Index

A

add_any_missing_node_features() (in module neuron_morphology_tools.neuron_nx_feature_processing) (in module neuron_morphology_tools.neuron_nx_stats) add_density_to_graph_data() (in module neuron_morphology_tools.neuron_nx_io) add_density_to_graph_data_in_df() (in module neuron_morphology_tools.neuron_nx_io) add_node_feature() (in module neuron_morphology_tools.neuron_nx_feature_processing) add_skeletal_length_xyz_to_df_x_features_x_pool() (in module neuron_morphology_tools.neuron_nx_io) add_skeleton_vector_features() (in module neuron_morphology_tools.neuron_nx_feature_processing) add_summary_statistic_over_dynamic_attributes_to_G() (in module neuron_morphology_tools.neuron_nx_stats) adjusted_scholl_coordinates() (in module neuron_morphology_tools.neuron_nx_utils) aggregate_embedding_df_by_seg_split() (in module neuron_morphology_tools.neuron_nx_io) all_compartment_conn_comp_subgraph_vector_stats() (in module neuron_morphology_tools.neuron_nx_utils) all_compartment_conn_comp_subgraphs() (in module neuron_morphology_tools.neuron_nx_utils) all_compartment_skeletons() (in module neuron_morphology_tools.neuron_nx_utils)

all_compartment_subgraphs() (in module neuron_morphology_tools.neuron_nx_utils) all_limb_graphs() (in module neuron_morphology_tools.neuron_nx_utils) all_limb_graphs_off_soma() (in module neuron_morphology_tools.neuron_nx_utils) all_limb_idxs_in_G() (in module neuron_morphology_tools.neuron_nx_utils) all_node_graphs() (in module neuron_morphology_tools.neuron_nx_utils) apical_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) attribute_graph_from_graph_obj() (in module neuron_morphology_tools.neuron_nx_utils) auto_proof_filter_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) axon_dendrite_nodes() (in module neuron_morphology_tools.neuron_nx_utils) axon_dendrite_subgraph() (in module neuron_morphology_tools.neuron_nx_utils) axon_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) axon_nodes() (in module neuron_morphology_tools.neuron_nx_utils) axon_skeleton() (in module neuron_morphology_tools.neuron_nx_utils) axon_subgraph() (in module neuron_morphology_tools.neuron_nx_utils)

B

basal_label() (in module neuron_morphology_tools.neuron_nx_feature_processing)

branch_from_node_name() (in module neuron_morphology_tools.neuron_nx_utils)

C

calculate_soma_distance_to_data_objs() (in module neuron_morphology_tools.neuron_nx_utils) cirle_intersections() (in module neuron_morphology_tools.neuron_skeleton_utils) clean_G() (in module neuron_morphology_tools.neuron_nx_utils) clear_nodes_auto_proof_filter_feature() (in module neuron_morphology_tools.neuron_nx_utils) closest_node_to_coordinates() (in module neuron_morphology_tools.neuron_nx_utils) cluster_and_downstream_filter_coordinates() (in module neuron_morphology_tools.neuron_nx_utils) combine_limb_graph_data() (in module neuron_morphology_tools.neuron_nx_io) compartment_from_node() (in module neuron_morphology_tools.neuron_nx_utils) compartment_nodes() (in module neuron_morphology_tools.neuron_nx_utils)

compartment_one_hot() (in module neuron_morphology_tools.neuron_nx_feature_processing) compartment_proof() (in module neuron_morphology_tools.neuron_nx_feature_processing) compartment_skeleton() (in module neuron_morphology_tools.neuron_nx_utils) compartment_subgraph() (in module neuron_morphology_tools.neuron_nx_utils) compartment_vector_width_stats_from_G() (in module neuron_morphology_tools.neuron_nx_utils) compressed_dict_from_G() (in module neuron_morphology_tools.neuron_nx_io) coordinate_array_with_node_map_from_G() (in module neuron_morphology_tools.neuron_nx_utils) coordinate_estimation_from_upstream_dist_from_node() (in module neuron_morphology_tools.neuron_nx_utils) coordinates_from_coordinate_type() (in module neuron_morphology_tools.neuron_nx_utils)

D

delete_attributes() (in module neuron_morphology_tools.neuron_nx_utils) dendrite_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) dendrite_nodes() (in module neuron_morphology_tools.neuron_nx_utils) dendrite_subgraph() (in module neuron_morphology_tools.neuron_nx_utils) distance_downstream_from_soma() (in module neuron_morphology_tools.neuron_nx_utils) distance_downstream_from_soma_df() (in module neuron_morphology_tools.neuron_nx_utils)

distance_from_node_to_soma() (in module neuron_morphology_tools.neuron_nx_utils) distance_from_soma_df() (in module neuron_morphology_tools.neuron_nx_utils) distance_upstream_from_soma() (in module neuron_morphology_tools.neuron_nx_utils) distance_upstream_from_soma_df() (in module neuron_morphology_tools.neuron_nx_utils) downstream_limb_branch() (in module neuron_morphology_tools.neuron_nx_utils) draw_tree() (in module neuron_morphology_tools.neuron_nx_utils)

E

export_GNN_info_dict() (in module neuron_morphology_tools.neuron_nx_io) export_swc_df() (in module neuron_morphology_tools.neuron_nx_utils)

export_swc_dicts() (in module neuron_morphology_tools.neuron_nx_utils) export_swc_file() (in module neuron_morphology_tools.neuron_nx_utils)

F

feature_clip() (in module neuron_morphology_tools.neuron_nx_feature_processing) feature_df_from_adj_feature_dict() (in module neuron_morphology_tools.neuron_nx_io) feature_df_from_gnn_info() (in module neuron_morphology_tools.neuron_nx_io) features_list() (in module neuron_morphology_tools.neuron_nx_feature_processing) filter_axon_on_dendrite_splits_to_most_upstream() (in module neuron_morphology_tools.neuron_nx_utils) filter_G_features() (in module neuron_morphology_tools.neuron_nx_feature_processing)

filter_graph() (in module neuron_morphology_tools.neuron_nx_utils) filter_small_starter_branches() (in module neuron_morphology_tools.neuron_nx_utils) fix_attribute() (in module neuron_morphology_tools.neuron_nx_utils) fix_flipped_skeleton() (in module neuron_morphology_tools.neuron_nx_utils) fix_flipped_skeletons() (in module neuron_morphology_tools.neuron_nx_utils) fix_width_inf_nan() (in module neuron_morphology_tools.neuron_nx_utils)

G

G_from_adj_feature_dict() (in module neuron_morphology_tools.neuron_nx_io) G_no_soma() (in module neuron_morphology_tools.neuron_nx_utils) GNN_info_axon_vs_dendrite() (in module neuron_morphology_tools.neuron_nx_io)

GNN_info_cell_type_fine() (in module neuron_morphology_tools.neuron_nx_io) GNN_info_compartment_proof() (in module neuron_morphology_tools.neuron_nx_io) GNN_info_merge_errors() (in module neuron_morphology_tools.neuron_nx_io)

I

inter_attribute_G_preprocessing() (in module neuron_morphology_tools.neuron_nx_utils) inter_attribute_intervals_dict_from_neuron_G() (in module neuron_morphology_tools.neuron_nx_utils) inter_attribute_intervals_from_G() (in module neuron_morphology_tools.neuron_nx_utils)

internal_branching_coordinates() (in module neuron_morphology_tools.neuron_nx_utils) internal_branching_coordinates_max_min() (in module neuron_morphology_tools.neuron_nx_utils) internal_branching_stats() (in module neuron_morphology_tools.neuron_nx_utils)

L

limb_branch_nodes() (in module neuron_morphology_tools.neuron_nx_utils) limb_branch_subgraph() (in module neuron_morphology_tools.neuron_nx_utils) limb_df_for_train_from_limb_df() (in module neuron_morphology_tools.neuron_nx_io)

limb_from_node_name() (in module neuron_morphology_tools.neuron_nx_utils) limb_graph() (in module neuron_morphology_tools.neuron_nx_utils) limb_graphs_from_soma_connected_nodes() (in module neuron_morphology_tools.neuron_nx_utils) load_G() (in module neuron_morphology_tools.neuron_nx_utils)

M

merge_axon_on_dendrite_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) merge_clean() (in module neuron_morphology_tools.neuron_nx_feature_processing) merge_double_back_dendrite_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) merge_high_degree_branching_dendrite_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) merge_high_degree_branching_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) merge_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) merge_low_degree_branching_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) merge_width_jump_up_axon_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) merge_width_jump_up_dendrite_label() (in module neuron_morphology_tools.neuron_nx_feature_processing) min_dist_synapses_pre_downstream_clip() (in module neuron_morphology_tools.neuron_nx_feature_processing) min_dist_synapses_pre_upstream_clip() (in module neuron_morphology_tools.neuron_nx_feature_processing) module neuron_morphology_tools neuron_morphology_tools.morphopy_utils neuron_morphology_tools.neuron_nx_feature_processing neuron_morphology_tools.neuron_nx_io neuron_morphology_tools.neuron_nx_stats neuron_morphology_tools.neuron_nx_utils neuron_morphology_tools.neuron_skeleton_utils

morphometrics() (in module neuron_morphology_tools.morphopy_utils) (in module neuron_morphology_tools.neuron_nx_utils) most_upstream_coordinate() (in module neuron_morphology_tools.neuron_nx_utils) most_upstream_node() (in module neuron_morphology_tools.neuron_nx_utils) most_upstream_node_on_axon_limb() (in module neuron_morphology_tools.neuron_nx_utils) most_upstream_node_vector_stats() (in module neuron_morphology_tools.neuron_nx_utils) most_upstream_nodes() (in module neuron_morphology_tools.neuron_nx_utils)

N

n_branches() (in module neuron_morphology_tools.neuron_nx_stats) n_data_attribues() (in module neuron_morphology_tools.neuron_nx_utils) n_internal_branching_coordinates() (in module neuron_morphology_tools.neuron_nx_utils) n_scholl_dict_from_scholl_dict() (in module neuron_morphology_tools.neuron_nx_utils) name_from_G() (in module neuron_morphology_tools.neuron_nx_utils) neuron_df_for_train_from_limb_df() (in module neuron_morphology_tools.neuron_nx_io) neuron_morphology_tools module neuron_morphology_tools.morphopy_utils module neuron_morphology_tools.neuron_nx_feature_processing module neuron_morphology_tools.neuron_nx_io module neuron_morphology_tools.neuron_nx_stats module

neuron_morphology_tools.neuron_nx_utils module neuron_morphology_tools.neuron_skeleton_utils module node_compartment_color_dict() (in module neuron_morphology_tools.neuron_nx_utils) node_endpoint() (in module neuron_morphology_tools.neuron_nx_utils) node_map() (in module neuron_morphology_tools.neuron_nx_utils) node_match_by_dict() (in module neuron_morphology_tools.neuron_nx_utils) nodes_between_soma_and_nodes() (in module neuron_morphology_tools.neuron_nx_utils) nodes_distance_query_from_soma() (in module neuron_morphology_tools.neuron_nx_utils) nodes_farther_than_distance_from_soma() (in module neuron_morphology_tools.neuron_nx_utils) nodes_with_auto_proof_filter() (in module neuron_morphology_tools.neuron_nx_utils) nodes_with_auto_proof_filter_type() (in module neuron_morphology_tools.neuron_nx_utils) nodes_within_distance_from_soma() (in module neuron_morphology_tools.neuron_nx_utils) nodes_within_distance_upstream_from_soma() (in module neuron_morphology_tools.neuron_nx_utils) nodes_without_match() (in module neuron_morphology_tools.neuron_nx_utils) ntree_obj_from_swc() (in module neuron_morphology_tools.morphopy_utils)

P

plot() (in module neuron_morphology_tools.neuron_nx_utils) plot_all_skeleton_compartments() (in module neuron_morphology_tools.neuron_nx_utils) plot_inter_attribute_intervals() (in module neuron_morphology_tools.neuron_nx_utils)

plot_inter_attribute_intervals_from_dicts() (in module neuron_morphology_tools.neuron_nx_utils) plot_ntree() (in module neuron_morphology_tools.morphopy_utils) plot_skeleton() (in module neuron_morphology_tools.neuron_nx_utils) print_compartment_colors() (in module neuron_morphology_tools.neuron_nx_utils)

R

remove_node() (in module neuron_morphology_tools.neuron_nx_utils)

remove_small_endnode_branches() (in module neuron_morphology_tools.neuron_nx_utils) remove_small_starter_branches() (in module neuron_morphology_tools.neuron_nx_utils)

S

save_G() (in module neuron_morphology_tools.neuron_nx_utils) scholl_coordinates() (in module neuron_morphology_tools.neuron_nx_utils) segment_id_from_G() (in module neuron_morphology_tools.neuron_nx_utils) set_auto_proof_filter_attribute() (in module neuron_morphology_tools.neuron_nx_utils) shortest_path_from_most_upstream() (in module neuron_morphology_tools.neuron_nx_utils) shuffle_upstream_dist_on_data_attribute() (in module neuron_morphology_tools.neuron_nx_utils) skeletal_length() (in module neuron_morphology_tools.neuron_nx_utils) (in module neuron_morphology_tools.neuron_skeleton_utils) skeletal_length_downstream() (in module neuron_morphology_tools.neuron_nx_stats) skeletal_length_on_path() (in module neuron_morphology_tools.neuron_nx_utils) skeleton() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_bbox() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_bounding_box() (in module neuron_morphology_tools.neuron_nx_stats) skeleton_coordinates_from_G() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_downstream_of_node() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_edge_df_with_edge_graph_with_compartments() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_from_node() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_graph() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_nodes() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_soma_to_limb_start() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_vector_downstream_phi() (in module neuron_morphology_tools.neuron_nx_feature_processing) skeleton_vector_downstream_theta() (in module neuron_morphology_tools.neuron_nx_feature_processing) skeleton_vector_downstream_x() (in module neuron_morphology_tools.neuron_nx_feature_processing) skeleton_vector_downstream_y() (in module neuron_morphology_tools.neuron_nx_feature_processing) skeleton_vector_downstream_z() (in module neuron_morphology_tools.neuron_nx_feature_processing) skeleton_vector_upstream_and_width_from_node() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_vector_upstream_phi() (in module neuron_morphology_tools.neuron_nx_feature_processing)

skeleton_vector_upstream_theta() (in module neuron_morphology_tools.neuron_nx_feature_processing) skeleton_vector_upstream_x() (in module neuron_morphology_tools.neuron_nx_feature_processing) skeleton_vector_upstream_y() (in module neuron_morphology_tools.neuron_nx_feature_processing) skeleton_vector_upstream_z() (in module neuron_morphology_tools.neuron_nx_feature_processing) skeleton_width_compartment_arrays_from_G() (in module neuron_morphology_tools.neuron_nx_utils) skeleton_width_data_from_node() (in module neuron_morphology_tools.neuron_nx_utils) small_endnode_branches() (in module neuron_morphology_tools.neuron_nx_utils) small_starter_branches() (in module neuron_morphology_tools.neuron_nx_utils) soma_center() (in module neuron_morphology_tools.neuron_nx_utils) soma_connected_nodes() (in module neuron_morphology_tools.neuron_nx_utils) soma_filter_by_complete_graph() (in module neuron_morphology_tools.neuron_nx_utils) soma_only_graph() (in module neuron_morphology_tools.neuron_nx_utils) soma_radius() (in module neuron_morphology_tools.neuron_nx_utils) soma_start_angle_max() (in module neuron_morphology_tools.neuron_nx_utils) soma_vector_from_node() (in module neuron_morphology_tools.neuron_nx_utils) spine_shaft_coordinates() (in module neuron_morphology_tools.neuron_nx_utils) split_location_node_map_df() (in module neuron_morphology_tools.neuron_nx_utils) starting_coordinate() (in module neuron_morphology_tools.neuron_nx_stats) starting_coordinates_all_limbs() (in module neuron_morphology_tools.neuron_nx_utils) statistics_survey_from_graph() (in module neuron_morphology_tools.neuron_nx_stats) subgraph_df_and_endnodes_df() (in module neuron_morphology_tools.neuron_nx_utils) summary_statistic_over_attributes() (in module neuron_morphology_tools.neuron_nx_stats) summary_statistic_over_dynamic_attribute() (in module neuron_morphology_tools.neuron_nx_stats) summary_statistic_over_spines() (in module neuron_morphology_tools.neuron_nx_stats) summary_statistic_over_synapses() (in module neuron_morphology_tools.neuron_nx_stats) swc_df() (in module neuron_morphology_tools.neuron_nx_utils) swc_df_from_file() (in module neuron_morphology_tools.morphopy_utils) swc_rotated_resampled() (in module neuron_morphology_tools.morphopy_utils)

U

upstream_limb_branch() (in module neuron_morphology_tools.neuron_nx_utils)

V

vector_stats_from_G() (in module neuron_morphology_tools.neuron_nx_utils)

W

width_from_node() (in module neuron_morphology_tools.neuron_nx_utils)

width_no_spine() (in module neuron_morphology_tools.neuron_nx_feature_processing)