neurd
- neurd package
- Subpackages
- neurd.parameter_configs package
- Submodules
- 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_h01_old module
- neurd.parameter_configs.parameters_config_microns module
- Module contents
- neurd.parameter_configs package
- Submodules
- neurd.ais_utils module
- neurd.apical_utils module
- Compartment List and Description
add_compartment_coarse_fine_to_df()apical_classification()apical_classification_high_soma_center()apical_limb_branch_dict()apical_shaft_classification_old()apical_shaft_direct_downstream()apical_shaft_like_limb_branch()apical_shaft_limb_branch_dict()apical_total_limb_branch_dict()apical_tuft_classification()apical_tuft_limb_branch_dict()axon_limb_branch_dict()basal_classfication()basal_limb_branch_dict()coarse_fine_compartment_from_label()colors_from_compartments()compartment_classification_by_cell_type()compartment_feature_over_limb_branch_dict()compartment_features_from_skeleton_and_soma_center()compartment_from_branch()compartment_from_face_overlap_with_comp_faces_dict()compartment_label_from_branch_obj()compartment_label_to_all_labels()compartment_labels_for_externals()compartment_labels_for_stats()compartment_labels_for_synapses_stats()compartment_limb_branch_dict()compartment_mesh()compartment_skeleton()compartments_feature_over_limb_branch_dict()compartments_from_cell_type()compartments_mesh()compartments_skeleton()compartments_stats()compartments_to_plot()dendrite_compartment_labels()dendrite_limb_branch_dict()expand_candidate_branches_to_soma()filter_apical_candidates()filter_apical_candidates_to_one()limb_branch_compartment_dict_from_limb_branch_face_and_compartment_faces_dict()limb_features_from_compartment()limb_features_from_compartment_over_neuron()max_height_for_multi_soma()multi_soma_y()non_upward_skeletal_distance_upstream()oblique_classification()oblique_limb_branch_dict()plot_compartment_mesh_and_skeleton()print_compartment_features_dict_for_dj_table()set_neuron_synapses_compartment()soma_angle_extrema_from_compartment()soma_angle_max_from_compartment()soma_angle_min_from_compartment()spine_labels_from_compartment()syn_type_from_compartment()
- neurd.axon_utils module
axon_angles()axon_angles_from_neuron()axon_branching_attributes()axon_classification_excitatory()axon_classification_inhibitory()axon_classification_using_synapses()axon_classification_without_synapses()axon_features_from_neuron_obj()axon_like_segments()axon_limb_branch_dict()axon_on_dendrite_limb_branch_dict()axon_spines_limb_branch_dict()axon_start_distance_from_soma()axon_width()bouton_meshes()calculate_axon_webbing()calculate_axon_webbing_on_branch()calculate_boutons()calculate_boutons_over_limb_branch_dict()complete_axon_processing()complete_axon_processing_old()compute_axon_on_dendrite_limb_branch_dict()compute_dendrite_on_axon_limb_branch_dict()compute_dendrite_on_axon_limb_branch_dict_excitatory()compute_dendrite_on_axon_limb_branch_dict_inhibitory()dendrite_limb_branch_dict()dendrite_on_axon_limb_branch_dict()filter_axon_limb_false_positive_end_nodes()filter_axon_neuron_false_positive_end_nodes()filter_candidate_branches_by_downstream_postsyn()filter_candidates_away_with_downstream_high_postsyn_branches_NOT_USED()myelination_limb_branch_dict()short_thick_branches_limb_branch_dict()valid_web_for_t()wide_angle_t_candidates()
- neurd.branch_attr_utils module
calculate_branch_attr_soma_distances_on_limb()calculate_endpoints_dist()calculate_neuron_soma_distance()calculate_neuron_soma_distance_euclidean()calculate_upstream_downstream_dist()calculate_upstream_downstream_dist_from_down_idx()calculate_upstream_downstream_dist_from_up_idx()set_limb_branch_idx_to_attr()
- neurd.branch_utils module
add_jitter_to_endpoint()branch_dynamics_attr_dict_dynamics_from_node()closest_mesh_skeleton_dist()combine_attr_lists()combine_branches()endpoint_downstream_idx()endpoint_downstream_with_offset()endpoint_type_with_offset()endpoint_upstream_idx()endpoint_upstream_with_offset()is_skeleton_upstream_to_downstream()mesh_shaft()mesh_shaft_idx()min_dist_synapse_endpoint()min_dist_synapses_post_downstream()min_dist_synapses_post_upstream()min_dist_synapses_pre_downstream()min_dist_synapses_pre_upstream()refine_width_array_to_match_skeletal_coordinates()set_branch_attr_on_limb()set_branch_attr_on_limb_on_neuron()set_branches_endpoints_upstream_downstream_idx()set_branches_endpoints_upstream_downstream_idx_on_limb()set_endpoints_upstream_downstream_idx_from_upstream_coordinate()set_endpoints_upstream_downstream_idx_on_branch()skeletal_coordinates_dist_upstream_to_downstream()skeletal_coordinates_upstream_to_downstream()skeleton_adjust()skeleton_angle_from_top()skeleton_vector_downstream()skeleton_vector_endpoint()skeleton_vector_upstream()width_array_skeletal_lengths_upstream_to_downstream()width_array_upstream_to_downstream()width_array_upstream_to_dowstream_with_skeletal_points()width_array_value_closest_to_coordinate()width_downstream()width_endpoint()width_upstream()
- neurd.cave_client_utils module
CaveInterfaceCaveInterface.get_table()CaveInterface.get_tables()CaveInterface.load_cave_token()CaveInterface.mesh_from_seg_id()CaveInterface.neuron_nucleus_df()CaveInterface.postsyn_df_from_seg_id()CaveInterface.pre_post_df_from_seg_id()CaveInterface.presyn_df_from_seg_id()CaveInterface.segment_ids_with_nucleus()CaveInterface.set_cave_auth()CaveInterface.synapse_df_from_seg_id()CaveInterface.table_size()
get_table()get_tables()init_cave_client()load_cave_token()mesh_from_seg_id()neuron_nucleus_df()postsyn_df_from_seg_id()pre_post_df_from_seg_id()prepost_syn_df_from_cave_syn_df()presyn_df_from_seg_id()release_from_release_name()release_name_from_client()release_name_from_release()save_cave_token_to_cloudvolume_secrets()segment_ids_with_nucleus()set_cave_auth()set_global_table_names()synapse_df_from_seg_id()table_dict_from_release_name()table_name_from_table_str()table_size()
- neurd.cave_interface module
- neurd.cell_type_utils module
accuracy_df_by_cell_type_fine()all_training_df()border_training_df()cell_type_fine_classifier_map_derived()cell_type_fine_for_clustering_inhcell_type_fine_mapping_publishable()cell_type_fine_name_cleaner()cell_type_from_feature_df()cell_type_high_probability_df_from_df()cell_type_names_str()classes_from_cell_type_name()clean_cell_type_fine()coarse_cell_type_from_coarse()coarse_cell_type_from_fine()dendrite_branch_stats_near_soma()df_cell_type_fine()e_i_classification_from_neuron_obj()e_i_classification_from_neuron_obj_old()e_i_classification_single()e_i_color_dict()e_i_label_from_cell_type_fine()e_i_model_as_logistic_reg_on_border_df()excitatory_high_probability_df_from_df()export_cell_type_abbreviations_csv()filter_cell_type_df_for_most_complete_duplicates()load_border_exc_inh_df()load_manual_exc_inh_df()map_cell_type_fine_publishable()plot_cell_type_gnn_embedding()plot_classifier_map()plot_e_i_model_classifier_map()postsyn_branches_near_soma()postsyn_branches_near_soma_for_syn_post_density()predict_class_single_datapoint()rename_cell_type_fine_column()rename_dict_for_cell_type_fine()set_e_i_model()set_e_i_model_as_kNN()soma_stats_for_cell_type()spine_density_near_soma()synapse_density_near_soma()synapse_density_stats()
- neurd.classification_utils module
apical_branch_candidates_on_limb()apical_classification()axon_candidates()axon_classification()axon_faces_from_labels_on_original_mesh()axon_like_limb_branch_dict()axon_limb_branch_dict()axon_mesh_from_labels()axon_starting_branch()axon_starting_coordinate()axon_width_like_query_revised()axon_width_like_segments()candidate_starting_skeletal_angle()clear_axon_labels_from_dendritic_paths_to_starter_node()contains_excitatory_apical()contains_excitatory_axon()dendrite_branches_on_limb()dendrite_limb_branch_dict()filter_axon_candiates()filter_axon_candiates_old()inhibitory_excitatory_classifier()spine_level_classifier()
- neurd.concept_network_utils module
G_weighted_from_limb()all_downstream_branches_from_branches()all_downstream_nodes()all_downtream_branches()all_downtream_branches_including_branch()all_upstream_branches()all_upstream_branches_from_branches()all_upstream_branches_including_branch()attribute_upstream_downstream()branches_with_parent_branching()branches_with_parent_non_branching()branches_within_distance()branches_within_distance_downstream()branches_within_distance_upstream()distance_between_nodes_di()distance_between_nodes_di_downstream()distance_between_nodes_di_upstream()downstream_nodes()downstream_nodes_mesh_connected()downstream_nodes_without_branching()endnode_branches_of_branches_within_distance_downtream()feature_over_branches()nodes_downstream()nodes_upstream()nodes_upstream_downstream()other_direction()skeletal_length_downstream()skeletal_length_upstream()skeletal_length_upstream_downstream()skeleton_downstream()skeleton_downstream_restricted()skeleton_upstream()skeleton_upstream_downstream()subgraph_around_branch()sum_feature_over_branches()synapse_density_downstream()synapse_density_upstream()synapse_density_upstream_downstream()synapses_downstream()synapses_upstream()synapses_upstream_downstream()upstream_branches_in_branches_list()upstream_nodes_without_branching()weighted_attribute_upstream_downstream()weighted_feature_over_branches()width_downstream()width_downstream_restricted()width_upstream()width_upstream_downstream()
- neurd.connectome_analysis_utils module
- neurd.connectome_query_utils module
- neurd.connectome_utils module
add_axes_subset_soma_to_syn_euclidean_dist_to_edge_df()add_compartment_syn_flag_columns_to_edge_df()add_delta_ori_edge_features()add_presyn_postsyn_syn_dist_signed_to_edge_df()add_spine_syn_flag_columns_to_edge_df()add_synapse_xyz_to_edge_df()attribute_from_edge_dict()basic_connectivity_axon_dendrite_stats_from_G()compute_edge_statistic()compute_presyn_postsyn_walk_euclidean_skeletal_dist()compute_presyn_soma_postsyn_soma_euclid_dist_axis()computed_presyn_postsyn_soma_relative_synapse_coordinate()exc_to_exc_edge_df()excitatory_nodes()filter_away_presyns_with_soma_postsyns()inhibitory_nodes()mean_axon_skeletal_length()mean_dendrite_skeletal_length()n_compartment_syn_from_edge_df()n_spine_syn_from_edge_df()neuroglancer_df_from_edge_df()plot_3D_distribution_attribute()plot_3d_attribute()plot_cell_type_pre_post_attribute_hist()plot_functional_connection_from_df()plot_restricted_edge_df_delta_ori()plot_soma_dist_distr()plotting_edge_df_delta_ori()postsyn_skeletal_distance_to_soma_from_edge_dict()pre_post_node_names_from_synapse_id()presyn_postsyn_skeletal_path_from_synapse_id()presyn_postsyn_soma_relative_synapse_coordinate()presyn_postsyn_walk_euclidean_skeletal_dist()presyn_soma_postsyn_soma_euclid_dist_axis()presyns_with_soma_postsyns()radius_cell_type_sampling()restrict_edge_df()restrict_edge_df_by_cell_type_and_layer()segment_id_from_seg_split_id()segment_ids_from_synapse_ids()set_edge_attribute_from_node_attribute()set_edge_presyn_postsyn_centroid()soma_center_from_segment_id()soma_centers_from_node_df()soma_centers_from_segment_ids()syn_coordinate_from_edge_dict()synapse_coordinate_from_seg_split_syn_id()synapse_ids_and_coord_from_segment_ids_edge()synapses_from_segment_id_edges()visualize_graph_connections_by_method()
- neurd.dandi_utils module
- neurd.documentation_utils module
- neurd.error_detection module
attempt_width_matching_for_fork_divergence()axon_fork_divergence_errors_limb_branch_dict()calculate_skip_distance()calculate_skip_distance_poly()cut_kissing_graph_edges()debug_branches_high_degree()debug_branches_low_degree()dendrite_branch_restriction()double_back_axon_thick()double_back_axon_thin()double_back_dendrite()double_back_edges()double_back_edges_path()double_back_error_limb_branch_dict()double_back_threshold_axon_by_width()downstream_nodes_from_G()error_branches_by_axons()error_faces_by_axons()high_degree_branch_errors_dendrite_limb_branch_dict()high_degree_branch_errors_limb_branch_dict()high_degree_false_positive_low_sibling_filter()high_degree_upstream_match()high_low_degree_upstream_match_preprocessing()low_degree_branch_errors_limb_branch_dict()low_degree_upstream_match()matched_branches_by_angle()matched_branches_by_angle_at_coordinate()path_to_edges()resolving_crossovers()skip_distance_from_branch_width()thick_t_errors_limb_branch_dict()upstream_node_from_G()webbing_t_errors_limb_branch_dict()webbing_t_errors_limb_branch_dict_old()width_jump_double_back_edges_path()width_jump_edges()width_jump_edges_path()width_jump_from_upstream_min()width_jump_up_axon()width_jump_up_dendrite()width_jump_up_error_limb_branch_dict()
- neurd.functional_tuning_utils module
- neurd.gnn_cell_typing_utils module
- neurd.gnn_embedding_utils module
- neurd.graph_filters module
axon_double_back_filter()axon_double_back_inh_filter()axon_spine_at_intersection_filter()axon_webbing_filter()fork_divergence_filter()fork_min_skeletal_distance_filter()graph_filter_adapter()min_synapse_dist_to_branch_point_filter()thick_t_filter()upstream_pair_singular()wide_angle_t_motif()
- neurd.h01_volume_utils module
DataInterfacealign_array()align_attribute()align_matrix_from_rotation()align_matrix_from_soma_coordinate()align_mesh()align_mesh_from_rotation()align_neuron_obj()align_neuron_obj_from_align_matrix()align_skeleton()aligning_matrix_3D()radius_for_rotation_from_proj_magn()rotate_mesh_from_matrix()rotation_from_proj_error_and_radius()rotation_from_soma_center()rotation_signed_from_middle_vector()unalign_neuron_obj()
- neurd.limb_utils module
all_paths_to_leaf_nodes()best_feature_match_in_descendents()children_skeletal_angle()children_skeletal_angle_max()children_skeletal_angle_min()most_upstream_endpoints_of_limb_branch()most_usptream_endpoints_of_branches_on_limb()parent_skeletal_angle()relation_skeletal_angle()root_skeleton_vector_from_soma()root_width()siblings_skeletal_angle()siblings_skeletal_angle_max()siblings_skeletal_angle_min()skeletal_angles_df()width_upstream()
- neurd.microns_graph_query_utils module
- neurd.microns_volume_utils module
DataInterfaceEM_coordinates_to_layer()EM_coordinates_to_visual_areas()add_node_attributes_to_proofread_graph()align_array()align_mesh()align_neuron_obj()align_skeleton()coordinates_to_layer_height()distance_from_microns_volume_bbox_midpoint()em_alignment_coordinates_info()em_alignment_data_raw()em_voxels_to_nm()layer_from_em_centroid_xyz()microns_volume_bbox_corners()microns_volume_bbox_midpoint()neuron_soma_layer_height()nm_to_em_voxels()plot_visual_area_xz_projection()soma_distances_from_microns_volume_bbox_midpoint()unalign_neuron_obj()visual_area_from_em_centroid_xyz()
- neurd.motif_null_utils module
- neurd.motif_utils module
annotated_motif_df()counts_df_from_motif_df()dotmotif_str_from_G_motif()edges_from_motif_dict()edges_from_str()filter_G_attributes()filter_motif_df()motif_G()motif_column_mapping()motif_data()motif_dicts_from_motif_from_database()motif_nodes_from_motif()motif_segment_df_from_motifs()n_nodes_from_motif()node_attributes_from_G()node_attributes_strs()nodes_from_motif_dict()nodes_from_str()nodes_mapping_from_G()query_with_edge_col()set_compartment_flat()str_from_G_motif()subgraph_from_motif_dict()unique_motif_reduction()visualize_graph_connections()
- neurd.nature_paper_plotting module
- neurd.neuron module
BranchBranch.__init__()Branch.areaBranch.axon_compartmentBranch.calculate_endpoints()Branch.compartmentBranch.compute_boutons_volume()Branch.compute_spines_volume()Branch.endpoint_downstreamBranch.endpoint_downstream_with_offsetBranch.endpoint_downstream_xBranch.endpoint_downstream_yBranch.endpoint_downstream_zBranch.endpoint_upstreamBranch.endpoint_upstream_with_offsetBranch.endpoint_upstream_xBranch.endpoint_upstream_yBranch.endpoint_upstream_zBranch.endpoints_nodesBranch.mesh_center_xBranch.mesh_center_yBranch.mesh_center_zBranch.mesh_shaftBranch.mesh_shaft_idxBranch.mesh_volumeBranch.min_dist_synapses_post_downstreamBranch.min_dist_synapses_post_upstreamBranch.min_dist_synapses_pre_downstreamBranch.min_dist_synapses_pre_upstreamBranch.n_boutonsBranch.n_spinesBranch.n_synapsesBranch.n_synapses_headBranch.n_synapses_neckBranch.n_synapses_no_headBranch.n_synapses_postBranch.n_synapses_preBranch.n_synapses_shaftBranch.n_synapses_spineBranch.n_webBranch.order_skeleton_by_smallest_endpoint()Branch.skeletal_coordinates_dist_upstream_to_downstreamBranch.skeletal_coordinates_upstream_to_downstreamBranch.skeletal_lengthBranch.skeletal_length_eligibleBranch.skeleton_graphBranch.skeleton_vector_downstreamBranch.skeleton_vector_upstreamBranch.spine_densityBranch.spine_volume_densityBranch.spine_volume_medianBranch.synapse_densityBranch.synapse_density_postBranch.synapse_density_preBranch.synapses_headBranch.synapses_neckBranch.synapses_no_headBranch.synapses_postBranch.synapses_preBranch.synapses_shaftBranch.synapses_spineBranch.total_spine_volumeBranch.width_array_skeletal_lengths_upstream_to_downstreamBranch.width_array_upstream_to_downstreamBranch.width_downstreamBranch.width_overallBranch.width_upstream
LimbLimb.__init__()Limb.all_starting_coordinatesLimb.all_starting_nodesLimb.areaLimb.boutonsLimb.boutons_volumeLimb.branch_objectsLimb.branchesLimb.compute_boutons_volume()Limb.compute_spines_volume()Limb.concept_network_data_by_somaLimb.concept_network_data_by_starting_nodeLimb.convert_concept_network_to_directional()Limb.current_starting_soma_verticesLimb.divided_skeletonsLimb.find_branch_by_skeleton_coordinate()Limb.get_attribute_dict()Limb.get_branch_names()Limb.get_computed_attribute_data()Limb.get_concept_network_data_by_soma()Limb.get_concept_network_data_by_soma_and_idx()Limb.get_skeleton()Limb.get_skeleton_soma_starting_node()Limb.get_soma_by_starting_node()Limb.get_soma_group_by_starting_node()Limb.get_starting_branch_by_soma()Limb.limb_correspondenceLimb.mesh_volumeLimb.n_boutonsLimb.n_branchesLimb.n_spinesLimb.n_synapsesLimb.n_synapses_postLimb.n_synapses_preLimb.n_webLimb.network_starting_infoLimb.nodes_to_excludeLimb.set_attribute_dict()Limb.set_branches_endpoints_upstream_downstream_idx()Limb.set_computed_attribute_data()Limb.set_concept_network_directional()Limb.set_concept_network_edges_from_current_starting_data()Limb.skeletal_lengthLimb.skeletonLimb.spinesLimb.spines_objLimb.spines_volumeLimb.synapse_density_postLimb.synapse_density_preLimb.synapsesLimb.synapses_postLimb.synapses_preLimb.touching_somas()Limb.web
NeuronNeuron.__init__()Neuron.apical_limb_branch_dictNeuron.apical_shaft_limb_branch_dictNeuron.apical_tuft_limb_branch_dictNeuron.areaNeuron.area_with_somasNeuron.axon_areaNeuron.axon_classification()Neuron.axon_lengthNeuron.axon_limbNeuron.axon_limb_branch_dictNeuron.axon_limb_idxNeuron.axon_limb_nameNeuron.axon_meshNeuron.axon_on_dendrite_limb_branch_dictNeuron.axon_skeletonNeuron.axon_starting_branchNeuron.axon_starting_coordinateNeuron.basal_limb_branch_dictNeuron.boutonsNeuron.boutons_volumeNeuron.calculate_decomposition_products()Neuron.calculate_multi_soma_split_suggestions()Neuron.calculate_new_width()Neuron.calculate_spines_old()Neuron.compute_boutons_volume()Neuron.compute_spines_volume()Neuron.dendrite_limb_branch_dictNeuron.dendrite_meshNeuron.dendrite_on_axon_limb_branch_dictNeuron.dendrite_skeletonNeuron.distance_errored_synapses_postNeuron.distance_errored_synapses_preNeuron.get_attribute_dict()Neuron.get_branch_node_names()Neuron.get_computed_attribute_data()Neuron.get_limb_names()Neuron.get_limb_node_names()Neuron.get_limbs_touching_soma()Neuron.get_skeleton()Neuron.get_soma_indexes()Neuron.get_soma_meshes()Neuron.get_soma_node_names()Neuron.get_somas()Neuron.get_somas_touching_limbs()Neuron.get_total_n_branches()Neuron.label_limb_branch_dict()Neuron.limb_areaNeuron.limb_branch_dictNeuron.limb_mesh_volumeNeuron.limbsNeuron.max_limb_n_branchesNeuron.max_limb_skeletal_lengthNeuron.max_soma_areaNeuron.max_soma_n_facesNeuron.max_soma_volumeNeuron.median_branch_lengthNeuron.merge_filter_locationsNeuron.merge_filter_suggestionsNeuron.mesh_errored_synapses_postNeuron.mesh_errored_synapses_preNeuron.mesh_from_branchesNeuron.mesh_kdtreeNeuron.mesh_volumeNeuron.mesh_volume_with_somasNeuron.multi_soma_split_execution()Neuron.multi_soma_touching_limbsNeuron.n_boutonsNeuron.n_branchesNeuron.n_branches_per_limbNeuron.n_distance_errored_synapsesNeuron.n_distance_errored_synapses_postNeuron.n_distance_errored_synapses_preNeuron.n_error_limbsNeuron.n_facesNeuron.n_limbsNeuron.n_mesh_errored_synapsesNeuron.n_mesh_errored_synapses_postNeuron.n_mesh_errored_synapses_preNeuron.n_somasNeuron.n_spine_eligible_branchesNeuron.n_spinesNeuron.n_synapsesNeuron.n_synapses_errorNeuron.n_synapses_postNeuron.n_synapses_preNeuron.n_synapses_somasNeuron.n_synapses_totalNeuron.n_synapses_validNeuron.n_verticesNeuron.neuron_stats()Neuron.neuron_stats_old()Neuron.non_axon_like_limb_branch_on_dendriteNeuron.oblique_limb_branch_dictNeuron.plot_limb_concept_network()Neuron.plot_soma_limb_concept_network()Neuron.same_soma_multi_touching_limbsNeuron.save_compressed_neuron()Neuron.save_neuron_object()Neuron.set_attribute_dict()Neuron.set_computed_attribute_data()Neuron.skeletal_lengthNeuron.skeletal_length_eligibleNeuron.skeletonNeuron.skeleton_length_per_limbNeuron.soma_areaNeuron.soma_mesh_volumeNeuron.spine_densityNeuron.spine_density_eligibleNeuron.spine_eligible_branch_lengthsNeuron.spine_volume_densityNeuron.spine_volume_density_eligibleNeuron.spine_volume_medianNeuron.spine_volume_per_branch_eligibleNeuron.spinesNeuron.spines_already_computed()Neuron.spines_objNeuron.spines_per_branchNeuron.spines_per_branch_eligibleNeuron.spines_volumeNeuron.suNeuron.synapse_density_postNeuron.synapse_density_preNeuron.synapsesNeuron.synapses_errorNeuron.synapses_postNeuron.synapses_preNeuron.synapses_somasNeuron.synapses_totalNeuron.synapses_validNeuron.total_spine_volumeNeuron.valid_error_split_points_by_limbNeuron.webNeuron.width_90_percNeuron.width_medianNeuron.width_no_spine_90_percNeuron.width_no_spine_median
Somaconvert_soma_to_piece_connectivity_to_graph()copy_concept_network()dc_check()export_mesh_labels()export_skeleton()
- neurd.neuron_geometry_utils module
- neurd.neuron_graph_lite_utils module
G_with_attrs_from_neuron_obj()array_shape_from_radius()attr_activation_map()attr_value_by_node()attr_value_soma()axes_limits_coordinates()axes_limits_from_df()axon_compartment_extract()boutons_cdfs_extract()boutons_volume_extract()closest_node_idx_to_sample_idx()feature_map_df()filter_df_by_axon_dendrite()filter_df_by_skeletal_length()filter_df_by_soma_distance()filter_df_by_xyz_window()idx_for_col()idx_xyz_to_df()labels_extract()load_G_with_attrs()mesh_center_xyz()no_spatial_df_from_df_filtered()plot_df_xyz()save_G_with_attrs()soma_branch_df_split()soma_center_from_df()stats_df_from_G()symmetric_window()width_new_extract()
- neurd.neuron_pipeline_utils module
- neurd.neuron_searching module
apply_function_to_neuron()area()average_branch_length()axon_label()axon_merge_error_width_like_query()axon_segment()axon_segment_clean_false_positives()axon_segment_downstream_dendrites()axon_segments_after_checks()axon_width()axon_width_like_query()axon_width_like_segments_old()children_axon_width_max()children_skeletal_lengths_min()closest_mesh_skeleton_dist()convert_limb_function_return_to_dict()convert_limb_function_return_to_limb_branch_dict()convert_neuron_to_branches_dataframe()distance_from_soma()downstream_nodes_mesh_connected()downstream_upstream_diff_of_most_downstream_syn()farthest_distance_from_skeleton_to_mesh()flip_dendrite_to_axon()fork_divergence()functions_list_from_query()generate_neuron_dataframe()get_run_type()is_apical_shaft_in_downstream_branches()is_axon()is_axon_in_downstream_branches()is_axon_like()is_branch_mesh_connected_to_neighborhood()labels()labels_restriction()limb_error_branches()map_new_limb_node_value()matching_label()mean_mesh_center()median_mesh_center()merge_limbs()min_synapse_dist_to_branch_point()n_boutons()n_boutons_above_thresholds()n_downstream_nodes()n_downstream_nodes_with_skip()n_faces_branch()n_faces_limb()n_siblings()n_small_children()n_spines()n_synapses()n_synapses_downstream()n_synapses_downstream_within_dist()n_synapses_offset_endpoint_upstream()n_synapses_post()n_synapses_post_downstream()n_synapses_post_downstream_within_dist()n_synapses_post_head()n_synapses_post_spine()n_synapses_pre()n_synapses_pre_downstream()n_synapses_pre_offset_endpoint_upstream()n_synapses_spine()n_synapses_spine_offset_endpoint_upstream()n_synapses_spine_within_distance_of_endpoint_downstream()no_spine_average_mesh_center()no_spine_mean_mesh_center()no_spine_median_mesh_center()no_spine_width()parent_angle()parent_width()query_neuron()query_neuron_by_labels()ray_trace_perc()restrict_by_branch_and_upstream_skeletal_length()run_limb_function()run_optionsset_limb_functions_for_search()sibling_angle_max()sibling_angle_min()skeletal_distance_from_soma()skeletal_distance_from_soma_excluding_node()skeletal_length()skeletal_length_downstream()skeleton_dist_match_ref_vector()skeleton_distance_branch()skeleton_distance_limb()skeleton_perc_match_ref_vector()soma_starting_angle()spine_density()spines_per_skeletal_length()synapse_closer_to_downstream_endpoint_than_upstream()synapse_density()synapse_density_offset_endpoint_upstream()synapse_density_post()synapse_density_post_near_endpoint_downstream()synapse_density_post_offset_endpoint_upstream()synapse_density_pre()synapse_post_perc()synapse_post_perc_downstream()synapse_pre_perc()synapse_pre_perc_downstream()test_limb()total_upstream_skeletal_length()two_children_angle()upstream_axon_width()upstream_node_has_label()upstream_node_is_apical_shaft()upstream_skeletal_length()width()width_jump()width_jump_from_upstream_min()width_neuron()width_new()
- neurd.neuron_simplification module
all_concept_network_data_updated()branch_idx_map_from_branches_to_delete_on_limb()branching_simplification()combine_path_branches()combine_path_branches_on_limb()delete_branches_from_limb()delete_branches_from_neuron()floating_end_nodes_limb_branch()merge_floating_end_nodes_to_parent()reset_concept_network_branch_endpoints()
- neurd.neuron_statistics module
angle_from_top()branch_stats_dict_from_df()branch_stats_over_limb_branch()centroid_stats_from_neuron_obj()child_angles()children_axon_width()children_axon_width_max()children_feature()children_skeletal_lengths()children_skeletal_lengths_min()compute_edge_attributes_around_node()compute_edge_attributes_globally()compute_edge_attributes_locally()compute_edge_attributes_locally_upstream_downstream()compute_node_attributes()compute_node_attributes_upstream_downstream()coordinates_function_list()coordinates_stats_df()distance_from_soma()distance_from_soma_candidate()distance_from_soma_euclidean()downstream_dist_match_ref_vector_over_candidate()downstream_upstream_diff_of_most_downstream_syn()edges_to_delete_from_threshold_and_buffer()edges_to_delete_on_node_above_threshold_if_one_below()euclidean_distance_close_to_soma_limb_branch()euclidean_distance_farther_than_soma_limb_branch()euclidean_distance_from_soma_limb_branch()farthest_dendrite_branch_from_soma()farthest_distance_from_skeleton_to_mesh()features_from_neuron_skeleton_and_soma_center()features_from_skeleton_and_soma_center()filter_limbs_by_soma_starting_angle()find_parent_child_skeleton_angle_upstream_downstream()fork_divergence()fork_divergence_from_branch()fork_divergence_from_skeletons()fork_min_skeletal_distance()fork_min_skeletal_distance_from_skeletons()get_stat()is_apical_shaft_in_downstream_branches()is_axon_in_downstream_branches()is_label_in_downstream_branches()limb_branch_from_stats_df()max_layer_distance_above_soma_over_candidate()max_layer_height_over_candidate()min_synapse_dist_to_branch_point()n_small_children()n_synapses_diff()n_synapses_downstream()n_synapses_downstream_total()n_synapses_downstream_within_dist()n_synapses_offset_endpoint_upstream()n_synapses_post_downstream_within_dist()n_synapses_pre_downstream_within_dist()n_synapses_pre_offset_endpoint_upstream()n_synapses_spine_offset_endpoint_upstream()n_synapses_spine_within_distance_of_endpoint_downstream()n_synapses_upstream()n_synapses_upstream_total()neuron_path_analysis()neuron_stats()node_functions_default()parent_child_sk_angle()parent_width()ray_trace_perc()shortest_distance_from_soma_multi_soma()sibling_sk_angle()skeletal_length_along_path()skeletal_length_downstream()skeletal_length_downstream_total()skeletal_length_over_candidate()skeletal_length_upstream()skeletal_length_upstream_total()skeleton_dist_match_ref_vector()skeleton_dist_match_ref_vector_sum_over_branches()skeleton_dist_match_ref_vector_sum_over_branches_downstream()skeleton_dist_match_ref_vector_sum_over_branches_upstream()skeleton_downstream()skeleton_perc_dist_match_ref_vector()skeleton_perc_match_ref_vector()skeleton_stats_axon()skeleton_stats_compartment()skeleton_stats_dendrite()skeleton_stats_from_neuron_obj()skeleton_upstream()soma_distance_branch_set()soma_distance_euclidean_branch_set()soma_distance_skeletal_branch_set()soma_starting_angle()soma_starting_vector()stats_df()stats_dict_over_limb_branch()synapse_closer_to_downstream_endpoint_than_upstream()synapse_density_diff()synapse_density_offset_endpoint_upstream()synapse_density_post_near_endpoint_downstream()synapse_density_post_offset_endpoint_upstream()synapses_downstream()synapses_downstream_total()synapses_downstream_within_dist()synapses_post_downstream_within_dist()synapses_pre_downstream_within_dist()synapses_upstream()synapses_upstream_total()total_upstream_skeletal_length()trajectory_angle_from_start_branch_and_subtree()upstream_axon_width()upstream_endpoint_branch_set()upstream_node_is_apical()upstream_node_is_apical_shaft()upstream_skeletal_length()width_basic()width_diff()width_diff_basic()width_diff_percentage()width_diff_percentage_basic()width_downstream()width_max()width_near_branch_endpoint()width_new()width_over_candidate()width_upstream()width_weighted_over_branches()
- neurd.neuron_utils module
add_branch_label()add_limb_branch_combined_name_to_df()align_and_restrict_branch()align_array()align_attribute()align_mesh()align_neuron_obj_from_align_matrix()align_neuron_objs_at_soma()align_skeleton()all_concept_network_data_to_dict()all_concept_network_data_to_limb_network_stating_info()all_donwstream_branches_from_limb_branch()all_downstream_branches()all_downstream_branches_from_candidate()all_downstream_branches_from_multiple_branhes()all_medain_mesh_center_widths()all_no_spine_median_mesh_center_widths()all_skeletal_lengths()all_soma_connnecting_endpionts_from_starting_info()all_soma_meshes_from_limb()all_soma_names_from_limb()all_soma_soma_connections_from_limb()all_starting_attr_by_limb_and_soma()all_starting_dicts_by_soma()apply_adaptive_mesh_correspondence_to_neuron()area_over_limb_branch()axon_area()axon_length()axon_mesh()axon_only_group()axon_skeleton()boutons_above_thresholds()branch_attr_dict_from_node()branch_boundary_transition()branch_boundary_transition_old()branch_mesh_no_spines()branch_neighbors()branch_neighbors_attribute()branch_neighbors_mesh()branch_path_to_node()branch_path_to_soma()branch_path_to_start_node()branch_skeletal_distance_from_soma()branches_at_high_degree_coordinates()branches_combined_mesh()branches_on_limb_after_edges_deleted_and_created()branches_to_concept_network()branches_within_skeletal_distance()calculate_decomposition_products()calculate_spines_skeletal_length()candidate_from_branches()candidate_groups_from_limb_branch()candidate_limb_branch_dict_branch_intersection()candidates_from_limb_branch_candidates()check_concept_network()check_points_inside_soma_bbox()children_nodes()classify_endpoint_error_branches_from_limb_concept_network()classify_error_branch()classify_upstream_downsream()clean_all_concept_network_data()clean_neuron_all_concept_network_data()clear_all_branch_labels()clear_certain_branch_labels()closest_branch_endpoint_to_limb_starting_coordinate()closest_branch_to_coordinates()combined_somas_neuron_obj()compartment_root_skeleton_angle_max()compartment_root_skeleton_angle_min()compartment_root_width_max()compartment_root_width_min()compartment_roots_stat()compartment_roots_stat_extrema()compartment_roots_stat_max()compartment_roots_stat_min()compute_all_concept_network_data_from_limb()compute_feature_over_object()compute_mesh_attribute_volume()concatenate_feature_over_limb_branch_dict()concept_network_data_from_soma()connected_components_from_branches()convert_concept_network_to_directional()convert_concept_network_to_skeleton()convert_concept_network_to_undirectional()convert_int_names_to_string_names()convert_limb_concept_network_to_neuron_skeleton()convert_string_names_to_int_names()coordinate_to_offset_skeletons()coordinates_to_closest_limb_branch()copy_neuron()decompress_neuron()dendrite_mesh()dendrite_skeleton()distance_to_soma_from_coordinate_close_to_branch()downstream_endpoint()downstream_labels()downstream_nodes()empty_limb_object()error_limb_indexes()error_limbs()feature_list_over_object()feature_over_branches()feature_over_limb_branch_dict()filter_away_neuron_limbs()filter_away_neuron_limbs_by_min_skeletal_length()filter_branches_by_restriction_mesh()filter_limb_branch_dict_by_limb()filter_limbs_below_soma_percentile()find_branch_with_specific_coordinate()find_branch_with_specific_endpoint()find_face_idx_and_check_recovery()find_parent_child_skeleton_angle()find_sibling_child_skeleton_angle()generate_limb_concept_networks_from_global_connectivity()get_limb_int_name()get_limb_names_from_concept_network()get_limb_starting_angle_dict()get_limb_string_name()get_limb_to_soma_border_vertices()get_matching_concept_network_data()get_soma_int_name()get_soma_meshes()get_soma_names_from_concept_network()get_soma_skeleton()get_soma_string_name()get_starting_info_from_concept_network()get_starting_node_from_limb_concept_network()get_whole_neuron_skeleton()high_degree_branching_coordinates_on_limb()high_degree_branching_coordinates_on_neuron()in_limb_branch_dict()is_branch_mesh_connected_to_neighborhood()is_branch_obj()is_limb_obj()is_neuron_obj()label_limb_branch_dict()limb_branch_after_limb_branch_removal()limb_branch_after_limb_edge_removal()limb_branch_combining()limb_branch_dict_to_connected_components()limb_branch_dict_to_faces()limb_branch_dict_to_limb_true_false_dict()limb_branch_dict_to_skeleton()limb_branch_dict_valid()limb_branch_face_idx_dict_from_neuron_obj_overlap_with_face_idx_on_reference_mesh()limb_branch_from_candidate()limb_branch_from_edge_function()limb_branch_from_keywords()limb_branch_from_limbs()limb_branch_get()limb_branch_intersection()limb_branch_invert()limb_branch_list_to_limb_branch_dict()limb_branch_removed_after_limb_branch_removal()limb_branch_setdiff()limb_branch_str_names_from_limb_branch_dict()limb_branch_union()limb_correspondence_on_limb()limb_correspondence_on_neuron()limb_edge_dict_with_function()limb_idx()limb_label()limb_mesh_from_branches()limb_to_soma_mapping()limb_true_false_dict_to_limb_branch_dict()low_branch_length_clusters()max_limb_n_branches()max_limb_skeletal_length()max_soma_area()max_soma_n_faces()max_soma_volume()median_branch_length()mesh_not_in_neuron_branches()mesh_over_candidate()mesh_over_limb_branch_dict()mesh_without_boutons()mesh_without_mesh_attribute()min_width_upstream()most_upstream_branch()most_upstream_conn_comp_node()most_upstream_conn_comp_node_stat()multi_soma_touching_limbs()n_boutons()n_branches()n_branches_over_limb_branch_dict()n_branches_per_limb()n_downstream_nodes()n_error_limbs()n_limbs()n_somas()n_spine_eligible_branches()n_spines()n_web()neighbor_endpoint()neighborhood_mesh()neuron_limb_branch_dict()neuron_limb_overwrite()neuron_mesh_from_branches()neuron_spine_density()non_axon_like_limb_branch_on_dendrite()non_soma_touching_meshes_not_stitched()non_soma_touching_meshes_stitched()order_branches_by_skeletal_distance_from_soma()ordered_endpoints_on_branch_path()original_mesh_face_to_limb_branch()pair_branch_connected_components()pair_branch_connected_components_by_common_upstream()pair_neuron_obj_to_nuclei()parent_node()recalculate_endpoints_and_order_skeletons_for_branch()recalculate_endpoints_and_order_skeletons_over_neuron()restrict_skeleton_from_start_plus_offset_downstream()restrict_skeleton_from_start_plus_offset_upstream()return_concept_network()roots_stat()same_soma_multi_touching_limbs()save_compressed_neuron()sdf_filter()set_branch_attribute_over_neuron()set_preprocessed_data_from_limb_no_mesh_change()shared_skeleton_endpoints_for_connected_branches()shortest_path()sibling_nodes()skeletal_distance_from_soma()skeletal_length()skeletal_length_eligible()skeletal_length_over_candidate()skeletal_length_over_downstream_branches()skeletal_length_over_limb_branch()skeleton_coordinate_connecting_to_downstream_branches()skeleton_length_per_limb()skeleton_nodes_from_branches_on_limb()skeleton_nodes_from_limb_branch()skeleton_over_candidate()skeleton_over_limb_branch_dict()skeleton_points_along_path()skeleton_touching_branches()smaller_preprocessed_data()soma_centers()soma_idx_and_group_from_name()soma_label()spine_density()spine_density_eligible()spine_eligible_branch_lengths()spine_volume_density()spine_volume_density_eligible()spine_volume_median()spine_volume_per_branch_eligible()spines_per_branch()spines_per_branch_eligible()starting_node_combinations_of_limb_sorted_by_microns_midpoint()starting_node_from_soma()statistic_per_branch()sum_feature_over_branches()sum_feature_over_limb_branch_dict()synapse_skeletal_distances_to_soma()total_spine_volume()translate_neuron_obj()unalign_neuron_obj_from_align_matrix()upstream_downstream_endpoint_idx()upstream_endpoint()upstream_labels()upstream_node()upstream_node_has_label()viable_axon_limbs_by_starting_angle()viable_axon_limbs_by_starting_angle_old()volume_over_limb_branch()whole_neuron_branch_concept_network()whole_neuron_branch_concept_network_old()width()width_average_from_limb_correspondence()width_median()width_no_spine_median()width_no_spine_perc()width_perc()
- neurd.neuron_visualizations module
add_scatter_to_current_plot()limb_branch_dicts_to_combined_color_dict()limb_correspondence_plottable()plot_axon()plot_axon_merge_errors()plot_boutons()plot_branch()plot_branch_groupings()plot_branch_mesh_attribute()plot_branch_on_whole_mesh()plot_branch_pieces()plot_branch_spines()plot_branch_with_boutons_old()plot_branch_with_neighbors()plot_branches_with_boutons()plot_branches_with_colors()plot_branches_with_mesh_attribute()plot_branches_with_spines()plot_candidates()plot_compartments()plot_concept_network()plot_dendrite_and_synapses()plot_intermediates()plot_ipv_mesh()plot_ipv_scatter()plot_ipv_skeleton()plot_labeled_limb_branch_dicts()plot_limb()plot_limb_branch_dict()plot_limb_branch_dict_multiple()plot_limb_concept_network_2D()plot_limb_correspondence()plot_limb_correspondence_multiple()plot_limb_idx()plot_limb_path()plot_merge_filter_suggestions()plot_mesh_face_idx()plot_meshes_skeletons()plot_original_vs_proofread()plot_soma_extraction_meshes()plot_soma_limb_concept_network()plot_soma_meshes()plot_spines()plot_spines_head_neck()plot_split_suggestions_per_limb()plot_synapses()plot_valid_error_synapses()plot_web_intersection()plottable_from_branches()plottable_meshes()plottable_meshes_skeletons()plottable_skeletons()set_zoom()set_zoom_to_limb_branch()vector_to_scatter_line()visualize_axon_dendrite()visualize_branch_at_downstream_split()visualize_concept_map()visualize_limb_obj()visualize_neuron()visualize_neuron_axon_dendrite()visualize_neuron_axon_merge_errors()visualize_neuron_limbs()visualize_neuron_lite()visualize_neuron_path()visualize_neuron_specific_limb()visualize_subset_neuron_limbs()
- neurd.nwb_utils module
- neurd.parameter_utils module
PackageParametersParametersadd_global_name_to_dict()category_param_from_module()clean_modules_dict()config_directory()export_csv()export_df()export_package_param_dict_to_file()global_param_and_attributes_dict_to_separate_mode_jsons()injest_nested_dict()jsonable_dict()modes_global_param_and_attributes_dict_all_modules()modes_global_param_and_attributes_dict_from_module()parameter_config_folder()parameter_dict_from_module_and_obj()parameter_list_from_module()parameters_from_filepath()set_parameters_for_directory_modules_from_obj()this_directory()
- neurd.preprocess_neuron module
attach_floating_pieces_to_limb_correspondence()calculate_limb_concept_networks()check_skeletonization_and_decomp()closest_dist_from_floating_mesh_to_skeleton()correspondence_1_to_1()filter_limb_correspondence_for_end_nodes()filter_soma_touching_vertices_dict_by_mesh()find_if_stitch_point_on_end_or_branch()high_fidelity_axon_decomposition()limb_meshes_expansion()mesh_correspondence_first_pass()plot_correspondence()plot_correspondence_on_single_mesh()preprocess_limb()preprocess_neuron()
- neurd.proofreading_utils module
apply_proofreading_filters_to_neuron()axon_on_dendrite_plus_downstream()calculate_error_rate()collapse_branches_on_limb()crossover_elimination_limb_branch_dict()cut_limb_network_by_edges()cut_limb_network_by_suggestions()delete_branches_from_limb()delete_branches_from_neuron()doubling_back_and_width_elimination_limb_branch_dict()edges_to_create_and_delete_by_doubling_back_and_width()edges_to_create_and_delete_crossover()edges_to_create_and_delete_high_degree_coordinates()edges_to_cut_by_doubling_back_and_width_change()exc_axon_on_dendrite_merges_filter()exc_double_back_dendrite_filter()exc_high_degree_branching_dendrite_filter()exc_high_degree_branching_filter()exc_low_degree_branching_filter()exc_width_jump_up_axon_filter()exc_width_jump_up_dendrite_filter()extract_blue_red_points_from_limb_branch_dict_to_cancel()extract_from_filter_info()filter_away_axon_on_dendrite_merges()filter_away_axon_on_dendrite_merges_old()filter_away_crossovers()filter_away_dendrite_on_axon_merges()filter_away_dendrite_on_axon_merges_old()filter_away_double_back_axon_thick()filter_away_double_back_axon_thin()filter_away_double_back_dendrite()filter_away_high_degree_branching()filter_away_high_degree_branching_dendrite()filter_away_high_degree_coordinates()filter_away_large_double_back_or_width_changes()filter_away_limb_branch_dict()filter_away_limb_branch_dict_with_function()filter_away_low_branch_length_clusters()filter_away_low_branch_length_clusters_axon()filter_away_low_branch_length_clusters_dendrite()filter_away_low_degree_branching()filter_away_small_axon_fork_divergence()filter_away_thick_t_merge()filter_away_webbing_t_merges()filter_away_width_jump_up_axon()filter_away_width_jump_up_dendrite()find_high_degree_coordinates_on_path()get_all_coordinate_suggestions()get_all_cut_and_not_cut_path_coordinates()get_attribute_from_suggestion()get_best_cut_edge()get_edges_to_create_from_suggestion()get_edges_to_delete_from_suggestion()get_exc_filters()get_exc_filters_high_fidelity_axon_postprocessing_old()get_exc_filters_high_fidelity_axon_preprocessing()get_exc_filters_high_fidelity_axon_preprocessing_old()get_inh_filters()get_n_paths_cut()get_n_paths_not_cut()get_removed_branches_from_suggestion()high_degree_coordinates_elimination_limb_branch_dict()inh_double_back_dendrite_filter()inh_high_degree_branching_dendrite_filter()inh_high_degree_branching_filter()inh_low_degree_branching_filter()limb_branch_dict_to_cancel_to_red_blue_groups()limb_errors_to_cancel_to_red_blue_group()low_branch_length_large_clusters()low_branch_length_large_clusters_axon()low_branch_length_large_clusters_dendrite()make_filter_dict()merge_error_red_blue_suggestions_clean()merge_type_to_color()multi_soma_split_suggestions()plot_limb_to_red_blue_groups()print_merge_type_color_map()proofread_neuron()proofread_neuron_class_predetermined()proofread_neuron_full()proofreading_table_processing()refine_axon_for_high_fidelity_skeleton()save_off_meshes_skeletons()soma_connections_from_split_title()soma_names_from_split_title()split_disconnected_neuron()split_neuron()split_neuron_limb_by_seperated_network()split_neuron_limbs_by_suggestions()split_success()split_suggestions_to_concept_networks()split_suggestions_to_concept_networks_old()split_type_from_title()synapse_filtering()v4_exc_filters()v5_exc_filters()v6_exc_filters()v6_exc_filters_old()v6_inh_filters()v7_exc_filters()v7_inh_filters()valid_synapse_records_to_unique_synapse_df()
- neurd.proximity_analysis_utils module
add_euclidean_dist_to_prox_df()conversion_df()conversion_df_from_proximity_df()conversion_rate()conversion_rate_by_attribute_and_cell_type_pairs()example_basal_conversion_rate()example_pairwise_postsyn_analysis()pairwise_presyn_proximity_onto_postsyn()plot_prox_func_vs_attribute_from_edge_df()print_n_dict()str_of_n_prox_n_syn()
- neurd.proximity_utils module
- neurd.soma_extraction_utils module
extract_soma_center()filter_away_inside_soma_pieces()find_soma_centroid_containing_meshes()find_soma_centroids()glia_nuclei_faces_from_mesh()grouping_containing_mesh_indices()largest_mesh_piece()original_mesh_soma()original_mesh_soma_old()output_global_parameters_glia()output_global_parameters_nuclei()output_global_parameters_soma()plot_soma_products()remove_nuclei_and_glia_meshes()side_length_check()side_length_ratios()soma_connectivitysoma_indentification()soma_volume_check()soma_volume_ratio()subtract_soma()
- neurd.soma_splitting_utils module
- neurd.spine_utils module
SpineSpine.mesh_face_idxSpine.meshSpine.neck_face_idxSpine.head_face_idxSpine.neck_sdfSpine.head_sdfSpine.head_widthSpine.neck_widthSpine.volumeSpine.spine_idSpine.sdfSpine.endpoints_distSpine.upstream_distSpine.downstream_distSpine.coordinate_border_vertsSpine.coordinateSpine.bbox_oriented_side_lengthsSpine.head_bbox_oriented_side_lengthsSpine.neck_bbox_oriented_side_lengthsSpine.head_mesh_splitsSpine.head_mesh_splits_face_idxSpine.branch_width_overallSpine.branch_skeletal_lengthSpine.branch_width_at_baseSpine.skeletonSpine.skeletal_lengthSpine.closest_branch_face_idxSpine.closest_sk_coordinateSpine.closest_face_coordinateSpine.closest_face_distSpine.soma_distanceSpine.soma_distance_euclideanSpine.compartmentSpine.limb_idxSpine.branch_idxSpine.__init__()Spine.areaSpine.area_of_border_vertsSpine.base_coordinateSpine.base_coordinate_x_nmSpine.base_coordinate_y_nmSpine.base_coordinate_z_nmSpine.bbox_oriented_side_lengthsSpine.bbox_oriented_side_maxSpine.bbox_oriented_side_middleSpine.bbox_oriented_side_minSpine.border_areaSpine.calculate_closest_mesh_sk_coordinates()Spine.calculate_face_idx()Spine.calculate_head_neck()Spine.calculate_skeleton()Spine.calculate_spine_attributes()Spine.calculate_volume()Spine.coordinate_border_verts_areaSpine.endpoint_dist_0Spine.endpoint_dist_1Spine.export()Spine.head_areaSpine.head_bbox_max_x_nmSpine.head_bbox_max_y_nmSpine.head_bbox_max_z_nmSpine.head_bbox_min_x_nmSpine.head_bbox_min_y_nmSpine.head_bbox_min_z_nmSpine.head_bbox_oriented_side_lengthsSpine.head_bbox_oriented_side_maxSpine.head_bbox_oriented_side_middleSpine.head_bbox_oriented_side_minSpine.head_existSpine.head_meshSpine.head_mesh_splitsSpine.head_mesh_splits_face_idxSpine.head_mesh_splits_from_index()Spine.head_mesh_splits_maxSpine.head_mesh_splits_minSpine.head_n_facesSpine.head_skeletal_lengthSpine.head_volumeSpine.head_width_raySpine.head_width_ray_80_percSpine.mesh_centerSpine.mesh_center_x_nmSpine.mesh_center_y_nmSpine.mesh_center_z_nmSpine.n_facesSpine.n_faces_headSpine.n_faces_neckSpine.n_headsSpine.neck_areaSpine.neck_bbox_max_x_nmSpine.neck_bbox_max_y_nmSpine.neck_bbox_max_z_nmSpine.neck_bbox_min_x_nmSpine.neck_bbox_min_y_nmSpine.neck_bbox_min_z_nmSpine.neck_bbox_oriented_side_lengthsSpine.neck_bbox_oriented_side_maxSpine.neck_bbox_oriented_side_middleSpine.neck_bbox_oriented_side_minSpine.neck_meshSpine.neck_n_facesSpine.neck_skeletal_lengthSpine.neck_volumeSpine.neck_width_raySpine.neck_width_ray_80_percSpine.no_head_face_idxSpine.no_head_meshSpine.plot_head_neck()Spine.sdf_70_percSpine.sdf_90_percSpine.sdf_meanSpine.sdf_medianSpine.shaft_border_areaSpine.skeletal_lengthSpine.skeletonSpine.spine_areaSpine.spine_bbox_max_x_nmSpine.spine_bbox_max_y_nmSpine.spine_bbox_max_z_nmSpine.spine_bbox_min_x_nmSpine.spine_bbox_min_y_nmSpine.spine_bbox_min_z_nmSpine.spine_bbox_oriented_side_maxSpine.spine_bbox_oriented_side_middleSpine.spine_bbox_oriented_side_minSpine.spine_n_facesSpine.spine_skeletal_lengthSpine.spine_volumeSpine.spine_width_raySpine.spine_width_ray_80_perc
add_head_neck_shaft_spine_objs()add_spine_densities_to_spine_stats_df()add_synapse_densities_to_spine_synapse_stats_df()adjust_obj_with_face_offset()apply_sdf_filter()area_from_compartment()area_of_border_verts()bbox_max_x_nm_from_compartment()bbox_max_y_nm_from_compartment()bbox_max_z_nm_from_compartment()bbox_min_x_nm_from_compartment()bbox_min_y_nm_from_compartment()bbox_min_z_nm_from_compartment()bouton_non_bouton_idx_from_branch()calculate_branch_overall_features()calculate_branch_width_at_base()calculate_endpoints_dist()calculate_face_idx()calculate_soma_distance_euclidean()calculate_soma_distance_skeletal()calculate_spine_attributes()calculate_spine_attributes_for_list()calculate_spine_obj_attr_for_neuron()calculate_spine_obj_mesh_skeleton_coordinates()calculate_spine_obj_mesh_skeleton_coordinates_for_branch()calculate_spines_on_branch()calculate_spines_on_neuron()calculate_upstream_downstream_dist_from_up_idx()colors_from_spine_bouton_labels()compartment_idx_for_mesh_face_idx_of_spine()compartment_index_from_id()complete_spine_processing()connectivityconvert_number_of_columns_to_dtype()decode_head_neck_shaft_idx()df_from_spine_objs()examle_plot_spines_from_spine_df_query()example_comparing_mesh_segmentation_vs_spine_head_segmentation()example_plot_coordinates_from_spine_df_idx()example_plot_small_volume_spines_from_spine_df()example_syn_df_spine_correlations()example_trying_to_skeletonize_spine()export()face_idx_map_from_spine_objs()false_positive_queries()feature_summed_over_compartments()features_to_export_for_db()filter_and_scale_spine_syn_df()filter_away_fp_from_df()filter_for_high_confidence_df()filter_out_border_spines()filter_out_soma_touching_spines()filter_spine_df_samples()filter_spine_meshes()filter_spine_objs_by_size_bare_minimum()filter_spine_objs_from_restrictions()filter_spines_by_size()filter_spines_by_size_branch()get_spine_meshes_unfiltered()get_spine_meshes_unfiltered_from_mesh()head_exist()head_mesh()head_mesh_splits_face_idx_by_index()head_mesh_splits_from_index()head_neck_shaft_idx_from_branch()id_from_compartment_index()id_from_idx()is_spine_obj()limb_branch_dict_to_search_for_spines()mesh_attribute_from_compartment()mesh_from_compartment()mesh_from_name_or_idx()mesh_minus_spine_objs()n_faces()n_shaft_synapses()n_spine_compartment_synapses()n_spines()n_spines_head()n_spines_neck()n_spines_no_head()neck_mesh()no_head_mesh()number_of_columns()plot_connetion_type_head_vs_spine_size_by_conn_type_kde()plot_feature_histograms_with_ct_overlay()plot_head_neck()plot_spine_attribute_vs_category_from_spine_df_samples()plot_spine_coordinates_from_spine_df()plot_spine_embeddings_kde()plot_spine_face_idx_dict()plot_spine_feature_hist()plot_spine_objs()plot_spine_objs_and_syn_from_syn_df()plot_spine_objs_on_branch()plot_spine_synapse_coords_dict()plot_spines_head_neck()plot_spines_objs_with_head_neck_and_coordinates()print_filter_spine_thresholds()query_spine_objs()restrict_meshes_to_shaft_meshes_without_coordinates()scale_stats_df()sdf_median_mean_difference()seg_split_spine()seg_split_spine_from_df()set_branch_head_neck_shaft_idx()set_branch_spines_obj()set_branch_synapses_head_neck_shaft()set_neuron_head_neck_shaft_idx()set_neuron_spine_attribute()set_neuron_spines_obj()set_neuron_synapses_head_neck_shaft()set_shaft_synapses_from_spine_query()set_soma_synapses_spine_label()shaft_synapses()skeletal_length_from_compartment()skeletal_length_from_spine()skeleton_from_spine()spine_and_syn_df_computed_from_neuron_obj()spine_bouton_labels_to_plot()spine_compartment_mesh_functions()spine_compartment_mesh_functions_dict()spine_compartment_synapses()spine_compartments_face_idx_for_neuron_mesh()spine_counts_from_spine_df()spine_density()spine_density_over_limb_branch()spine_df_for_db_from_spine_objs()spine_features_to_print()spine_head_neck()spine_id_add_from_limb_branch_idx()spine_id_from_limb_branch_spine_idx()spine_id_range_from_limb_branch_idx()spine_int_label()spine_labels()spine_length()spine_mesh()spine_objs_and_synapse_df_computed_from_branch_idx()spine_objs_and_synapse_df_computed_from_neuron_obj()spine_objs_and_synapse_df_total_from_limb_branch_spine_dict()spine_objs_bare_minimum_filt_with_attr_from_branch_obj()spine_objs_near_endpoints()spine_objs_with_border_sk_endpoint_and_soma_filter_from_scratch_on_branch_obj()spine_objs_with_border_sk_endpoint_and_soma_filter_from_scratch_on_mesh()spine_stats_from_spine_df()spine_str_label()spine_synapse_stats_from_synapse_df()spine_table_restriction_high_confidence()spine_volume_density()spine_volume_to_spine_area()spines()spines_head()spines_head_meshes()spines_neck()spines_neck_meshes()spines_no_head()spines_no_head_meshes()split_head_mesh()split_mesh_into_spines_shaft()split_mesh_into_spines_shaft_old()surface_area_to_volume()synapse_attribute_dict_from_synapse_df()synapse_coords_from_synapse_df()synapse_df_with_spine_match()synapse_ids_from_synapse_df()synapse_spine_match_df_filtering()update_spines_obj()volume_from_compartment()volume_from_spine()width_ray_80_perc_from_compartment()width_ray_from_compartment()
- neurd.synapse_utils module
SynapseSynapse.synapse_idSynapse.upstream_distSynapse.downstream_distSynapse.coordinateSynapse.closest_sk_coordinateSynapse.closest_face_coordinateSynapse.closest_face_distSynapse.soma_distanceSynapse.soma_distance_euclideanSynapse.head_neck_shaftSynapse.compartmentSynapse.limb_idxSynapse.branch_idxSynapse.NoteSynapse.__init__()Synapse.export()
add_error_synapses_to_neuron_obj()add_nm_to_synapse_df()add_synapses_to_neuron_obj()add_valid_soma_synapses_to_neuron_obj()add_valid_synapses_to_neuron_obj()adjust_obj_with_face_offset()annotate_synapse_df()append_synapses_to_plot()axon_ais_synapses()axon_on_dendrite_synapses()axon_synapses()calculate_endpoints_dist()calculate_limb_synapse_soma_distances()calculate_neuron_soma_distance()calculate_neuron_soma_distance_euclidean()calculate_upstream_downstream_dist()calculate_upstream_downstream_dist_from_down_idx()calculate_upstream_downstream_dist_from_up_idx()combine_synapse_dict_into_presyn_postsyn_valid_error_dict()compartment_groups_from_synapses_obj()complete_n_synapses_analysis()downstream_dist_max_over_syn()downstream_dist_min_over_syn()endpoint_dist_extrema_over_syn()error_query()error_synapses_to_scatter_info()export()exports_to_synapses()fetch_synapse_dict_by_mesh_labels()get_errored_synapses_names()get_synapse_types()get_synapses_compartment()limb_branch_synapses_to_scatter_info()limb_branch_with_synapses()n_axon_ais_synapses()n_presyns_on_dendrite()n_synapses()n_synapses_all_compartment_spine_type()n_synapses_all_compartments()n_synapses_all_spine_labels()n_synapses_all_valid_error()n_synapses_analysis_axon_dendrite()n_synapses_by_compartment_spine_type()n_synapses_distance_errored()n_synapses_downstream()n_synapses_error()n_synapses_error_post()n_synapses_error_pre()n_synapses_head()n_synapses_mesh_errored()n_synapses_neck()n_synapses_no_head()n_synapses_offset_distance_of_endpoint_downstream()n_synapses_offset_distance_of_endpoint_upstream()n_synapses_offset_distance_of_endpoint_upstream_downstream()n_synapses_over_limb_branch_dict()n_synapses_post()n_synapses_post_downstream()n_synapses_post_head()n_synapses_post_neck()n_synapses_post_no_head()n_synapses_post_offset_distance_of_endpoint_downstream()n_synapses_post_offset_distance_of_endpoint_upstream()n_synapses_post_over_limb_branch_dict()n_synapses_post_shaft()n_synapses_post_spine()n_synapses_post_within_distance_of_endpoint_downstream()n_synapses_post_within_distance_of_endpoint_upstream()n_synapses_pre()n_synapses_pre_downstream()n_synapses_pre_offset_distance_of_endpoint_downstream()n_synapses_pre_offset_distance_of_endpoint_upstream()n_synapses_pre_over_limb_branch_dict()n_synapses_pre_shaft()n_synapses_pre_within_distance_of_endpoint_downstream()n_synapses_pre_within_distance_of_endpoint_upstream()n_synapses_shaft()n_synapses_somas_postsyn()n_synapses_spine()n_synapses_spine_offset_distance_of_endpoint_downstream()n_synapses_spine_offset_distance_of_endpoint_upstream()n_synapses_spine_within_distance_of_endpoint_downstream()n_synapses_valid()n_synapses_valid_post()n_synapses_valid_pre()n_synapses_within_distance_of_endpoint_downstream()n_synapses_within_distance_of_endpoint_upstream()n_synapses_within_distance_of_endpoint_upstream_downstream()plot_head_neck_shaft_synapses()plot_synapses()plot_synapses_compartment()plot_synapses_error_from_neuron_obj()plot_synapses_objs()plot_synapses_on_limb()plot_synapses_presyn_dendrite_errors()plot_synapses_query()plot_synapses_soma()plot_synapses_valid_from_neuron_obj()plot_valid_error_synpases()presyn_on_dendrite_synapses()presyn_on_dendrite_synapses_after_axon_on_dendrite_filter_away()presyn_on_dendrite_synapses_non_axon_like()presyn_postsyn_groups_from_synapses_obj()presyns_on_dendrite()query_synapses()restrict_synapses_df_by_limb_branch_dict()set_branch_synapses_attribute()set_branch_synapses_compartment()set_limb_branch_idx_to_synapses()set_neuron_synapses_compartment()set_presyns_on_dendrite_as_errors()set_presyns_on_dendrite_as_errors_default()soma_face_offset_value()soma_synapses()soma_synapses_to_scatter_info()spine_bouton_groups_from_synapses_obj()synapse_compartment_spine_type_title()synapse_coordinates_from_synapse_df()synapse_density()synapse_density_head()synapse_density_neck()synapse_density_no_head()synapse_density_offset_distance_of_endpoint_upstream()synapse_density_over_limb_branch()synapse_density_post()synapse_density_post_offset_distance_of_endpoint_downstream()synapse_density_post_offset_distance_of_endpoint_upstream()synapse_density_post_within_distance_of_endpoint_downstream()synapse_density_pre()synapse_density_shaft()synapse_density_spine()synapse_df()synapse_df_abridged()synapse_df_from_csv()synapse_df_from_synapse_dict()synapse_dict_from_synapse_csv()synapse_dict_from_synapse_df()synapse_dict_mesh_labels_to_synapse_attribute_dict()synapse_dict_mesh_labels_to_synapse_coordinate_dict()synapse_dict_mesh_labels_to_synapse_volume_dict()synapse_endpoint_dist_downstream()synapse_endpoint_dist_upstream()synapse_endpoint_dist_upstream_downstream()synapse_filtering_vp2()synapse_head_perc()synapse_ids_to_synapses()synapse_indexes_to_synapses()synapse_obj_from_dj_synapse_dict()synapse_plot_items_by_type_or_query()synapse_post_perc()synapse_post_perc_downstream()synapse_post_perc_over_limb_branch_dict()synapse_pre_perc()synapse_pre_perc_downstream()synapse_pre_perc_over_limb_branch_dict()synapse_pre_post_valid_errror_coordinates_dict()synapse_pre_post_valid_errror_stats_dict()synapse_spine_perc()synapses()synapses_bouton()synapses_by_compartment_spine_type()synapses_df()synapses_distance_errored()synapses_dj_export_dict_error()synapses_dj_export_dict_valid()synapses_downstream()synapses_error()synapses_error_ids()synapses_error_old()synapses_error_post()synapses_error_post_coordinates()synapses_error_pre()synapses_error_pre_coordinates()synapses_head()synapses_mesh_errored()synapses_neck()synapses_no_head()synapses_non_bouton()synapses_obj_groups_from_queries()synapses_offset_distance_of_endpoint_upstream_downstream()synapses_over_limb_branch_dict()synapses_post()synapses_post_downstream()synapses_post_head()synapses_post_neck()synapses_post_no_head()synapses_post_shaft()synapses_post_spine()synapses_pre()synapses_pre_downstream()synapses_pre_shaft()synapses_shaft()synapses_somas()synapses_somas_postsyn()synapses_spine()synapses_to_coordinates()synapses_to_dj_keys()synapses_to_dj_keys_old()synapses_to_exports()synapses_to_feature()synapses_to_synapse_ids()synapses_to_synapses_df()synapses_total()synapses_type_and_head_neck_shaft()synapses_valid()synapses_valid_old()synapses_valid_post()synapses_valid_post_coordinates()synapses_valid_pre()synapses_valid_pre_coordinates()synapses_with_feature()synapses_within_distance_of_endpoint_upstream_downstream()valid_error_groups_from_synapses_obj()valid_query()
- neurd.vdi_default module
DataInterfaceBoilerplateDataInterfaceBoilerplate.__init__()DataInterfaceBoilerplate.add_nm_to_synapse_df()DataInterfaceBoilerplate.align_array()DataInterfaceBoilerplate.align_mesh()DataInterfaceBoilerplate.align_neuron_obj()DataInterfaceBoilerplate.align_neuron_obj_from_align_matrix()DataInterfaceBoilerplate.align_skeleton()DataInterfaceBoilerplate.cell_type()DataInterfaceBoilerplate.load_neuron_obj()DataInterfaceBoilerplate.multiplicity()DataInterfaceBoilerplate.nucleus_id()DataInterfaceBoilerplate.pre_post_synapse_ids_coords_from_connectome()DataInterfaceBoilerplate.proof_versionDataInterfaceBoilerplate.save_neuron_obj()DataInterfaceBoilerplate.segment_id_and_split_index()DataInterfaceBoilerplate.segment_id_to_synapse_dict()DataInterfaceBoilerplate.segment_id_to_synapse_table_optimized()DataInterfaceBoilerplate.set_parameters_for_directory_modules()DataInterfaceBoilerplate.set_parameters_obj()DataInterfaceBoilerplate.set_parameters_obj_from_dict()DataInterfaceBoilerplate.set_parameters_obj_from_filepath()DataInterfaceBoilerplate.unalign_neuron_obj()DataInterfaceBoilerplate.unalign_neuron_obj_from_align_matrix()DataInterfaceBoilerplate.vdi
DataInterfaceDefaultDataInterfaceDefault.__init__()DataInterfaceDefault.default_low_degree_graph_filtersDataInterfaceDefault.exc_filters_auto_proof()DataInterfaceDefault.fetch_proofread_mesh()DataInterfaceDefault.fetch_segment_id_mesh()DataInterfaceDefault.fetch_soma_mesh()DataInterfaceDefault.fetch_undecimated_segment_id_mesh()DataInterfaceDefault.get_align_matrix()DataInterfaceDefault.graph_obj_from_proof_stage()DataInterfaceDefault.inh_filters_auto_proof()DataInterfaceDefault.load_neuron_obj_auto_proof()DataInterfaceDefault.nuclei_classification_info_from_nucleus_id()DataInterfaceDefault.nuclei_from_segment_id()DataInterfaceDefault.save_neuron_obj_auto_proof()DataInterfaceDefault.segment_id_to_synapse_df()DataInterfaceDefault.segment_id_to_synapse_table_optimized_connectome()DataInterfaceDefault.segment_id_to_synapse_table_optimized_proofread()DataInterfaceDefault.set_synapse_filepath()DataInterfaceDefault.soma_nm_coordinate()DataInterfaceDefault.voxel_to_nm_scaling
neuron_obj_func()
- neurd.vdi_h01 module
- neurd.vdi_microns module
- neurd.vdi_microns_cave module
- neurd.version module
- neurd.volume_utils module
DataInterfaceDataInterface.__init__()DataInterface.align_array()DataInterface.align_mesh()DataInterface.align_neuron_obj()DataInterface.align_skeleton()DataInterface.nuclei_classification_info_from_nucleus_id()DataInterface.nuclei_from_segment_id()DataInterface.segment_id_to_synapse_dict()DataInterface.set_synapse_filepath()DataInterface.unalign_neuron_obj()
- neurd.width_utils module
- Module contents
- Subpackages