neuron_morphology_tools

• neuron_morphology_tools package
  • Submodules
  • neuron_morphology_tools.morphopy_utils module
    • morphometrics()
    • ntree_obj_from_swc()
    • plot_ntree()
    • swc_df_from_file()
    • swc_rotated_resampled()
  • neuron_morphology_tools.neuron_nx_feature_processing module
    • add_any_missing_node_features()
    • add_node_feature()
    • add_skeleton_vector_features()
    • apical_label()
    • auto_proof_filter_label()
    • axon_label()
    • basal_label()
    • compartment_one_hot()
    • compartment_proof()
    • dendrite_label()
    • feature_clip()
    • features_list()
    • filter_G_features()
    • merge_axon_on_dendrite_label()
    • merge_clean()
    • merge_double_back_dendrite_label()
    • merge_high_degree_branching_dendrite_label()
    • merge_high_degree_branching_label()
    • merge_label()
    • merge_low_degree_branching_label()
    • merge_width_jump_up_axon_label()
    • merge_width_jump_up_dendrite_label()
    • min_dist_synapses_pre_downstream_clip()
    • min_dist_synapses_pre_upstream_clip()
    • skeleton_vector_downstream_phi()
    • skeleton_vector_downstream_theta()
    • skeleton_vector_downstream_x()
    • skeleton_vector_downstream_y()
    • skeleton_vector_downstream_z()
    • skeleton_vector_upstream_phi()
    • skeleton_vector_upstream_theta()
    • skeleton_vector_upstream_x()
    • skeleton_vector_upstream_y()
    • skeleton_vector_upstream_z()
    • width_no_spine()
  • neuron_morphology_tools.neuron_nx_io module
    • GNN_info_axon_vs_dendrite()
    • GNN_info_cell_type_fine()
    • GNN_info_compartment_proof()
    • GNN_info_merge_errors()
    • G_from_adj_feature_dict()
    • add_density_to_graph_data()
    • add_density_to_graph_data_in_df()
    • add_skeletal_length_xyz_to_df_x_features_x_pool()
    • aggregate_embedding_df_by_seg_split()
    • combine_limb_graph_data()
    • compressed_dict_from_G()
    • export_GNN_info_dict()
    • feature_df_from_adj_feature_dict()
    • feature_df_from_gnn_info()
    • limb_df_for_train_from_limb_df()
    • neuron_df_for_train_from_limb_df()
  • neuron_morphology_tools.neuron_nx_stats module
    • add_any_missing_node_features()
    • add_summary_statistic_over_dynamic_attributes_to_G()
    • n_branches()
    • skeletal_length_downstream()
    • skeleton_bounding_box()
    • starting_coordinate()
    • statistics_survey_from_graph()
    • summary_statistic_over_attributes()
    • summary_statistic_over_dynamic_attribute()
    • summary_statistic_over_spines()
    • summary_statistic_over_synapses()
  • neuron_morphology_tools.neuron_nx_utils module
    • G_no_soma()
    • adjusted_scholl_coordinates()
    • all_compartment_conn_comp_subgraph_vector_stats()
    • all_compartment_conn_comp_subgraphs()
    • all_compartment_skeletons()
    • all_compartment_subgraphs()
    • all_limb_graphs()
    • all_limb_graphs_off_soma()
    • all_limb_idxs_in_G()
    • all_node_graphs()
    • attribute_graph_from_graph_obj()
    • axon_dendrite_nodes()
    • axon_dendrite_subgraph()
    • axon_nodes()
    • axon_skeleton()
    • axon_subgraph()
    • branch_from_node_name()
    • calculate_soma_distance_to_data_objs()
    • clean_G()
    • clear_nodes_auto_proof_filter_feature()
    • closest_node_to_coordinates()
    • cluster_and_downstream_filter_coordinates()
    • compartment_from_node()
    • compartment_nodes()
    • compartment_skeleton()
    • compartment_subgraph()
    • compartment_vector_width_stats_from_G()
    • coordinate_array_with_node_map_from_G()
    • coordinate_estimation_from_upstream_dist_from_node()
    • coordinates_from_coordinate_type()
    • delete_attributes()
    • dendrite_nodes()
    • dendrite_subgraph()
    • distance_downstream_from_soma()
    • distance_downstream_from_soma_df()
    • distance_from_node_to_soma()
    • distance_from_soma_df()
    • distance_upstream_from_soma()
    • distance_upstream_from_soma_df()
    • downstream_limb_branch()
    • draw_tree()
    • export_swc_df()
    • export_swc_dicts()
    • export_swc_file()
    • filter_axon_on_dendrite_splits_to_most_upstream()
    • filter_graph()
    • filter_small_starter_branches()
    • fix_attribute()
    • fix_flipped_skeleton()
    • fix_flipped_skeletons()
    • fix_width_inf_nan()
    • inter_attribute_G_preprocessing()
    • inter_attribute_intervals_dict_from_neuron_G()
    • inter_attribute_intervals_from_G()
    • internal_branching_coordinates()
    • internal_branching_coordinates_max_min()
    • internal_branching_stats()
    • limb_branch_nodes()
    • limb_branch_subgraph()
    • limb_from_node_name()
    • limb_graph()
    • limb_graphs_from_soma_connected_nodes()
    • load_G()
    • morphometrics()
    • most_upstream_coordinate()
    • most_upstream_node()
    • most_upstream_node_on_axon_limb()
    • most_upstream_node_vector_stats()
    • most_upstream_nodes()
    • n_data_attribues()
    • n_internal_branching_coordinates()
    • n_scholl_dict_from_scholl_dict()
    • name_from_G()
    • node_compartment_color_dict()
    • node_endpoint()
    • node_map()
    • node_match_by_dict()
    • nodes_between_soma_and_nodes()
    • nodes_distance_query_from_soma()
    • nodes_farther_than_distance_from_soma()
    • nodes_with_auto_proof_filter()
    • nodes_with_auto_proof_filter_type()
    • nodes_within_distance_from_soma()
    • nodes_within_distance_upstream_from_soma()
    • nodes_without_match()
    • plot()
    • plot_all_skeleton_compartments()
    • plot_inter_attribute_intervals()
    • plot_inter_attribute_intervals_from_dicts()
    • plot_skeleton()
    • print_compartment_colors()
    • remove_node()
    • remove_small_endnode_branches()
    • remove_small_starter_branches()
    • save_G()
    • scholl_coordinates()
    • segment_id_from_G()
    • set_auto_proof_filter_attribute()
    • shortest_path_from_most_upstream()
    • shuffle_upstream_dist_on_data_attribute()
    • skeletal_length()
    • skeletal_length_on_path()
    • skeleton()
    • skeleton_bbox()
    • skeleton_coordinates_from_G()
    • skeleton_downstream_of_node()
    • skeleton_edge_df_with_edge_graph_with_compartments()
    • skeleton_from_node()
    • skeleton_graph()
    • skeleton_nodes()
    • skeleton_soma_to_limb_start()
    • skeleton_vector_upstream_and_width_from_node()
    • skeleton_width_compartment_arrays_from_G()
    • skeleton_width_data_from_node()
    • small_endnode_branches()
    • small_starter_branches()
    • soma_center()
    • soma_connected_nodes()
    • soma_filter_by_complete_graph()
    • soma_only_graph()
    • soma_radius()
    • soma_start_angle_max()
    • soma_vector_from_node()
    • spine_shaft_coordinates()
    • split_location_node_map_df()
    • starting_coordinates_all_limbs()
    • subgraph_df_and_endnodes_df()
    • swc_df()
    • upstream_limb_branch()
    • vector_stats_from_G()
    • width_from_node()
  • neuron_morphology_tools.neuron_skeleton_utils module
    • cirle_intersections()
    • skeletal_length()
  • Module contents