.spine_utils) mesh_not_in_neuron_branches() (in module neurd.neuron_utils) mesh_over_candidate() (in module neurd.neuron_utils) mesh_over_limb_branch_dict() (in module neurd.neuron_utils) mesh_shaft (neurd.neuron.Branch property) mesh_shaft() (in module neurd.branch_utils) mesh_shaft_idx (neurd.neuron.Branch property) mesh_shaft_idx() (in module neurd.branch_utils) mesh_volume (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) (neurd.neuron.Soma property) mesh_volume_with_somas (neurd.neuron.Neuron property) mesh_without_boutons() (in module neurd.neuron_utils) mesh_without_mesh_attribute() (in module neurd.neuron_utils) microns_volume_bbox_corners() (in module neurd.microns_volume_utils) microns_volume_bbox_midpoint() (in module neurd.microns_volume_utils) min_dist_synapse_endpoint() (in module neurd.branch_utils) min_dist_synapses_post_downstream (neurd.neuron.Branch property) min_dist_synapses_post_downstream() (in module neurd.branch_utils) min_dist_synapses_post_upstream (neurd.neuron.Branch property) min_dist_synapses_post_upstream() (in module neurd.branch_utils) min_dist_synapses_pre_downstream (neurd.neuron.Branch property) min_dist_synapses_pre_downstream() (in module neurd.branch_utils) min_dist_synapses_pre_upstream (neurd.neuron.Branch property) min_dist_synapses_pre_upstream() (in module neurd.branch_utils) min_synapse_dist_to_branch_point() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) min_synapse_dist_to_branch_point_filter() (in module neurd.graph_filters) min_width_upstream() (in module neurd.neuron_utils)

modes_global_param_and_attributes_dict_all_modules() (in module neurd.parameter_utils) modes_global_param_and_attributes_dict_from_module() (in module neurd.parameter_utils) module neurd neurd.ais_utils neurd.apical_utils neurd.axon_utils neurd.branch_attr_utils neurd.branch_utils neurd.cave_client_utils neurd.cave_interface neurd.cell_type_utils neurd.classification_utils neurd.concept_network_utils neurd.connectome_analysis_utils neurd.connectome_query_utils neurd.connectome_utils neurd.dandi_utils neurd.documentation_utils neurd.error_detection neurd.functional_tuning_utils neurd.graph_filters neurd.h01_volume_utils neurd.limb_utils neurd.microns_graph_query_utils neurd.microns_volume_utils neurd.motif_null_utils neurd.motif_utils neurd.nature_paper_plotting neurd.neuron neurd.neuron_geometry_utils neurd.neuron_graph_lite_utils neurd.neuron_pipeline_utils neurd.neuron_searching neurd.neuron_simplification neurd.neuron_statistics neurd.neuron_utils neurd.neuron_visualizations neurd.nwb_utils neurd.parameter_configs neurd.parameter_configs.parameters_config_default neurd.parameter_configs.parameters_config_default_old neurd.parameter_configs.parameters_config_h01 neurd.parameter_configs.parameters_config_microns neurd.parameter_utils neurd.preprocess_neuron neurd.proofreading_utils neurd.proximity_analysis_utils neurd.proximity_utils neurd.soma_extraction_utils neurd.soma_splitting_utils neurd.spine_utils neurd.synapse_utils neurd.vdi_default neurd.vdi_h01 neurd.vdi_microns neurd.vdi_microns_cave neurd.version neurd.volume_utils neurd.width_utils module_attr_map() (neurd.parameter_utils.PackageParameters method) module_attr_map_requested() (neurd.parameter_utils.PackageParameters method) most_upstream_branch() (in module neurd.neuron_utils) most_upstream_conn_comp_node() (in module neurd.neuron_utils) most_upstream_conn_comp_node_stat() (in module neurd.neuron_utils) most_upstream_endpoints_of_limb_branch() (in module neurd.limb_utils) most_usptream_endpoints_of_branches_on_limb() (in module neurd.limb_utils) motif_column_mapping() (in module neurd.motif_utils) motif_data() (in module neurd.motif_utils) motif_dicts_from_motif_from_database() (in module neurd.motif_utils) motif_G() (in module neurd.motif_utils) motif_nodes_from_motif() (in module neurd.motif_utils) motif_segment_df_from_motifs() (in module neurd.motif_utils) multi_soma_split_execution() (in module neurd.soma_splitting_utils) (neurd.neuron.Neuron method) multi_soma_split_suggestions() (in module neurd.proofreading_utils) multi_soma_touching_limbs (neurd.neuron.Neuron property) multi_soma_touching_limbs() (in module neurd.neuron_utils) multi_soma_y() (in module neurd.apical_utils) multiplicity() (neurd.vdi_default.DataInterfaceBoilerplate method) myelination_limb_branch_dict() (in module neurd.axon_utils)

N

n_ais_columns() (in module neurd.ais_utils) n_ais_sum_from_min_max_dist() (in module neurd.ais_utils) n_axon_ais_synapses() (in module neurd.synapse_utils) n_boutons (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) n_boutons() (in module neurd.neuron_searching) (in module neurd.neuron_utils) n_boutons_above_thresholds() (in module neurd.neuron_searching) n_branches (neurd.neuron.Limb property) (neurd.neuron.Neuron property) n_branches() (in module neurd.neuron_utils) n_branches_over_limb_branch_dict() (in module neurd.neuron_utils) n_branches_per_limb (neurd.neuron.Neuron property) n_branches_per_limb() (in module neurd.neuron_utils) n_compartment_syn_from_edge_df() (in module neurd.connectome_utils) n_distance_errored_synapses (neurd.neuron.Neuron property) n_distance_errored_synapses_post (neurd.neuron.Neuron property) n_distance_errored_synapses_pre (neurd.neuron.Neuron property) n_downstream_nodes() (in module neurd.neuron_searching) (in module neurd.neuron_utils) n_downstream_nodes_with_skip() (in module neurd.neuron_searching) n_error_limbs (neurd.neuron.Neuron property) n_error_limbs() (in module neurd.neuron_utils) n_excitatory_n_inhibitory_nodes() (in module neurd.connectome_query_utils) (in module neurd.microns_graph_query_utils) n_faces (neurd.neuron.Neuron property) (neurd.spine_utils.Spine property) n_faces() (in module neurd.spine_utils) n_faces_branch() (in module neurd.neuron_searching) n_faces_head (neurd.spine_utils.Spine property) n_faces_limb() (in module neurd.neuron_searching) n_faces_neck (neurd.spine_utils.Spine property) n_heads (neurd.spine_utils.Spine property) n_limbs (neurd.neuron.Neuron property) n_limbs() (in module neurd.neuron_utils) n_mesh_errored_synapses (neurd.neuron.Neuron property) n_mesh_errored_synapses_post (neurd.neuron.Neuron property) n_mesh_errored_synapses_pre (neurd.neuron.Neuron property) n_nodes_from_motif() (in module neurd.motif_utils) n_presyns_on_dendrite() (in module neurd.synapse_utils) n_shaft_synapses() (in module neurd.spine_utils) n_siblings() (in module neurd.neuron_searching) n_small_children() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) n_somas (neurd.neuron.Neuron property) n_somas() (in module neurd.neuron_utils) n_spine_compartment_synapses() (in module neurd.spine_utils) n_spine_eligible_branches (neurd.neuron.Neuron property) n_spine_eligible_branches() (in module neurd.neuron_utils) n_spine_syn_from_edge_df() (in module neurd.connectome_utils) n_spines (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) n_spines() (in module neurd.neuron_searching) (in module neurd.neuron_utils) (in module neurd.spine_utils) n_spines_head() (in module neurd.spine_utils) n_spines_neck() (in module neurd.spine_utils) n_spines_no_head() (in module neurd.spine_utils) n_synapses (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) (neurd.neuron.Soma property) n_synapses() (in module neurd.neuron_searching) (in module neurd.synapse_utils) n_synapses_all_compartment_spine_type() (in module neurd.synapse_utils) n_synapses_all_compartments() (in module neurd.synapse_utils) n_synapses_all_spine_labels() (in module neurd.synapse_utils) n_synapses_all_valid_error() (in module neurd.synapse_utils) n_synapses_analysis_axon_dendrite() (in module neurd.synapse_utils) n_synapses_by_compartment_spine_type() (in module neurd.synapse_utils) n_synapses_diff() (in module neurd.neuron_statistics) n_synapses_distance_errored() (in module neurd.synapse_utils) n_synapses_downstream() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) (in module neurd.synapse_utils) n_synapses_downstream_total() (in module neurd.neuron_statistics) n_synapses_downstream_within_dist() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) n_synapses_error (neurd.neuron.Neuron property) n_synapses_error() (in module neurd.synapse_utils) n_synapses_error_post() (in module neurd.synapse_utils) n_synapses_error_pre() (in module neurd.synapse_utils) n_synapses_head (neurd.neuron.Branch property) n_synapses_head() (in module neurd.synapse_utils) n_synapses_mesh_errored() (in module neurd.synapse_utils) n_synapses_neck (neurd.neuron.Branch property) n_synapses_neck() (in module neurd.synapse_utils) n_synapses_no_head (neurd.neuron.Branch property) n_synapses_no_head() (in module neurd.synapse_utils) n_synapses_offset_distance_of_endpoint_downstream() (in module neurd.synapse_utils) n_synapses_offset_distance_of_endpoint_upstream() (in module neurd.synapse_utils) n_synapses_offset_distance_of_endpoint_upstream_downstream() (in module neurd.synapse_utils) n_synapses_offset_endpoint_upstream() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) n_synapses_over_limb_branch_dict() (in module neurd.synapse_utils) n_synapses_post (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) (neurd.neuron.Soma property) n_synapses_post() (in module neurd.neuron_searching) (in module neurd.synapse_utils) n_synapses_post_downstream() (in module neurd.neuron_searching) (in module neurd.synapse_utils) n_synapses_post_downstream_within_dist() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) n_synapses_post_head() (in module neurd.neuron_searching) (in module neurd.synapse_utils) n_synapses_post_neck() (in module neurd.synapse_utils) n_synapses_post_no_head() (in module neurd.synapse_utils) n_synapses_post_offset_distance_of_endpoint_downstream() (in module neurd.synapse_utils) n_synapses_post_offset_distance_of_endpoint_upstream() (in module neurd.synapse_utils) n_synapses_post_over_limb_branch_dict() (in module neurd.synapse_utils) n_synapses_post_shaft() (in module neurd.synapse_utils) n_synapses_post_spine() (in module neurd.neuron_searching) (in module neurd.synapse_utils) n_synapses_post_within_distance_of_endpoint_downstream() (in module neurd.synapse_utils) n_synapses_post_within_distance_of_endpoint_upstream() (in module neurd.synapse_utils) n_synapses_pre (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) (neurd.neuron.Soma property) n_synapses_pre() (in module neurd.neuron_searching) (in module neurd.synapse_utils) n_synapses_pre_downstream() (in module neurd.neuron_searching) (in module neurd.synapse_utils) n_synapses_pre_downstream_within_dist() (in module neurd.neuron_statistics) n_synapses_pre_offset_distance_of_endpoint_downstream() (in module neurd.synapse_utils) n_synapses_pre_offset_distance_of_endpoint_upstream() (in module neurd.synapse_utils) n_synapses_pre_offset_endpoint_upstream() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) n_synapses_pre_over_limb_branch_dict() (in module neurd.synapse_utils) n_synapses_pre_shaft() (in module neurd.synapse_utils) n_synapses_pre_within_distance_of_endpoint_downstream() (in module neurd.synapse_utils) n_synapses_pre_within_distance_of_endpoint_upstream() (in module neurd.synapse_utils) n_synapses_shaft (neurd.neuron.Branch property) n_synapses_shaft() (in module neurd.synapse_utils) n_synapses_somas (neurd.neuron.Neuron property) n_synapses_somas_postsyn() (in module neurd.synapse_utils) n_synapses_spine (neurd.neuron.Branch property) n_synapses_spine() (in module neurd.neuron_searching) (in module neurd.synapse_utils) n_synapses_spine_offset_distance_of_endpoint_downstream() (in module neurd.synapse_utils) n_synapses_spine_offset_distance_of_endpoint_upstream() (in module neurd.synapse_utils) n_synapses_spine_offset_endpoint_upstream() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) n_synapses_spine_within_distance_of_endpoint_downstream() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) (in module neurd.synapse_utils) n_synapses_total (neurd.neuron.Neuron property) n_synapses_upstream() (in module neurd.neuron_statistics) n_synapses_upstream_total() (in module neurd.neuron_statistics) n_synapses_valid (neurd.neuron.Neuron property) n_synapses_valid() (in module neurd.synapse_utils) n_synapses_valid_post() (in module neurd.synapse_utils) n_synapses_valid_pre() (in module neurd.synapse_utils) n_synapses_within_distance_of_endpoint_downstream() (in module neurd.synapse_utils) n_synapses_within_distance_of_endpoint_upstream() (in module neurd.synapse_utils) n_synapses_within_distance_of_endpoint_upstream_downstream() (in module neurd.synapse_utils) n_vertices (neurd.neuron.Neuron property) n_web (neurd.neuron.Branch property) (neurd.neuron.Limb property) n_web() (in module neurd.neuron_utils) name() (in module neurd.documentation_utils) neck_area (neurd.spine_utils.Spine property) neck_bbox_max_x_nm (neurd.spine_utils.Spine property) neck_bbox_max_y_nm (neurd.spine_utils.Spine property) neck_bbox_max_z_nm (neurd.spine_utils.Spine property) neck_bbox_min_x_nm (neurd.spine_utils.Spine property) neck_bbox_min_y_nm (neurd.spine_utils.Spine property) neck_bbox_min_z_nm (neurd.spine_utils.Spine property) neck_bbox_oriented_side_lengths (neurd.spine_utils.Spine attribute) (neurd.spine_utils.Spine property) neck_bbox_oriented_side_max (neurd.spine_utils.Spine property) neck_bbox_oriented_side_middle (neurd.spine_utils.Spine property) neck_bbox_oriented_side_min (neurd.spine_utils.Spine property)

neck_face_idx (neurd.spine_utils.Spine attribute) neck_mesh (neurd.spine_utils.Spine property) neck_mesh() (in module neurd.spine_utils) neck_n_faces (neurd.spine_utils.Spine property) neck_sdf (neurd.spine_utils.Spine attribute) neck_skeletal_length (neurd.spine_utils.Spine property) neck_volume (neurd.spine_utils.Spine property) neck_width (neurd.spine_utils.Spine attribute) neck_width_ray (neurd.spine_utils.Spine property) neck_width_ray_80_perc (neurd.spine_utils.Spine property) neighbor_endpoint() (in module neurd.neuron_utils) neighborhood_mesh() (in module neurd.neuron_utils) network_starting_info (neurd.neuron.Limb property) neurd module neurd.ais_utils module neurd.apical_utils module neurd.axon_utils module neurd.branch_attr_utils module neurd.branch_utils module neurd.cave_client_utils module neurd.cave_interface module neurd.cell_type_utils module neurd.classification_utils module neurd.concept_network_utils module neurd.connectome_analysis_utils module neurd.connectome_query_utils module neurd.connectome_utils module neurd.dandi_utils module neurd.documentation_utils module neurd.error_detection module neurd.functional_tuning_utils module neurd.graph_filters module neurd.h01_volume_utils module neurd.limb_utils module neurd.microns_graph_query_utils module neurd.microns_volume_utils module neurd.motif_null_utils module neurd.motif_utils module neurd.nature_paper_plotting module neurd.neuron module neurd.neuron_geometry_utils module neurd.neuron_graph_lite_utils module neurd.neuron_pipeline_utils module neurd.neuron_searching module neurd.neuron_simplification module neurd.neuron_statistics module neurd.neuron_utils module neurd.neuron_visualizations module neurd.nwb_utils module neurd.parameter_configs module neurd.parameter_configs.parameters_config_default module neurd.parameter_configs.parameters_config_default_old module neurd.parameter_configs.parameters_config_h01 module neurd.parameter_configs.parameters_config_microns module neurd.parameter_utils module neurd.preprocess_neuron module neurd.proofreading_utils module neurd.proximity_analysis_utils module neurd.proximity_utils module neurd.soma_extraction_utils module neurd.soma_splitting_utils module neurd.spine_utils module neurd.synapse_utils module neurd.vdi_default module neurd.vdi_h01 module neurd.vdi_microns module neurd.vdi_microns_cave module neurd.version module neurd.volume_utils module neurd.width_utils module neuroglancer_df_from_edge_df() (in module neurd.connectome_utils) Neuron (class in neurd.neuron) neuron_limb_branch_dict() (in module neurd.neuron_utils) neuron_limb_overwrite() (in module neurd.neuron_utils) neuron_mesh_from_branches() (in module neurd.neuron_utils) neuron_nucleus_df() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) neuron_obj_func() (in module neurd.vdi_default) neuron_path_analysis() (in module neurd.neuron_statistics) neuron_soma_layer_height() (in module neurd.microns_volume_utils) neuron_spine_density() (in module neurd.neuron_utils) neuron_stats() (in module neurd.neuron_statistics) (neurd.neuron.Neuron method) neuron_stats_old() (neurd.neuron.Neuron method) neuron_width_calculation_standard() (in module neurd.width_utils) new_width_from_mesh_skeleton() (in module neurd.width_utils) nm_to_em_voxels() (in module neurd.microns_volume_utils) no_head_face_idx (neurd.spine_utils.Spine property) no_head_mesh (neurd.spine_utils.Spine property) no_head_mesh() (in module neurd.spine_utils) no_spatial_df_from_df_filtered() (in module neurd.neuron_graph_lite_utils) no_spine_average_mesh_center() (in module neurd.neuron_searching) no_spine_mean_mesh_center() (in module neurd.neuron_searching) no_spine_median_mesh_center() (in module neurd.neuron_searching) no_spine_width() (in module neurd.neuron_searching) node_attributes_from_G() (in module neurd.motif_utils) node_attributes_strs() (in module neurd.motif_utils) node_df_from_attribute_value() (in module neurd.connectome_query_utils) (in module neurd.microns_graph_query_utils) node_df_from_query() (in module neurd.connectome_query_utils) (in module neurd.microns_graph_query_utils) node_functions_default() (in module neurd.neuron_statistics) nodes_downstream() (in module neurd.concept_network_utils) nodes_from_motif_dict() (in module neurd.motif_utils) nodes_from_str() (in module neurd.motif_utils) nodes_mapping_from_G() (in module neurd.motif_utils) nodes_to_exclude (neurd.neuron.Limb property) nodes_upstream() (in module neurd.concept_network_utils) nodes_upstream_downstream() (in module neurd.concept_network_utils) non_axon_like_limb_branch_on_dendrite (neurd.neuron.Neuron property) non_axon_like_limb_branch_on_dendrite() (in module neurd.neuron_utils) non_soma_touching_meshes_not_stitched() (in module neurd.neuron_utils) non_soma_touching_meshes_stitched() (in module neurd.neuron_utils) non_upward_skeletal_distance_upstream() (in module neurd.apical_utils) Note (neurd.synapse_utils.Synapse attribute) nuclei_classification_info_from_nucleus_id() (neurd.vdi_default.DataInterfaceDefault method) (neurd.volume_utils.DataInterface method) nuclei_from_segment_id() (neurd.vdi_default.DataInterfaceDefault method) (neurd.volume_utils.DataInterface method) nucleus_id() (neurd.vdi_default.DataInterfaceBoilerplate method) number_of_columns() (in module neurd.spine_utils)

O

oblique_classification() (in module neurd.apical_utils) oblique_limb_branch_dict (neurd.neuron.Neuron property) oblique_limb_branch_dict() (in module neurd.apical_utils) order_branches_by_skeletal_distance_from_soma() (in module neurd.neuron_utils) order_skeleton_by_smallest_endpoint() (neurd.neuron.Branch method) ordered_endpoints_on_branch_path() (in module neurd.neuron_utils)

original_mesh_face_to_limb_branch() (in module neurd.neuron_utils) original_mesh_soma() (in module neurd.soma_extraction_utils) original_mesh_soma_old() (in module neurd.soma_extraction_utils) other_direction() (in module neurd.concept_network_utils) output_global_parameters_glia() (in module neurd.soma_extraction_utils) output_global_parameters_nuclei() (in module neurd.soma_extraction_utils) output_global_parameters_soma() (in module neurd.soma_extraction_utils)

P

PackageParameters (class in neurd.parameter_utils) pair_branch_connected_components() (in module neurd.neuron_utils) pair_branch_connected_components_by_common_upstream() (in module neurd.neuron_utils) pair_neuron_obj_to_nuclei() (in module neurd.neuron_utils) pairwise_presyn_proximity_onto_postsyn() (in module neurd.proximity_analysis_utils) parameter_config_folder() (in module neurd.parameter_utils) parameter_dict_from_module_and_obj() (in module neurd.parameter_utils) parameter_list_from_module() (in module neurd.parameter_utils) Parameters (class in neurd.parameter_utils) parameters_from_filepath() (in module neurd.parameter_utils) parent_angle() (in module neurd.neuron_searching) parent_child_sk_angle() (in module neurd.neuron_statistics) parent_node() (in module neurd.neuron_utils) parent_skeletal_angle() (in module neurd.limb_utils) parent_width() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) path_to_cut_and_coord_dict_from_split_suggestions() (in module neurd.soma_splitting_utils) path_to_edges() (in module neurd.error_detection) plot_3d_attribute() (in module neurd.connectome_utils) plot_3D_distribution_attribute() (in module neurd.connectome_utils) plot_axon() (in module neurd.neuron_visualizations) plot_axon_merge_errors() (in module neurd.neuron_visualizations) plot_boutons() (in module neurd.neuron_visualizations) plot_branch() (in module neurd.neuron_visualizations) plot_branch_groupings() (in module neurd.neuron_visualizations) plot_branch_mesh_attribute() (in module neurd.neuron_visualizations) plot_branch_on_whole_mesh() (in module neurd.neuron_visualizations) plot_branch_pieces() (in module neurd.neuron_visualizations) plot_branch_spines() (in module neurd.neuron_visualizations) plot_branch_with_boutons_old() (in module neurd.neuron_visualizations) plot_branch_with_neighbors() (in module neurd.neuron_visualizations) plot_branches_with_boutons() (in module neurd.neuron_visualizations) plot_branches_with_colors() (in module neurd.neuron_visualizations) plot_branches_with_mesh_attribute() (in module neurd.neuron_visualizations) plot_branches_with_spines() (in module neurd.neuron_visualizations) plot_candidates() (in module neurd.neuron_visualizations) plot_cell_type_edge_stat() (in module neurd.connectome_analysis_utils) plot_cell_type_gnn_embedding() (in module neurd.cell_type_utils) plot_cell_type_pre_post_attribute_hist() (in module neurd.connectome_utils) plot_classifier_map() (in module neurd.cell_type_utils) plot_compartment_mesh_and_skeleton() (in module neurd.apical_utils) plot_compartment_vector_distribution() (in module neurd.neuron_geometry_utils) plot_compartments() (in module neurd.neuron_visualizations) plot_concept_network() (in module neurd.neuron_visualizations) plot_connetion_type_head_vs_spine_size_by_conn_type_kde() (in module neurd.spine_utils) plot_correspondence() (in module neurd.preprocess_neuron) plot_correspondence_on_single_mesh() (in module neurd.preprocess_neuron) plot_dendrite_and_synapses() (in module neurd.neuron_visualizations) plot_df_xyz() (in module neurd.neuron_graph_lite_utils) plot_e_i_model_classifier_map() (in module neurd.cell_type_utils) plot_edit_labels_subset() (in module neurd.nature_paper_plotting) plot_feature_histograms_with_ct_overlay() (in module neurd.spine_utils) plot_functional_connection_from_df() (in module neurd.connectome_utils) plot_head_neck() (in module neurd.spine_utils) (neurd.spine_utils.Spine method) plot_head_neck_shaft_synapses() (in module neurd.synapse_utils) plot_histogram_discrete_labels() (in module neurd.connectome_analysis_utils) plot_intermediates() (in module neurd.neuron_visualizations) plot_ipv_mesh() (in module neurd.neuron_visualizations) plot_ipv_scatter() (in module neurd.neuron_visualizations) plot_ipv_skeleton() (in module neurd.neuron_visualizations) plot_labeled_limb_branch_dicts() (in module neurd.neuron_visualizations) plot_limb() (in module neurd.neuron_visualizations) plot_limb_branch_dict() (in module neurd.neuron_visualizations) plot_limb_branch_dict_multiple() (in module neurd.neuron_visualizations) plot_limb_concept_network() (neurd.neuron.Neuron method) plot_limb_concept_network_2D() (in module neurd.neuron_visualizations) plot_limb_correspondence() (in module neurd.neuron_visualizations) plot_limb_correspondence_multiple() (in module neurd.neuron_visualizations) plot_limb_idx() (in module neurd.neuron_visualizations) plot_limb_path() (in module neurd.neuron_visualizations) plot_limb_to_red_blue_groups() (in module neurd.proofreading_utils) plot_merge_filter_suggestions() (in module neurd.neuron_visualizations) plot_mesh_face_idx() (in module neurd.neuron_visualizations) plot_meshes_skeletons() (in module neurd.neuron_visualizations) plot_original_vs_proofread() (in module neurd.neuron_visualizations) plot_prox_func_vs_attribute_from_edge_df() (in module neurd.proximity_analysis_utils) plot_proximity() (in module neurd.proximity_utils) plot_red_blue_split_suggestions_per_limb() (in module neurd.soma_splitting_utils)

plot_restricted_edge_df_delta_ori() (in module neurd.connectome_utils) plot_soma_dist_distr() (in module neurd.connectome_utils) plot_soma_extraction_meshes() (in module neurd.neuron_visualizations) plot_soma_limb_concept_network() (in module neurd.neuron_visualizations) (neurd.neuron.Neuron method) plot_soma_meshes() (in module neurd.neuron_visualizations) plot_soma_products() (in module neurd.soma_extraction_utils) plot_spine_attribute_vs_category_from_spine_df_samples() (in module neurd.spine_utils) plot_spine_coordinates_from_spine_df() (in module neurd.spine_utils) plot_spine_embeddings_kde() (in module neurd.spine_utils) plot_spine_face_idx_dict() (in module neurd.spine_utils) plot_spine_feature_hist() (in module neurd.spine_utils) plot_spine_objs() (in module neurd.spine_utils) plot_spine_objs_and_syn_from_syn_df() (in module neurd.spine_utils) plot_spine_objs_on_branch() (in module neurd.spine_utils) plot_spine_synapse_coords_dict() (in module neurd.spine_utils) plot_spines() (in module neurd.neuron_visualizations) plot_spines_head_neck() (in module neurd.neuron_visualizations) (in module neurd.spine_utils) plot_spines_objs_with_head_neck_and_coordinates() (in module neurd.spine_utils) plot_split_suggestions_per_limb() (in module neurd.neuron_visualizations) plot_synapses() (in module neurd.neuron_visualizations) (in module neurd.synapse_utils) plot_synapses_compartment() (in module neurd.synapse_utils) plot_synapses_error_from_neuron_obj() (in module neurd.synapse_utils) plot_synapses_objs() (in module neurd.synapse_utils) plot_synapses_on_limb() (in module neurd.synapse_utils) plot_synapses_presyn_dendrite_errors() (in module neurd.synapse_utils) plot_synapses_query() (in module neurd.synapse_utils) plot_synapses_soma() (in module neurd.synapse_utils) plot_synapses_valid_from_neuron_obj() (in module neurd.synapse_utils) plot_valid_error_synapses() (in module neurd.neuron_visualizations) plot_valid_error_synpases() (in module neurd.synapse_utils) plot_visual_area_xz_projection() (in module neurd.microns_volume_utils) plot_web_intersection() (in module neurd.neuron_visualizations) plottable_from_branches() (in module neurd.neuron_visualizations) plottable_meshes() (in module neurd.neuron_visualizations) plottable_meshes_skeletons() (in module neurd.neuron_visualizations) plottable_skeletons() (in module neurd.neuron_visualizations) plotting_edge_df_delta_ori() (in module neurd.connectome_utils) postsyn_branches_near_soma() (in module neurd.cell_type_utils) postsyn_branches_near_soma_for_syn_post_density() (in module neurd.cell_type_utils) postsyn_df_from_seg_id() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) postsyn_proximity_data() (in module neurd.proximity_utils) postsyn_skeletal_distance_to_soma_from_edge_dict() (in module neurd.connectome_utils) pre_post_df_from_seg_id() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) pre_post_node_names_from_synapse_id() (in module neurd.connectome_utils) pre_post_synapse_ids_coords_from_connectome() (neurd.vdi_default.DataInterfaceBoilerplate method) predict_class_single_datapoint() (in module neurd.cell_type_utils) prepost_syn_df_from_cave_syn_df() (in module neurd.cave_client_utils) preprocess_limb() (in module neurd.preprocess_neuron) preprocess_neuron() (in module neurd.preprocess_neuron) presyn_df_from_seg_id() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) presyn_on_dendrite_synapses() (in module neurd.synapse_utils) presyn_on_dendrite_synapses_after_axon_on_dendrite_filter_away() (in module neurd.synapse_utils) presyn_on_dendrite_synapses_non_axon_like() (in module neurd.synapse_utils) presyn_postsyn_groups_from_synapses_obj() (in module neurd.synapse_utils) presyn_postsyn_skeletal_path_from_synapse_id() (in module neurd.connectome_utils) presyn_postsyn_soma_relative_synapse_coordinate() (in module neurd.connectome_utils) presyn_postsyn_walk_euclidean_skeletal_dist() (in module neurd.connectome_utils) presyn_proximity_data() (in module neurd.proximity_utils) presyn_soma_postsyn_soma_euclid_dist_axis() (in module neurd.connectome_utils) presyns_on_dendrite() (in module neurd.synapse_utils) presyns_with_soma_postsyns() (in module neurd.connectome_utils) print_compartment_features_dict_for_dj_table() (in module neurd.apical_utils) print_filter_spine_thresholds() (in module neurd.spine_utils) print_merge_type_color_map() (in module neurd.proofreading_utils) print_n_dict() (in module neurd.proximity_analysis_utils) proof_version (neurd.vdi_default.DataInterfaceBoilerplate attribute) proofread_neuron() (in module neurd.proofreading_utils) proofread_neuron_class_predetermined() (in module neurd.proofreading_utils) proofread_neuron_full() (in module neurd.proofreading_utils) proofreading_table_processing() (in module neurd.proofreading_utils) proximity_pre_post() (in module neurd.proximity_utils) proximity_search_neurons_from_bounding_box() (in module neurd.proximity_utils) proximity_search_neurons_from_database() (in module neurd.proximity_utils)

Q

query_neuron() (in module neurd.neuron_searching) query_neuron_by_labels() (in module neurd.neuron_searching)

query_spine_objs() (in module neurd.spine_utils) query_synapses() (in module neurd.synapse_utils) query_with_edge_col() (in module neurd.motif_utils)

R

radius_cell_type_sampling() (in module neurd.connectome_utils) radius_for_rotation_from_proj_magn() (in module neurd.h01_volume_utils) ray_trace_perc() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) recalculate_endpoints_and_order_skeletons_for_branch() (in module neurd.neuron_utils) recalculate_endpoints_and_order_skeletons_over_neuron() (in module neurd.neuron_utils) red_blue_split_dict_by_limb_from_red_blue_split_results() (in module neurd.soma_splitting_utils) refine_axon_for_high_fidelity_skeleton() (in module neurd.proofreading_utils) refine_width_array_to_match_skeletal_coordinates() (in module neurd.branch_utils) relation_skeletal_angle() (in module neurd.limb_utils) release_from_release_name() (in module neurd.cave_client_utils) release_name_from_client() (in module neurd.cave_client_utils) release_name_from_release() (in module neurd.cave_client_utils) remove_nuclei_and_glia_meshes() (in module neurd.soma_extraction_utils) rename_cell_type_fine_column() (in module neurd.cell_type_utils) rename_dict_for_cell_type_fine() (in module neurd.cell_type_utils) reset_concept_network_branch_endpoints() (in module neurd.neuron_simplification) resolving_crossovers() (in module neurd.error_detection)

restrict_by_branch_and_upstream_skeletal_length() (in module neurd.neuron_searching) restrict_edge_df() (in module neurd.connectome_utils) restrict_edge_df_by_cell_type_and_layer() (in module neurd.connectome_utils) restrict_edge_df_by_types_compartment() (in module neurd.connectome_analysis_utils) restrict_meshes_to_shaft_meshes_without_coordinates() (in module neurd.spine_utils) restrict_skeleton_from_start_plus_offset_downstream() (in module neurd.neuron_utils) restrict_skeleton_from_start_plus_offset_upstream() (in module neurd.neuron_utils) restrict_synapses_df_by_limb_branch_dict() (in module neurd.synapse_utils) return_concept_network() (in module neurd.neuron_utils) root_skeleton_vector_from_soma() (in module neurd.limb_utils) root_width() (in module neurd.limb_utils) roots_stat() (in module neurd.neuron_utils) rotate_mesh_from_matrix() (in module neurd.h01_volume_utils) rotation_from_proj_error_and_radius() (in module neurd.h01_volume_utils) rotation_from_soma_center() (in module neurd.h01_volume_utils) rotation_signed_from_middle_vector() (in module neurd.h01_volume_utils) run_limb_function() (in module neurd.neuron_searching) run_options (class in neurd.neuron_searching)

S

same_soma_multi_touching_limbs (neurd.neuron.Neuron property) same_soma_multi_touching_limbs() (in module neurd.neuron_utils) save_cave_token_to_cloudvolume_secrets() (in module neurd.cave_client_utils) save_compressed_neuron() (in module neurd.neuron_utils) (neurd.neuron.Neuron method) save_G_with_attrs() (in module neurd.neuron_graph_lite_utils) save_neuron_obj() (neurd.vdi_default.DataInterfaceBoilerplate method) save_neuron_obj_auto_proof() (neurd.vdi_default.DataInterfaceDefault method) save_neuron_object() (neurd.neuron.Neuron method) save_off_meshes_skeletons() (in module neurd.proofreading_utils) scale_stats_df() (in module neurd.spine_utils) sdf (neurd.spine_utils.Spine attribute) sdf_70_perc (neurd.spine_utils.Spine property) sdf_90_perc (neurd.spine_utils.Spine property) sdf_filter() (in module neurd.neuron_utils) sdf_mean (neurd.spine_utils.Spine property) sdf_median (neurd.spine_utils.Spine property) sdf_median_mean_difference() (in module neurd.spine_utils) seg_split_spine() (in module neurd.spine_utils) seg_split_spine_from_df() (in module neurd.spine_utils) segment_id_and_split_index() (neurd.vdi_default.DataInterfaceBoilerplate method) segment_id_from_seg_split_id() (in module neurd.connectome_utils) segment_id_to_synapse_df() (neurd.vdi_default.DataInterfaceDefault method) (neurd.vdi_h01.DataInterfaceH01 method) (neurd.vdi_microns.DataInterfaceMicrons method) (neurd.vdi_microns_cave.DataInterfaceMicrons method) segment_id_to_synapse_dict() (neurd.h01_volume_utils.DataInterface method) (neurd.microns_volume_utils.DataInterface method) (neurd.vdi_default.DataInterfaceBoilerplate method) (neurd.volume_utils.DataInterface method) segment_id_to_synapse_table_optimized() (neurd.vdi_default.DataInterfaceBoilerplate method) segment_id_to_synapse_table_optimized_connectome() (neurd.vdi_default.DataInterfaceDefault method) segment_id_to_synapse_table_optimized_proofread() (neurd.vdi_default.DataInterfaceDefault method) segment_ids_from_synapse_ids() (in module neurd.connectome_utils) segment_ids_with_nucleus() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) set_attribute_dict() (neurd.neuron.Limb method) (neurd.neuron.Neuron method) set_branch_attr_on_limb() (in module neurd.branch_utils) set_branch_attr_on_limb_on_neuron() (in module neurd.branch_utils) set_branch_attribute_over_neuron() (in module neurd.neuron_utils) set_branch_head_neck_shaft_idx() (in module neurd.spine_utils) set_branch_spines_obj() (in module neurd.spine_utils) set_branch_synapses_attribute() (in module neurd.synapse_utils) set_branch_synapses_compartment() (in module neurd.synapse_utils) set_branch_synapses_head_neck_shaft() (in module neurd.spine_utils) set_branches_endpoints_upstream_downstream_idx() (in module neurd.branch_utils) (neurd.neuron.Limb method) set_branches_endpoints_upstream_downstream_idx_on_limb() (in module neurd.branch_utils) set_cave_auth() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) set_compartment_flat() (in module neurd.motif_utils) set_computed_attribute_data() (neurd.neuron.Limb method) (neurd.neuron.Neuron method) set_concept_network_directional() (neurd.neuron.Limb method) set_concept_network_edges_from_current_starting_data() (neurd.neuron.Limb method) set_e_i_model() (in module neurd.cell_type_utils) set_e_i_model_as_kNN() (in module neurd.cell_type_utils) set_edge_attribute_from_node_attribute() (in module neurd.connectome_utils) set_edge_presyn_postsyn_centroid() (in module neurd.connectome_utils) set_endpoints_upstream_downstream_idx_from_upstream_coordinate() (in module neurd.branch_utils) set_endpoints_upstream_downstream_idx_on_branch() (in module neurd.branch_utils) set_global_table_names() (in module neurd.cave_client_utils) set_limb_branch_idx_to_attr() (in module neurd.branch_attr_utils) set_limb_branch_idx_to_synapses() (in module neurd.synapse_utils) set_limb_functions_for_search() (in module neurd.neuron_searching) set_neuron_head_neck_shaft_idx() (in module neurd.spine_utils) set_neuron_spine_attribute() (in module neurd.spine_utils) set_neuron_spines_obj() (in module neurd.spine_utils) set_neuron_synapses_compartment() (in module neurd.apical_utils) (in module neurd.synapse_utils) set_neuron_synapses_head_neck_shaft() (in module neurd.spine_utils) set_parameters_for_directory_modules() (neurd.vdi_default.DataInterfaceBoilerplate method) set_parameters_for_directory_modules_from_obj() (in module neurd.parameter_utils) set_parameters_obj() (neurd.vdi_default.DataInterfaceBoilerplate method) set_parameters_obj_from_dict() (neurd.vdi_default.DataInterfaceBoilerplate method) set_parameters_obj_from_filepath() (neurd.vdi_default.DataInterfaceBoilerplate method) set_preprocessed_data_from_limb_no_mesh_change() (in module neurd.neuron_utils) set_presyns_on_dendrite_as_errors() (in module neurd.synapse_utils) set_presyns_on_dendrite_as_errors_default() (in module neurd.synapse_utils) set_shaft_synapses_from_spine_query() (in module neurd.spine_utils) set_soma_synapses_spine_label() (in module neurd.spine_utils) set_synapse_filepath() (neurd.vdi_default.DataInterfaceDefault method) (neurd.volume_utils.DataInterface method) set_volume_params() (in module neurd) set_zoom() (in module neurd.neuron_visualizations) set_zoom_to_limb_branch() (in module neurd.neuron_visualizations) shaft_border_area (neurd.spine_utils.Spine property) shaft_synapses() (in module neurd.spine_utils) shared_skeleton_endpoints_for_connected_branches() (in module neurd.neuron_utils) short_thick_branches_limb_branch_dict() (in module neurd.axon_utils) shortest_distance_from_soma_multi_soma() (in module neurd.neuron_statistics) shortest_path() (in module neurd.neuron_utils) sibling_angle_max() (in module neurd.neuron_searching) sibling_angle_min() (in module neurd.neuron_searching) sibling_nodes() (in module neurd.neuron_utils) sibling_sk_angle() (in module neurd.neuron_statistics) siblings_skeletal_angle() (in module neurd.limb_utils) siblings_skeletal_angle_max() (in module neurd.limb_utils) siblings_skeletal_angle_min() (in module neurd.limb_utils) side_length_check() (in module neurd.soma_extraction_utils) side_length_ratios() (in module neurd.soma_extraction_utils) skeletal_angles_df() (in module neurd.limb_utils) skeletal_coordinates_dist_upstream_to_downstream (neurd.neuron.Branch property) skeletal_coordinates_dist_upstream_to_downstream() (in module neurd.branch_utils) skeletal_coordinates_upstream_to_downstream (neurd.neuron.Branch property) skeletal_coordinates_upstream_to_downstream() (in module neurd.branch_utils) skeletal_distance_from_soma() (in module neurd.neuron_searching) (in module neurd.neuron_utils) skeletal_distance_from_soma_excluding_node() (in module neurd.neuron_searching) skeletal_length (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) (neurd.spine_utils.Spine attribute) (neurd.spine_utils.Spine property) skeletal_length() (in module neurd.neuron_searching) (in module neurd.neuron_utils) skeletal_length_along_path() (in module neurd.neuron_statistics) skeletal_length_downstream() (in module neurd.concept_network_utils) (in module neurd.neuron_searching) (in module neurd.neuron_statistics) skeletal_length_downstream_total() (in module neurd.neuron_statistics) skeletal_length_eligible (neurd.neuron.Branch property) (neurd.neuron.Neuron property) skeletal_length_eligible() (in module neurd.neuron_utils) skeletal_length_from_compartment() (in module neurd.spine_utils) skeletal_length_from_spine() (in module neurd.spine_utils) skeletal_length_over_candidate() (in module neurd.neuron_statistics) (in module neurd.neuron_utils) skeletal_length_over_downstream_branches() (in module neurd.neuron_utils) skeletal_length_over_limb_branch() (in module neurd.neuron_utils) skeletal_length_upstream() (in module neurd.concept_network_utils) (in module neurd.neuron_statistics) skeletal_length_upstream_downstream() (in module neurd.concept_network_utils) skeletal_length_upstream_total() (in module neurd.neuron_statistics) skeleton (neurd.neuron.Limb property) (neurd.neuron.Neuron property) (neurd.spine_utils.Spine attribute) (neurd.spine_utils.Spine property) skeleton_adjust() (in module neurd.branch_utils) skeleton_angle_from_top() (in module neurd.branch_utils) skeleton_coordinate_connecting_to_downstream_branches() (in module neurd.neuron_utils) skeleton_dist_match_ref_vector() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) skeleton_dist_match_ref_vector_sum_over_branches() (in module neurd.neuron_statistics) skeleton_dist_match_ref_vector_sum_over_branches_downstream() (in module neurd.neuron_statistics) skeleton_dist_match_ref_vector_sum_over_branches_upstream() (in module neurd.neuron_statistics) skeleton_distance_branch() (in module neurd.neuron_searching) skeleton_distance_limb() (in module neurd.neuron_searching) skeleton_downstream() (in module neurd.concept_network_utils) (in module neurd.neuron_statistics) skeleton_downstream_restricted() (in module neurd.concept_network_utils) skeleton_from_spine() (in module neurd.spine_utils) skeleton_graph (neurd.neuron.Branch property) skeleton_length_per_limb (neurd.neuron.Neuron property) skeleton_length_per_limb() (in module neurd.neuron_utils) skeleton_nodes_from_branches_on_limb() (in module neurd.neuron_utils) skeleton_nodes_from_limb_branch() (in module neurd.neuron_utils) skeleton_over_candidate() (in module neurd.neuron_utils) skeleton_over_limb_branch_dict() (in module neurd.neuron_utils) skeleton_perc_dist_match_ref_vector() (in module neurd.neuron_statistics) skeleton_perc_match_ref_vector() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) skeleton_points_along_path() (in module neurd.neuron_utils) skeleton_resized_ordered() (in module neurd.width_utils) skeleton_stats_axon() (in module neurd.neuron_statistics) skeleton_stats_compartment() (in module neurd.neuron_statistics) skeleton_stats_dendrite() (in module neurd.neuron_statistics) skeleton_stats_from_neuron_obj() (in module neurd.neuron_statistics) skeleton_touching_branches() (in module neurd.neuron_utils) skeleton_upstream() (in module neurd.concept_network_utils) (in module neurd.neuron_statistics) skeleton_upstream_downstream() (in module neurd.concept_network_utils) skeleton_vector_downstream (neurd.neuron.Branch property) skeleton_vector_downstream() (in module neurd.branch_utils) skeleton_vector_endpoint() (in module neurd.branch_utils) skeleton_vector_upstream (neurd.neuron.Branch property) skeleton_vector_upstream() (in module neurd.branch_utils) skip_distance_from_branch_width() (in module neurd.error_detection) smaller_preprocessed_data() (in module neurd.neuron_utils) Soma (class in neurd.neuron) soma_angle_extrema_from_compartment() (in module neurd.apical_utils) soma_angle_max_from_compartment() (in module neurd.apical_utils) soma_angle_min_from_compartment() (in module neurd.apical_utils) soma_area (neurd.neuron.Neuron property) soma_branch_df_split() (in module neurd.neuron_graph_lite_utils) soma_center_from_df() (in module neurd.neuron_graph_lite_utils) soma_center_from_segment_id() (in module neurd.connectome_utils) soma_centers() (in module neurd.neuron_utils) soma_centers_from_node_df() (in module neurd.connectome_query_utils) (in module neurd.connectome_utils) (in module neurd.microns_graph_query_utils) soma_centers_from_node_query() (in module neurd.connectome_query_utils) (in module neurd.microns_graph_query_utils) soma_centers_from_segment_ids() (in module neurd.connectome_utils) soma_connections_from_split_title() (in module neurd.proofreading_utils) soma_connectivity (in module neurd.soma_extraction_utils) soma_distance (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute) soma_distance_branch_set() (in module neurd.neuron_statistics) soma_distance_euclidean (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute) soma_distance_euclidean_branch_set() (in module neurd.neuron_statistics) soma_distance_skeletal_branch_set() (in module neurd.neuron_statistics) soma_distances_from_microns_volume_bbox_midpoint() (in module neurd.microns_volume_utils) soma_face_offset_value() (in module neurd.synapse_utils) soma_idx_and_group_from_name() (in module neurd.neuron_utils) soma_indentification() (in module neurd.soma_extraction_utils) soma_label() (in module neurd.neuron_utils) soma_mesh_volume (neurd.neuron.Neuron property) soma_names_from_split_title() (in module neurd.proofreading_utils) soma_nm_coordinate() (neurd.vdi_default.DataInterfaceDefault method) soma_starting_angle() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) soma_starting_vector() (in module neurd.neuron_statistics) soma_stats_for_cell_type() (in module neurd.cell_type_utils) soma_synapses() (in module neurd.synapse_utils) soma_synapses_to_scatter_info() (in module neurd.synapse_utils) soma_volume_check() (in module neurd.soma_extraction_utils) soma_volume_ratio() (in module neurd.soma_extraction_utils) Spine (class in neurd.spine_utils) spine_and_syn_df_computed_from_neuron_obj() (in module neurd.spine_utils) spine_area (neurd.spine_utils.Spine property) spine_bbox_max_x_nm (neurd.spine_utils.Spine property) spine_bbox_max_y_nm (neurd.spine_utils.Spine property) spine_bbox_max_z_nm (neurd.spine_utils.Spine property) spine_bbox_min_x_nm (neurd.spine_utils.Spine property) spine_bbox_min_y_nm (neurd.spine_utils.Spine property) spine_bbox_min_z_nm (neurd.spine_utils.Spine property) spine_bbox_oriented_side_max (neurd.spine_utils.Spine property) spine_bbox_oriented_side_middle (neurd.spine_utils.Spine property) spine_bbox_oriented_side_min (neurd.spine_utils.Spine property) spine_bouton_groups_from_synapses_obj() (in module neurd.synapse_utils) spine_bouton_labels_to_plot() (in module neurd.spine_utils) spine_compartment_mesh_functions() (in module neurd.spine_utils) spine_compartment_mesh_functions_dict() (in module neurd.spine_utils) spine_compartment_synapses() (in module neurd.spine_utils) spine_compartments_face_idx_for_neuron_mesh() (in module neurd.spine_utils) spine_counts_from_spine_df() (in module neurd.spine_utils) spine_density (neurd.neuron.Branch property) (neurd.neuron.Neuron property) spine_density() (in module neurd.neuron_searching) (in module neurd.neuron_utils) (in module neurd.spine_utils) spine_density_eligible (neurd.neuron.Neuron property) spine_density_eligible() (in module neurd.neuron_utils) spine_density_near_soma() (in module neurd.cell_type_utils) spine_density_over_limb_branch() (in module neurd.spine_utils) spine_df_for_db_from_spine_objs() (in module neurd.spine_utils) spine_eligible_branch_lengths (neurd.neuron.Neuron property) spine_eligible_branch_lengths() (in module neurd.neuron_utils) spine_features_to_print() (in module neurd.spine_utils) spine_head_neck() (in module neurd.spine_utils) spine_id (neurd.spine_utils.Spine attribute)

spine_id_add_from_limb_branch_idx() (in module neurd.spine_utils) spine_id_from_limb_branch_spine_idx() (in module neurd.spine_utils) spine_id_range_from_limb_branch_idx() (in module neurd.spine_utils) spine_int_label() (in module neurd.spine_utils) spine_labels() (in module neurd.spine_utils) spine_labels_from_compartment() (in module neurd.apical_utils) spine_length() (in module neurd.spine_utils) spine_level_classifier() (in module neurd.classification_utils) spine_mesh() (in module neurd.spine_utils) spine_n_faces (neurd.spine_utils.Spine property) spine_objs_and_synapse_df_computed_from_branch_idx() (in module neurd.spine_utils) spine_objs_and_synapse_df_computed_from_neuron_obj() (in module neurd.spine_utils) spine_objs_and_synapse_df_total_from_limb_branch_spine_dict() (in module neurd.spine_utils) spine_objs_bare_minimum_filt_with_attr_from_branch_obj() (in module neurd.spine_utils) spine_objs_near_endpoints() (in module neurd.spine_utils) spine_objs_with_border_sk_endpoint_and_soma_filter_from_scratch_on_branch_obj() (in module neurd.spine_utils) spine_objs_with_border_sk_endpoint_and_soma_filter_from_scratch_on_mesh() (in module neurd.spine_utils) spine_skeletal_length (neurd.spine_utils.Spine property) spine_stats_from_spine_df() (in module neurd.spine_utils) spine_str_label() (in module neurd.spine_utils) spine_synapse_stats_from_synapse_df() (in module neurd.spine_utils) spine_table_restriction_high_confidence() (in module neurd.spine_utils) spine_volume (neurd.spine_utils.Spine property) spine_volume_density (neurd.neuron.Branch property) (neurd.neuron.Neuron property) spine_volume_density() (in module neurd.neuron_utils) (in module neurd.spine_utils) spine_volume_density_eligible (neurd.neuron.Neuron property) spine_volume_density_eligible() (in module neurd.neuron_utils) spine_volume_median (neurd.neuron.Branch property) (neurd.neuron.Neuron property) spine_volume_median() (in module neurd.neuron_utils) spine_volume_per_branch_eligible (neurd.neuron.Neuron property) spine_volume_per_branch_eligible() (in module neurd.neuron_utils) spine_volume_to_spine_area() (in module neurd.spine_utils) spine_width_ray (neurd.spine_utils.Spine property) spine_width_ray_80_perc (neurd.spine_utils.Spine property) spines (neurd.neuron.Limb property) (neurd.neuron.Neuron property) spines() (in module neurd.spine_utils) spines_already_computed() (neurd.neuron.Neuron method) spines_head() (in module neurd.spine_utils) spines_head_meshes() (in module neurd.spine_utils) spines_neck() (in module neurd.spine_utils) spines_neck_meshes() (in module neurd.spine_utils) spines_no_head() (in module neurd.spine_utils) spines_no_head_meshes() (in module neurd.spine_utils) spines_obj (neurd.neuron.Limb property) (neurd.neuron.Neuron property) spines_per_branch (neurd.neuron.Neuron property) spines_per_branch() (in module neurd.neuron_utils) spines_per_branch_eligible (neurd.neuron.Neuron property) spines_per_branch_eligible() (in module neurd.neuron_utils) spines_per_skeletal_length() (in module neurd.neuron_searching) spines_volume (neurd.neuron.Limb property) (neurd.neuron.Neuron property) split_disconnected_neuron() (in module neurd.proofreading_utils) split_head_mesh() (in module neurd.spine_utils) split_mesh_into_spines_shaft() (in module neurd.spine_utils) split_mesh_into_spines_shaft_old() (in module neurd.spine_utils) split_neuron() (in module neurd.proofreading_utils) split_neuron_limb_by_seperated_network() (in module neurd.proofreading_utils) split_neuron_limbs_by_suggestions() (in module neurd.proofreading_utils) split_success() (in module neurd.proofreading_utils) split_suggestions_to_concept_networks() (in module neurd.proofreading_utils) split_suggestions_to_concept_networks_old() (in module neurd.proofreading_utils) split_type_from_title() (in module neurd.proofreading_utils) starting_node_combinations_of_limb_sorted_by_microns_midpoint() (in module neurd.neuron_utils) starting_node_from_soma() (in module neurd.neuron_utils) statistic_per_branch() (in module neurd.neuron_utils) stats_df() (in module neurd.neuron_statistics) stats_df_from_G() (in module neurd.neuron_graph_lite_utils) stats_dict_over_limb_branch() (in module neurd.neuron_statistics) str_from_G_motif() (in module neurd.motif_utils) str_of_n_prox_n_syn() (in module neurd.proximity_analysis_utils) su (neurd.neuron.Neuron attribute) subgraph_around_branch() (in module neurd.concept_network_utils) subgraph_from_motif_dict() (in module neurd.motif_utils) subtract_soma() (in module neurd.soma_extraction_utils) sum_feature_over_branches() (in module neurd.concept_network_utils) (in module neurd.neuron_utils) sum_feature_over_limb_branch_dict() (in module neurd.neuron_utils) surface_area_to_volume() (in module neurd.spine_utils) symmetric_window() (in module neurd.neuron_graph_lite_utils) syn_coordinate_from_edge_dict() (in module neurd.connectome_utils) syn_type_from_compartment() (in module neurd.apical_utils) Synapse (class in neurd.synapse_utils) synapse_attribute_dict_from_synapse_df() (in module neurd.spine_utils) synapse_closer_to_downstream_endpoint_than_upstream() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) synapse_compartment_spine_type_title() (in module neurd.synapse_utils) synapse_coordinate_from_seg_split_syn_id() (in module neurd.connectome_utils) synapse_coordinates_from_df() (in module neurd.proximity_utils) synapse_coordinates_from_synapse_df() (in module neurd.synapse_utils) synapse_coords_from_synapse_df() (in module neurd.spine_utils) synapse_density (neurd.neuron.Branch property) synapse_density() (in module neurd.neuron_searching) (in module neurd.synapse_utils) synapse_density_diff() (in module neurd.neuron_statistics) synapse_density_downstream() (in module neurd.concept_network_utils) synapse_density_head() (in module neurd.synapse_utils) synapse_density_near_soma() (in module neurd.cell_type_utils) synapse_density_neck() (in module neurd.synapse_utils) synapse_density_no_head() (in module neurd.synapse_utils) synapse_density_offset_distance_of_endpoint_upstream() (in module neurd.synapse_utils) synapse_density_offset_endpoint_upstream() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) synapse_density_over_limb_branch() (in module neurd.synapse_utils) synapse_density_post (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) synapse_density_post() (in module neurd.neuron_searching) (in module neurd.synapse_utils) synapse_density_post_near_endpoint_downstream() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) synapse_density_post_offset_distance_of_endpoint_downstream() (in module neurd.synapse_utils) synapse_density_post_offset_distance_of_endpoint_upstream() (in module neurd.synapse_utils) synapse_density_post_offset_endpoint_upstream() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) synapse_density_post_within_distance_of_endpoint_downstream() (in module neurd.synapse_utils) synapse_density_pre (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) synapse_density_pre() (in module neurd.neuron_searching) (in module neurd.synapse_utils) synapse_density_shaft() (in module neurd.synapse_utils) synapse_density_spine() (in module neurd.synapse_utils) synapse_density_stats() (in module neurd.cell_type_utils) synapse_density_upstream() (in module neurd.concept_network_utils) synapse_density_upstream_downstream() (in module neurd.concept_network_utils) synapse_df() (in module neurd.synapse_utils) synapse_df_abridged() (in module neurd.synapse_utils) synapse_df_from_csv() (in module neurd.synapse_utils) synapse_df_from_seg_id() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) synapse_df_from_synapse_dict() (in module neurd.synapse_utils) synapse_df_with_spine_match() (in module neurd.spine_utils) synapse_dict_from_synapse_csv() (in module neurd.synapse_utils) synapse_dict_from_synapse_df() (in module neurd.synapse_utils) synapse_dict_mesh_labels_to_synapse_attribute_dict() (in module neurd.synapse_utils) synapse_dict_mesh_labels_to_synapse_coordinate_dict() (in module neurd.synapse_utils) synapse_dict_mesh_labels_to_synapse_volume_dict() (in module neurd.synapse_utils) synapse_endpoint_dist_downstream() (in module neurd.synapse_utils) synapse_endpoint_dist_upstream() (in module neurd.synapse_utils) synapse_endpoint_dist_upstream_downstream() (in module neurd.synapse_utils) synapse_filtering() (in module neurd.proofreading_utils) synapse_filtering_vp2() (in module neurd.synapse_utils) synapse_head_perc() (in module neurd.synapse_utils) synapse_id (neurd.synapse_utils.Synapse attribute) synapse_ids_and_coord_from_segment_ids_edge() (in module neurd.connectome_utils) synapse_ids_from_synapse_df() (in module neurd.spine_utils) synapse_ids_to_synapses() (in module neurd.synapse_utils) synapse_indexes_to_synapses() (in module neurd.synapse_utils) synapse_obj_from_dj_synapse_dict() (in module neurd.synapse_utils) synapse_plot_items_by_type_or_query() (in module neurd.synapse_utils) synapse_post_perc() (in module neurd.neuron_searching) (in module neurd.synapse_utils) synapse_post_perc_downstream() (in module neurd.neuron_searching) (in module neurd.synapse_utils) synapse_post_perc_over_limb_branch_dict() (in module neurd.synapse_utils) synapse_pre_perc() (in module neurd.neuron_searching) (in module neurd.synapse_utils) synapse_pre_perc_downstream() (in module neurd.neuron_searching) (in module neurd.synapse_utils) synapse_pre_perc_over_limb_branch_dict() (in module neurd.synapse_utils) synapse_pre_post_valid_errror_coordinates_dict() (in module neurd.synapse_utils) synapse_pre_post_valid_errror_stats_dict() (in module neurd.synapse_utils) synapse_skeletal_distances_to_soma() (in module neurd.neuron_utils) synapse_spine_match_df_filtering() (in module neurd.spine_utils) synapse_spine_perc() (in module neurd.synapse_utils) synapses (neurd.neuron.Limb property) (neurd.neuron.Neuron property) synapses() (in module neurd.synapse_utils) synapses_bouton() (in module neurd.synapse_utils) synapses_by_compartment_spine_type() (in module neurd.synapse_utils) synapses_df() (in module neurd.synapse_utils) synapses_distance_errored() (in module neurd.synapse_utils) synapses_dj_export_dict_error() (in module neurd.synapse_utils) synapses_dj_export_dict_valid() (in module neurd.synapse_utils) synapses_downstream() (in module neurd.concept_network_utils) (in module neurd.neuron_statistics) (in module neurd.synapse_utils) synapses_downstream_total() (in module neurd.neuron_statistics) synapses_downstream_within_dist() (in module neurd.neuron_statistics) synapses_error (neurd.neuron.Neuron property) synapses_error() (in module neurd.synapse_utils) synapses_error_ids() (in module neurd.synapse_utils) synapses_error_old() (in module neurd.synapse_utils) synapses_error_post() (in module neurd.synapse_utils) synapses_error_post_coordinates() (in module neurd.synapse_utils) synapses_error_pre() (in module neurd.synapse_utils) synapses_error_pre_coordinates() (in module neurd.synapse_utils) synapses_from_segment_id_edges() (in module neurd.connectome_utils) synapses_head (neurd.neuron.Branch property) synapses_head() (in module neurd.synapse_utils) synapses_mesh_errored() (in module neurd.synapse_utils) synapses_neck (neurd.neuron.Branch property) synapses_neck() (in module neurd.synapse_utils) synapses_no_head (neurd.neuron.Branch property) synapses_no_head() (in module neurd.synapse_utils) synapses_non_bouton() (in module neurd.synapse_utils) synapses_obj_groups_from_queries() (in module neurd.synapse_utils) synapses_offset_distance_of_endpoint_upstream_downstream() (in module neurd.synapse_utils) synapses_over_limb_branch_dict() (in module neurd.synapse_utils) synapses_post (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) (neurd.neuron.Soma property) synapses_post() (in module neurd.synapse_utils) synapses_post_downstream() (in module neurd.synapse_utils) synapses_post_downstream_within_dist() (in module neurd.neuron_statistics) synapses_post_head() (in module neurd.synapse_utils) synapses_post_neck() (in module neurd.synapse_utils) synapses_post_no_head() (in module neurd.synapse_utils) synapses_post_shaft() (in module neurd.synapse_utils) synapses_post_spine() (in module neurd.synapse_utils) synapses_pre (neurd.neuron.Branch property) (neurd.neuron.Limb property) (neurd.neuron.Neuron property) (neurd.neuron.Soma property) synapses_pre() (in module neurd.synapse_utils) synapses_pre_downstream() (in module neurd.synapse_utils) synapses_pre_downstream_within_dist() (in module neurd.neuron_statistics) synapses_pre_shaft() (in module neurd.synapse_utils) synapses_shaft (neurd.neuron.Branch property) synapses_shaft() (in module neurd.synapse_utils) synapses_somas (neurd.neuron.Neuron property) synapses_somas() (in module neurd.synapse_utils) synapses_somas_postsyn() (in module neurd.synapse_utils) synapses_spine (neurd.neuron.Branch property) synapses_spine() (in module neurd.synapse_utils) synapses_to_coordinates() (in module neurd.synapse_utils) synapses_to_dj_keys() (in module neurd.synapse_utils) synapses_to_dj_keys_old() (in module neurd.synapse_utils) synapses_to_exports() (in module neurd.synapse_utils) synapses_to_feature() (in module neurd.synapse_utils) synapses_to_synapse_ids() (in module neurd.synapse_utils) synapses_to_synapses_df() (in module neurd.synapse_utils) synapses_total (neurd.neuron.Neuron property) synapses_total() (in module neurd.synapse_utils) synapses_type_and_head_neck_shaft() (in module neurd.synapse_utils) synapses_upstream() (in module neurd.concept_network_utils) (in module neurd.neuron_statistics) synapses_upstream_downstream() (in module neurd.concept_network_utils) synapses_upstream_total() (in module neurd.neuron_statistics) synapses_valid (neurd.neuron.Neuron property) synapses_valid() (in module neurd.synapse_utils) synapses_valid_old() (in module neurd.synapse_utils) synapses_valid_post() (in module neurd.synapse_utils) synapses_valid_post_coordinates() (in module neurd.synapse_utils) synapses_valid_pre() (in module neurd.synapse_utils) synapses_valid_pre_coordinates() (in module neurd.synapse_utils) synapses_with_feature() (in module neurd.synapse_utils) synapses_within_distance_of_endpoint_upstream_downstream() (in module neurd.synapse_utils)

T

table_dict_from_release_name() (in module neurd.cave_client_utils) table_name_from_table_str() (in module neurd.cave_client_utils) table_size() (in module neurd.cave_client_utils) (neurd.cave_client_utils.CaveInterface method) tag() (in module neurd.documentation_utils) test_limb() (in module neurd.neuron_searching) thick_t_errors_limb_branch_dict() (in module neurd.error_detection) thick_t_filter() (in module neurd.graph_filters) this_directory() (in module neurd.parameter_utils)

total_spine_volume (neurd.neuron.Branch property) (neurd.neuron.Neuron property) total_spine_volume() (in module neurd.neuron_utils) total_upstream_skeletal_length() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) touching_somas() (neurd.neuron.Limb method) trajectory_angle_from_start_branch_and_subtree() (in module neurd.neuron_statistics) translate_neuron_obj() (in module neurd.neuron_utils) two_children_angle() (in module neurd.neuron_searching)

U

unalign_neuron_obj() (in module neurd.h01_volume_utils) (in module neurd.microns_volume_utils) (neurd.h01_volume_utils.DataInterface method) (neurd.microns_volume_utils.DataInterface method) (neurd.vdi_default.DataInterfaceBoilerplate method) (neurd.volume_utils.DataInterface method) unalign_neuron_obj_from_align_matrix() (in module neurd.neuron_utils) (neurd.vdi_default.DataInterfaceBoilerplate method) unique_motif_reduction() (in module neurd.motif_utils) update() (neurd.parameter_utils.PackageParameters method) (neurd.parameter_utils.Parameters method) update_spines_obj() (in module neurd.spine_utils) upstream_axon_width() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) upstream_branches_in_branches_list() (in module neurd.concept_network_utils) upstream_dist (neurd.spine_utils.Spine attribute) (neurd.synapse_utils.Synapse attribute)

upstream_downstream_endpoint_idx() (in module neurd.neuron_utils) upstream_endpoint() (in module neurd.neuron_utils) upstream_endpoint_branch_set() (in module neurd.neuron_statistics) upstream_labels() (in module neurd.neuron_utils) upstream_node() (in module neurd.neuron_utils) upstream_node_from_G() (in module neurd.error_detection) upstream_node_has_label() (in module neurd.neuron_searching) (in module neurd.neuron_utils) upstream_node_is_apical() (in module neurd.neuron_statistics) upstream_node_is_apical_shaft() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) upstream_nodes_without_branching() (in module neurd.concept_network_utils) upstream_pair_singular() (in module neurd.graph_filters) upstream_skeletal_length() (in module neurd.neuron_searching) (in module neurd.neuron_statistics)

V

v4_exc_filters() (in module neurd.proofreading_utils) v5_exc_filters() (in module neurd.proofreading_utils) v6_exc_filters() (in module neurd.proofreading_utils) v6_exc_filters_old() (in module neurd.proofreading_utils) v6_inh_filters() (in module neurd.proofreading_utils) v7_exc_filters() (in module neurd.proofreading_utils) v7_inh_filters() (in module neurd.proofreading_utils) valid_error_groups_from_synapses_obj() (in module neurd.synapse_utils) valid_error_split_points_by_limb (neurd.neuron.Neuron property) valid_query() (in module neurd.synapse_utils) valid_synapse_records_to_unique_synapse_df() (in module neurd.proofreading_utils) valid_web_for_t() (in module neurd.axon_utils) vdi (neurd.vdi_default.DataInterfaceBoilerplate property) vec_df_from_compartment() (in module neurd.neuron_geometry_utils) vector_to_scatter_line() (in module neurd.neuron_visualizations) viable_axon_limbs_by_starting_angle() (in module neurd.neuron_utils) viable_axon_limbs_by_starting_angle_old() (in module neurd.neuron_utils) visual_area_from_em_centroid_xyz() (in module neurd.microns_volume_utils) visualize_axon_dendrite() (in module neurd.neuron_visualizations) visualize_branch_at_downstream_split() (in module neurd.neuron_visualizations)

visualize_concept_map() (in module neurd.neuron_visualizations) visualize_graph_connections() (in module neurd.motif_utils) visualize_graph_connections_by_method() (in module neurd.connectome_utils) visualize_limb_obj() (in module neurd.neuron_visualizations) visualize_neuron() (in module neurd.neuron_visualizations) visualize_neuron_axon_dendrite() (in module neurd.neuron_visualizations) visualize_neuron_axon_merge_errors() (in module neurd.neuron_visualizations) visualize_neuron_limbs() (in module neurd.neuron_visualizations) visualize_neuron_lite() (in module neurd.neuron_visualizations) visualize_neuron_path() (in module neurd.neuron_visualizations) visualize_neuron_specific_limb() (in module neurd.neuron_visualizations) visualize_subset_neuron_limbs() (in module neurd.neuron_visualizations) volume (neurd.neuron.Soma property) (neurd.spine_utils.Spine attribute) volume_from_compartment() (in module neurd.spine_utils) volume_from_spine() (in module neurd.spine_utils) volume_over_limb_branch() (in module neurd.neuron_utils) voxel_to_nm_scaling (neurd.vdi_default.DataInterfaceDefault property) (neurd.vdi_h01.DataInterfaceH01 property) (neurd.vdi_microns.DataInterfaceMicrons property) (neurd.vdi_microns_cave.DataInterfaceMicrons property)

W

web (neurd.neuron.Limb property) (neurd.neuron.Neuron property) webbing_t_errors_limb_branch_dict() (in module neurd.error_detection) webbing_t_errors_limb_branch_dict_old() (in module neurd.error_detection) weighted_attribute_upstream_downstream() (in module neurd.concept_network_utils) weighted_feature_over_branches() (in module neurd.concept_network_utils) whole_neuron_branch_concept_network() (in module neurd.neuron_utils) whole_neuron_branch_concept_network_old() (in module neurd.neuron_utils) wide_angle_t_candidates() (in module neurd.axon_utils) wide_angle_t_motif() (in module neurd.graph_filters) width() (in module neurd.neuron_searching) (in module neurd.neuron_utils) width_90_perc (neurd.neuron.Neuron property) width_array_skeletal_lengths_upstream_to_downstream (neurd.neuron.Branch property) width_array_skeletal_lengths_upstream_to_downstream() (in module neurd.branch_utils) width_array_upstream_to_downstream (neurd.neuron.Branch property) width_array_upstream_to_downstream() (in module neurd.branch_utils) width_array_upstream_to_dowstream_with_skeletal_points() (in module neurd.branch_utils) width_array_value_closest_to_coordinate() (in module neurd.branch_utils) width_average_from_limb_correspondence() (in module neurd.neuron_utils) width_basic() (in module neurd.neuron_statistics) width_diff() (in module neurd.neuron_statistics) width_diff_basic() (in module neurd.neuron_statistics) width_diff_percentage() (in module neurd.neuron_statistics) width_diff_percentage_basic() (in module neurd.neuron_statistics) width_downstream (neurd.neuron.Branch property) width_downstream() (in module neurd.branch_utils) (in module neurd.concept_network_utils) (in module neurd.neuron_statistics) width_downstream_restricted() (in module neurd.concept_network_utils) width_endpoint() (in module neurd.branch_utils) width_jump() (in module neurd.neuron_searching)

width_jump_double_back_edges_path() (in module neurd.error_detection) width_jump_edges() (in module neurd.error_detection) width_jump_edges_path() (in module neurd.error_detection) width_jump_from_upstream_min() (in module neurd.error_detection) (in module neurd.neuron_searching) width_jump_up_axon() (in module neurd.error_detection) width_jump_up_dendrite() (in module neurd.error_detection) width_jump_up_error_limb_branch_dict() (in module neurd.error_detection) width_max() (in module neurd.neuron_statistics) width_median (neurd.neuron.Neuron property) width_median() (in module neurd.neuron_utils) width_near_branch_endpoint() (in module neurd.neuron_statistics) width_neuron() (in module neurd.neuron_searching) width_new() (in module neurd.neuron_searching) (in module neurd.neuron_statistics) width_new_extract() (in module neurd.neuron_graph_lite_utils) width_no_spine_90_perc (neurd.neuron.Neuron property) width_no_spine_median (neurd.neuron.Neuron property) width_no_spine_median() (in module neurd.neuron_utils) width_no_spine_perc() (in module neurd.neuron_utils) width_over_candidate() (in module neurd.neuron_statistics) width_overall (neurd.neuron.Branch property) width_perc() (in module neurd.neuron_utils) width_ray_80_perc_from_compartment() (in module neurd.spine_utils) width_ray_from_compartment() (in module neurd.spine_utils) width_upstream (neurd.neuron.Branch property) width_upstream() (in module neurd.branch_utils) (in module neurd.concept_network_utils) (in module neurd.limb_utils) (in module neurd.neuron_statistics) width_upstream_downstream() (in module neurd.concept_network_utils) width_weighted_over_branches() (in module neurd.neuron_statistics)