Index

A

add() (syconn.utils.skeleton.SkeletonLoop method) add_annotation() (syconn.utils.skeleton.Skeleton method) add_path() (syconn.utils.segmentationdataset.SegmentationObject method) (syconn.utils.skeleton.SkeletonAnnotation method) add_voxel() (syconn.utils.segmentationdataset.SegmentationObject method) addChild() (syconn.utils.skeleton.SkeletonNode method) addEdge() (syconn.utils.skeleton.SkeletonAnnotation method) addMetaDataElem() (syconn.utils.skeleton.SkeletonNode method) addNode() (syconn.utils.skeleton.SkeletonAnnotation method) addParent() (syconn.utils.skeleton.SkeletonNode method) analyze_dataset() (in module syconn.brainqueries) annnotationChildrenBFS() (syconn.utils.skeleton_utils.AnnotationSearch method) annnotationNeighborsBFS() (syconn.utils.skeleton_utils.AnnotationSearch method) annnotationParentsBFS() (syconn.utils.skeleton_utils.AnnotationSearch method) anno (syconn.processing.mapper.SkeletonMapper attribute) annosToKDtree() (in module syconn.utils.skeleton_utils) annosToNMLFile() (in module syconn.utils.skeleton_utils)

annotate_object() (syconn.processing.mapper.SkeletonMapper method) annotate_objects() (syconn.processing.mapper.SkeletonMapper method) annotation_from_nodes() (in module syconn.utils.skeleton_utils) annotation_matcher() (in module syconn.utils.skeleton_utils) annotation_to_nx_graph() (in module syconn.utils.skeleton_utils) annotations (syconn.utils.skeleton.Skeleton attribute) AnnotationSearch (class in syconn.utils.skeleton_utils) annoToKDtree() (in module syconn.utils.skeleton_utils) annoToNXGraph() (in module syconn.utils.skeleton_utils) appendComment() (syconn.utils.skeleton.SkeletonAnnotation method) (syconn.utils.skeleton.SkeletonNode method) apply_merge_list() (in module syconn.processing.objectextraction) assign_neck() (in module syconn.processing.spiness) assign_property2node() (in module syconn.processing.features) average_coordinate() (in module syconn.utils.basics) avg_annotation_inter_node_distance() (in module syconn.utils.skeleton_utils) avg_inter_node_distance() (syconn.utils.skeleton.SkeletonAnnotation method)

B

BFS() (syconn.utils.skeleton_utils.AnnotationSearch method) bfs_search() (syconn.utils.skeleton_utils.AnnotationSearch method)

bounding_box (syconn.utils.segmentationdataset.SegmentationObject attribute) build_attributes() (in module syconn.utils.skeleton)

C

calc_cs_node() (in module syconn.contactsites) calc_distance2soma() (in module syconn.processing.axoness) calc_myelinisation() (syconn.processing.mapper.SkeletonMapper method) calc_neuron_feat() (in module syconn.processing.cell_types) calc_neuron_feat_star() (in module syconn.processing.cell_types) calc_overlap() (in module syconn.utils.basics) calc_prop_feat_dict() (in module syconn.processing.features) calc_syn_dict() (in module syconn.processing.mapper) calc_syn_feature() (in module syconn.processing.synapticity) calculate_chunk_numbers_for_box() (in module syconn.processing.objectextraction) calculate_rep_coord() (syconn.utils.segmentationdataset.SegmentationObject method) calculate_size() (syconn.utils.segmentationdataset.SegmentationObject method) calculateReducedPoints() (syconn.utils.skeleton.SkeletonLoop method) cell_classification() (in module syconn.processing.learning_rfc) cell_object_coord_parser() (in module syconn.utils.basics) cell_object_id_parser() (in module syconn.utils.datahandler) celltype_axoness_feature() (in module syconn.processing.features) check_all_hulls() (in module syconn.utils.segmentationdataset) check_all_hulls_loop() (in module syconn.utils.segmentationdataset) check_all_hulls_thread() (in module syconn.utils.segmentationdataset) check_if_coordinate_is_contained() (syconn.utils.segmentationdataset.SegmentationObject method) chunk_dataset (syconn.utils.segmentationdataset.UltrastructuralDataset attribute) class_ranges() (in module syconn.conmatrix)

clear_nodes() (syconn.utils.skeleton.SkeletonAnnotation method) clearEdges() (syconn.utils.skeleton.SkeletonAnnotation method) clearNodeEdges() (syconn.utils.skeleton.SkeletonAnnotation method) closest_point() (syconn.utils.segmentationdataset.SegmentationObject method) collect_contact_sites() (in module syconn.contactsites) collect_spineheads() (in module syconn.processing.spiness) compare_version() (in module syconn.utils.skeleton) concatenate_mappings() (in module syconn.processing.objectextraction) conn_dict_wrapper() (in module syconn.contactsites) connect_soma_tracing() (in module syconn.utils.datahandler) convert_to_standard_cs_name() (in module syconn.contactsites) convex_hull_area() (in module syconn.utils.basics) Coordinate (class in syconn.utils.basics) coordinate_from_string() (in module syconn.utils.basics) coordinate_to_ewkt() (in module syconn.utils.basics) create_datasets_from_objects() (in module syconn.processing.objectextraction) create_hull_ids() (syconn.utils.segmentationdataset.SegmentationObject method) create_hull_voxels() (syconn.utils.segmentationdataset.SegmentationObject method) create_objects_from_voxels() (in module syconn.processing.objectextraction) create_synapse_skeleton() (in module syconn.contactsites) cs_btw_annos() (in module syconn.processing.mapper) cs_path (syconn.utils.datahandler.DataHandler attribute) cset (syconn.processing.mapper.SkeletonMapper attribute) cut_array_in_one_dim() (in module syconn.utils.datahandler)

D

data_path (syconn.utils.datahandler.DataHandler attribute) DataHandler (class in syconn.utils.datahandler) degree() (syconn.utils.skeleton.SkeletonNode method) delCommentPart() (syconn.utils.skeleton.SkeletonNode method) delete_jobs_by_name() (in module syconn.multi_proc.multi_proc_main) detachAnnotation() (syconn.utils.skeleton.SkeletonNode method)

detect_similar_tracings() (in module syconn.brainqueries) detect_synapses() (in module syconn.brainqueries) dfs_search() (syconn.utils.skeleton_utils.AnnotationSearch method) distance_scaled() (syconn.utils.skeleton.SkeletonNode method) diverge_map() (in module syconn.conmatrix) draw_feat_hist() (in module syconn.processing.cell_types)

E

EnhancedAnnotation (class in syconn.utils.skeleton_utils) enrich_tracings() (in module syconn.brainqueries) enrich_tracings_all() (in module syconn.brainqueries) enrich_tracings_star() (in module syconn.brainqueries) estimateDisagreementRate() (in module syconn.utils.skeleton_utils) euclidian_distance() (in module syconn.utils.basics)

euclNodeDist() (in module syconn.utils.skeleton_utils) extract_and_save_all_hull_voxels() (in module syconn.utils.segmentationdataset) extract_and_save_all_hull_voxels_loop() (in module syconn.utils.segmentationdataset) extract_and_save_all_hull_voxels_thread() (in module syconn.utils.segmentationdataset) extract_main_tracings() (in module syconn.utils.skeleton_utils) extract_voxels() (in module syconn.processing.objectextraction)

F

feature_importance() (in module syconn.processing.learning_rfc) feature_valid_syns() (in module syconn.processing.mapper) file_md5_checksum() (in module syconn.utils.skeleton) fillHole() (syconn.utils.skeleton.SkeletonLoop method) filter_nodes() (in module syconn.utils.skeleton_utils) find_cell_types_from_dict() (in module syconn.processing.cell_types) find_object_with_coordinate() (syconn.utils.segmentationdataset.UltrastructuralDataset method) FloatCoordinate (class in syconn.utils.basics) from_annotation() (syconn.utils.skeleton_utils.ShortestPathSegment method) from_coordinate() (syconn.utils.skeleton.SkeletonNode method) from_id_lists_to_mergelist() (in module syconn.utils.skeleton) from_ids_to_objects() (in module syconn.processing.objectextraction) from_path() (syconn.utils.skeleton_utils.ShortestPathSegment method) from_probabilities_to_objects() (in module syconn.processing.objectextraction) from_probabilities_to_objects_parameter_sweeping() (in module syconn.processing.objectextraction)

from_scratch() (syconn.utils.skeleton.SkeletonNode method) from_skeleton_to_mergelist() (in module syconn.utils.skeleton) fromDom() (syconn.utils.skeleton.Skeleton method) fromNml() (syconn.utils.skeleton.Skeleton method) (syconn.utils.skeleton.SkeletonAnnotation method) (syconn.utils.skeleton.SkeletonNode method) fromNmlcTree() (syconn.utils.skeleton.Skeleton method) (syconn.utils.skeleton.SkeletonAnnotation method) (syconn.utils.skeleton.SkeletonLoop method) (syconn.utils.skeleton.SkeletonLoopPoint method) (syconn.utils.skeleton.SkeletonNode method) (syconn.utils.skeleton.SkeletonVolume method) fromNmlString() (syconn.utils.skeleton.Skeleton method) fromSWC() (syconn.utils.skeleton.Skeleton method) fscore() (in module syconn.processing.learning_rfc)

G

gauss_threshold_connected_components() (in module syconn.processing.objectextraction) genj0126SkelObj() (in module syconn.utils.skeleton_utils) genSeedNodes() (in module syconn.utils.skeleton_utils) genZColumnGridSkeleton() (in module syconn.utils.skeleton_utils) get_all_comment_nodes() (in module syconn.utils.skeleton_utils) get_all_node_comments() (in module syconn.utils.skeleton_utils) get_annotations_with_comment() (in module syconn.utils.skeleton_utils) get_box_coords() (in module syconn.utils.basics) get_cell_majority_synsign() (in module syconn.conmatrix) get_cell_type_classes_dict() (in module syconn.processing.cell_types) get_cell_type_labels() (in module syconn.processing.cell_types) get_closest_node() (in module syconn.utils.skeleton_utils) get_connectivity_list() (in module syconn.brainqueries) get_convex_hull() (in module syconn.utils.skeleton_utils) get_cum_pos() (in module syconn.conmatrix) get_end_nodes() (in module syconn.utils.skeleton_utils) get_filepaths_from_dir() (in module syconn.utils.datahandler) get_high_node_id() (syconn.utils.skeleton.Skeleton method) get_id_dict_from_skel_ids() (in module syconn.processing.cell_types) get_largest_annotation() (in module syconn.utils.skeleton_utils) get_max_node_id() (in module syconn.utils.skeleton_utils) get_nml_str_from_knossos_file() (in module syconn.utils.skeleton_utils) get_node_at_distance() (syconn.utils.skeleton_utils.ShortestPathSegment method) get_node_at_position() (in module syconn.utils.skeleton_utils) get_node_positions_as_nparray() (in module syconn.utils.skeleton_utils) get_nodes_with_comment() (in module syconn.utils.skeleton_utils) get_nodes_with_token() (in module syconn.utils.skeleton_utils) get_nonempty_annotations() (in module syconn.utils.skeleton_utils) get_normals() (in module syconn.utils.basics) get_number_cs_details() (in module syconn.contactsites) get_obj_density() (in module syconn.processing.features) get_orth_plane() (in module syconn.utils.basics) get_paths_of_skelID() (in module syconn.utils.datahandler) get_plot_obj() (syconn.processing.mapper.SkeletonMapper method) get_radii_hull() (in module syconn.processing.mapper) get_reachable_nodes() (in module syconn.utils.skeleton_utils) get_rel_path() (in module syconn.utils.segmentationdataset) get_shortest_path() (syconn.utils.skeleton_utils.EnhancedAnnotation method) get_skelID_from_path() (in module syconn.utils.datahandler) get_spine_dict() (in module syconn.contactsites) get_spine_summary() (in module syconn.contactsites) get_subsegment() (syconn.utils.skeleton_utils.ShortestPathSegment method) get_subsegment_by_distance() (in module syconn.utils.skeleton_utils) get_the_nonempty_annotation() (in module syconn.utils.skeleton_utils)

get_the_nonempty_connected_annotation() (in module syconn.utils.skeleton_utils) get_version() (syconn.utils.skeleton.Skeleton method) getAnnosByCommentRegex() (in module syconn.utils.skeleton_utils) getAnnotations() (syconn.utils.skeleton.Skeleton method) getAnnoWithMostNodes() (in module syconn.utils.skeleton_utils) getChildren() (syconn.utils.skeleton.SkeletonNode method) getComment() (syconn.utils.skeleton.SkeletonAnnotation method) (syconn.utils.skeleton.SkeletonNode method) (syconn.utils.skeleton.SkeletonVolume method) getCoordinate() (syconn.utils.skeleton.SkeletonNode method) getCoordinate_scaled() (syconn.utils.skeleton.SkeletonNode method) getCoordinates() (syconn.utils.skeleton.SkeletonLoopPoint method) getData() (syconn.utils.skeleton.SkeletonNode method) getDataElem() (syconn.utils.skeleton.SkeletonNode method) getEdges() (syconn.utils.skeleton.SkeletonAnnotation method) getID() (syconn.utils.skeleton.SkeletonNode method) getIdleTime() (syconn.utils.skeleton.Skeleton method) getLimits() (syconn.utils.skeleton.SkeletonLoop method) (syconn.utils.skeleton.SkeletonVolume method) getLoops() (syconn.utils.skeleton.SkeletonVolume method) getMetaData() (syconn.utils.skeleton.SkeletonNode method) getNeighbors() (syconn.utils.skeleton.SkeletonNode method) getNMLannos() (in module syconn.utils.skeleton_utils) getNodeBaseID() (syconn.utils.skeleton.SkeletonAnnotation method) getNodeByID() (syconn.utils.skeleton.SkeletonAnnotation method) getNodeByUniqueID() (syconn.utils.skeleton.SkeletonAnnotation method) getNodeEdges() (syconn.utils.skeleton.SkeletonAnnotation method) getNodeReverseEdges() (syconn.utils.skeleton.SkeletonAnnotation method) getNodes() (syconn.utils.skeleton.Skeleton method) (syconn.utils.skeleton.SkeletonAnnotation method) getNodesByCommentRegex() (in module syconn.utils.skeleton_utils) getParents() (syconn.utils.skeleton.SkeletonNode method) getPoints() (syconn.utils.skeleton.SkeletonLoop method) getPureComment() (syconn.utils.skeleton.SkeletonNode method) getReducedPoints() (syconn.utils.skeleton.SkeletonLoop method) getReverseEdges() (syconn.utils.skeleton.SkeletonAnnotation method) getRoot() (syconn.utils.skeleton.SkeletonAnnotation method) getSingleParent() (syconn.utils.skeleton.SkeletonNode method) getSkeletonTime() (syconn.utils.skeleton.Skeleton method) getUniqueID() (syconn.utils.skeleton.SkeletonNode method) getVolumes() (syconn.utils.skeleton.Skeleton method) (syconn.utils.skeleton.SkeletonAnnotation method) getVP() (syconn.utils.skeleton.SkeletonLoop method) (syconn.utils.skeleton.SkeletonVolume method)

H

has_3_4_worktime_bug() (in module syconn.utils.skeleton_utils) has_comment_token() (syconn.utils.skeleton.SkeletonNode method) has_equal_dimensions() (in module syconn.utils.basics) has_node() (syconn.utils.skeleton.Skeleton method) (syconn.utils.skeleton.SkeletonAnnotation method) has_node_id_overflow_problem() (in module syconn.utils.skeleton_utils) has_node_id_overflow_problem_dir() (in module syconn.utils.skeleton_utils) helper_get_hull_voxels() (in module syconn.utils.datahandler)

helper_get_voxels() (in module syconn.utils.datahandler) helper_load_sj_feat() (in module syconn.processing.synapticity) helper_samllest_dist() (in module syconn.utils.basics) hull2text() (in module syconn.utils.datahandler) hull_coords (syconn.processing.mapper.SkeletonMapper attribute) hull_normals (syconn.processing.mapper.SkeletonMapper attribute) hull_sampling() (syconn.processing.mapper.SkeletonMapper method) hull_voxels (syconn.utils.segmentationdataset.SegmentationObject attribute)

I

id_lookup_in_one_chunk_thread() (in module syconn.utils.skeleton) ids (syconn.utils.segmentationdataset.UltrastructuralDataset attribute) implyMetadataAddRoot() (syconn.utils.skeleton.SkeletonNode method) implyMetadataRemoveRoot() (syconn.utils.skeleton.SkeletonNode method) init_clf() (in module syconn.processing.learning_rfc) init_properties() (syconn.utils.segmentationdataset.UltrastructuralDataset method) initialize_cset() (in module syconn.processing.initialization) integer_checksum() (in module syconn.utils.skeleton) interpolate_between() (in module syconn.utils.basics)

interpolate_nodes() (syconn.utils.skeleton.SkeletonAnnotation method) InvalidFileFormatException is_simple_skeleton() (in module syconn.utils.skeleton_utils) is_singly_connected() (in module syconn.utils.skeleton_utils) isEmpty() (syconn.utils.skeleton.SkeletonAnnotation method) iter_edges() (syconn.utils.skeleton.SkeletonAnnotation method) (syconn.utils.skeleton_utils.ShortestPathSegment method) iter_nodes_dfs() (in module syconn.utils.skeleton_utils) iter_nodes_regex() (in module syconn.utils.skeleton_utils) ix (syconn.processing.mapper.SkeletonMapper attribute)

K

KDtree (class in syconn.utils.skeleton_utils)

knossos_dataset (syconn.utils.segmentationdataset.UltrastructuralDataset attribute)

L

length() (syconn.utils.skeleton_utils.ShortestPathSegment method) load_anno_list() (in module syconn.utils.datahandler) load_cell_gt() (in module syconn.processing.cell_types) load_celltype_feats() (in module syconn.processing.cell_types) load_celltype_gt() (in module syconn.processing.cell_types) load_celltype_preds() (in module syconn.processing.cell_types) load_celltype_probas() (in module syconn.processing.cell_types) load_csv2feat() (in module syconn.processing.learning_rfc) load_dataset() (in module syconn.utils.segmentationdataset) load_files_from_kzip() (in module syconn.utils.datahandler) load_from_h5py() (in module syconn.utils.datahandler)

load_j0251_nml() (in module syconn.utils.skeleton_utils) load_j0256_nml() (in module syconn.utils.skeleton_utils) load_jk_NML() (in module syconn.utils.skeleton_utils) load_mapped_skeleton() (in module syconn.utils.datahandler) load_objpkl_from_kzip() (in module syconn.utils.datahandler) load_ordered_mapped_skeleton() (in module syconn.utils.datahandler) load_pkl2obj() (in module syconn.utils.datahandler) load_rfcs() (in module syconn.processing.learning_rfc) loadj0126ConsensusNMLsInDir() (in module syconn.utils.skeleton_utils) loadj0126NML() (in module syconn.utils.skeleton_utils) loadj0126NMLbyRegex() (in module syconn.utils.skeleton_utils) loo_proba() (in module syconn.processing.learning_rfc)

M

majority_vote() (in module syconn.processing.features) make_colormap() (in module syconn.conmatrix) make_merge_list() (in module syconn.processing.objectextraction) make_stitch_list() (in module syconn.processing.objectextraction) make_unique_labels() (in module syconn.processing.objectextraction) max_nodes_in_path() (in module syconn.processing.mapper) mem (syconn.utils.datahandler.DataHandler attribute)

mem_offset (syconn.utils.datahandler.DataHandler attribute) mem_path (syconn.utils.datahandler.DataHandler attribute) merge_annotations() (in module syconn.utils.skeleton_utils) merge_soma_tracing() (syconn.processing.mapper.SkeletonMapper method) morphology_feature() (in module syconn.processing.features) most_distant_voxel (syconn.utils.segmentationdataset.SegmentationObject attribute) myelin_ds_path (syconn.utils.datahandler.DataHandler attribute)

N

negative_to_zero() (in module syconn.multi_proc.multi_proc_main) (in module syconn.utils.basics) neighbour_next() (in module syconn.utils.skeleton_utils) node_branch_end_distance() (in module syconn.processing.features) node_id2key() (in module syconn.processing.mapper)

nodes_in_pathlength() (in module syconn.processing.features) nodes_to_NX_graph() (in module syconn.utils.skeleton_utils) NonSimpleNML novel_multiclass_prediction() (in module syconn.processing.learning_rfc) nx_graph_to_annotation() (in module syconn.utils.skeleton_utils)

O

obj_hull2text() (in module syconn.utils.datahandler) obj_id (syconn.utils.segmentationdataset.SegmentationObject attribute)

objfeat2skelnode() (in module syconn.processing.features) old_anno (syconn.processing.mapper.SkeletonMapper attribute) outlier_detection() (in module syconn.processing.mapper)

P

pairwise_syn_feature_calc() (in module syconn.processing.synapticity) parse_attributes() (in module syconn.utils.skeleton) parse_cET() (in module syconn.utils.skeleton) parse_synfeature_from_node() (in module syconn.processing.synapticity) parse_synfeature_from_txt() (in module syconn.processing.synapticity) path (syconn.utils.segmentationdataset.UltrastructuralDataset attribute) path_dataset (syconn.utils.segmentationdataset.SegmentationObject attribute) path_in_voxel_folder() (in module syconn.utils.segmentationdataset) path_to_hull_voxels (syconn.utils.segmentationdataset.SegmentationObject attribute) path_to_voxel (syconn.utils.segmentationdataset.SegmentationObject attribute) pathlength_of_property() (in module syconn.processing.features) physical_length() (syconn.utils.skeleton.SkeletonAnnotation method) plot_corr() (in module syconn.processing.learning_rfc) plot_pr() (in module syconn.processing.learning_rfc)

plot_wiring() (in module syconn.conmatrix) plot_wiring_cs() (in module syconn.conmatrix) plot_wiring_cum() (in module syconn.conmatrix) plot_wiring_cum_cs() (in module syconn.conmatrix) poly_area() (in module syconn.utils.basics) pre_process_volume() (in module syconn.utils.basics) predict_axoness_from_node_comments() (in module syconn.processing.axoness) predict_axoness_from_nodes() (in module syconn.processing.axoness) predict_celltype_label() (in module syconn.processing.cell_types) predict_property() (syconn.processing.mapper.SkeletonMapper method) prepare_syns_btw_annos() (in module syconn.processing.mapper) property_features (syconn.processing.mapper.SkeletonMapper attribute) propertyfeat2skelnode() (in module syconn.processing.features) prune_short_end_branches() (in module syconn.utils.skeleton_utils) prune_stub_branches() (in module syconn.utils.skeleton_utils)

Q

QSUB_script() (in module syconn.multi_proc.multi_proc_main) query_ball_point() (syconn.utils.skeleton_utils.KDtree method) query_ball_tree() (syconn.utils.skeleton_utils.KDtree method)

query_k_nearest() (syconn.utils.skeleton_utils.KDtree method) query_nearest_node() (syconn.utils.skeleton_utils.KDtree method) queryNN() (syconn.utils.skeleton_utils.KDtree method)

R

radfeat2skelnode() (in module syconn.processing.features) radius_feats_from_nodes() (in module syconn.processing.features) read_pair_cs() (in module syconn.processing.mapper) readout_cs_info() (in module syconn.processing.mapper) remap_tracings() (in module syconn.brainqueries) remap_tracings_all() (in module syconn.brainqueries) remap_tracings_star() (in module syconn.brainqueries) remove_all_node_comments() (in module syconn.utils.skeleton_utils) remove_from_zip() (in module syconn.utils.datahandler) (in module syconn.utils.skeleton) remove_voxel_file() (syconn.utils.segmentationdataset.SegmentationObject method) removeChild() (syconn.utils.skeleton.SkeletonNode method) removeEdge() (syconn.utils.skeleton.SkeletonAnnotation method) removeMetaData() (syconn.utils.skeleton.SkeletonNode method) removeMetaDataKey() (syconn.utils.skeleton.SkeletonNode method)

removeNode() (syconn.utils.skeleton.SkeletonAnnotation method) removeParent() (syconn.utils.skeleton.SkeletonNode method) removeSingleParent() (syconn.utils.skeleton.SkeletonNode method) rep_coord (syconn.utils.segmentationdataset.SegmentationObject attribute) rep_coords (syconn.utils.segmentationdataset.UltrastructuralDataset attribute) reset_all_ids() (syconn.utils.skeleton.Skeleton method) reset_all_times() (syconn.utils.skeleton.Skeleton method) reset_nml_for_heidelbrain_taskfile() (in module syconn.utils.skeleton_utils) resetObject() (syconn.utils.skeleton.SkeletonAnnotation method) (syconn.utils.skeleton.SkeletonLoop method) (syconn.utils.skeleton.SkeletonLoopPoint method) (syconn.utils.skeleton.SkeletonNode method) (syconn.utils.skeleton.SkeletonVolume method) resetRoot() (syconn.utils.skeleton.SkeletonAnnotation method) return_process() (in module syconn.utils.skeleton_utils) rotation_matrix() (in module syconn.utils.basics)

S

save_annotations() (in module syconn.utils.skeleton_utils) save_cell_type_clf() (in module syconn.processing.cell_types) save_cell_type_feats() (in module syconn.processing.cell_types) save_dataset() (in module syconn.utils.segmentationdataset) save_synapse_clf() (in module syconn.processing.synapticity) save_to_h5py() (in module syconn.utils.datahandler) save_train_clf() (in module syconn.processing.learning_rfc) scaling (syconn.utils.datahandler.DataHandler attribute) (syconn.utils.segmentationdataset.SegmentationObject attribute) (syconn.utils.skeleton.Skeleton attribute) search() (syconn.utils.skeleton_utils.AnnotationSearch method) SegmentationObject (class in syconn.utils.segmentationdataset) set_edit_position() (syconn.utils.skeleton.Skeleton method) set_scaling() (syconn.utils.skeleton.Skeleton method) setAnnotationStats() (in module syconn.utils.skeleton_utils) setComment() (syconn.utils.skeleton.SkeletonAnnotation method) (syconn.utils.skeleton.SkeletonNode method) (syconn.utils.skeleton.SkeletonVolume method) setCoordinate() (syconn.utils.skeleton.SkeletonNode method) setCoordinates() (syconn.utils.skeleton.SkeletonLoopPoint method) setData() (syconn.utils.skeleton.SkeletonNode method) setDataElem() (syconn.utils.skeleton.SkeletonNode method) setID() (syconn.utils.skeleton.SkeletonNode method) setLimits() (syconn.utils.skeleton.SkeletonLoop method) (syconn.utils.skeleton.SkeletonVolume method) setMetaData() (syconn.utils.skeleton.SkeletonNode method) setNodeBaseID() (syconn.utils.skeleton.SkeletonAnnotation method) setPureComment() (syconn.utils.skeleton.SkeletonNode method) setRoot() (syconn.utils.skeleton.SkeletonAnnotation method) (syconn.utils.skeleton.SkeletonNode method) setRootInternal() (syconn.utils.skeleton.SkeletonAnnotation method) setSingleParent() (syconn.utils.skeleton.SkeletonNode method) setVP() (syconn.utils.skeleton.SkeletonLoop method) (syconn.utils.skeleton.SkeletonVolume method) shortestPathBetNodes() (in module syconn.utils.skeleton_utils) ShortestPathSegment (class in syconn.utils.skeleton_utils) similarity_check() (in module syconn.processing.mapper) similarity_check_star() (in module syconn.processing.mapper) size (syconn.utils.segmentationdataset.SegmentationObject attribute) sizes (syconn.utils.segmentationdataset.UltrastructuralDataset attribute) sj_per_spinehead() (in module syconn.processing.features)

skel_radius (syconn.processing.mapper.SkeletonMapper attribute) Skeleton (class in syconn.utils.skeleton) skeleton_from_single_coordinate() (in module syconn.utils.skeleton_utils) skeleton_path (syconn.utils.datahandler.DataHandler attribute) SkeletonAnnotation (class in syconn.utils.skeleton) SkeletonLoop (class in syconn.utils.skeleton) SkeletonLoopPoint (class in syconn.utils.skeleton) SkeletonMapper (class in syconn.processing.mapper) SkeletonNode (class in syconn.utils.skeleton) SkeletonVolume (class in syconn.utils.skeleton) soma (syconn.processing.mapper.SkeletonMapper attribute) spiness_feats_from_nodes() (in module syconn.processing.features) split_by_connected_component() (in module syconn.utils.skeleton_utils) start_multiprocess() (in module syconn.multi_proc.multi_proc_main) SUBP_script() (in module syconn.multi_proc.multi_proc_main) supp_fname_from_fpath() (in module syconn.utils.datahandler) switch_array_entries() (in module syconn.utils.basics) (in module syconn.utils.datahandler) syconn.brainqueries (module) syconn.conmatrix (module) syconn.contactsites (module) syconn.multi_proc.multi_proc_main (module) syconn.processing.axoness (module) syconn.processing.cell_types (module) syconn.processing.features (module) syconn.processing.initialization (module) syconn.processing.learning_rfc (module) syconn.processing.mapper (module) syconn.processing.objectextraction (module) syconn.processing.spiness (module) syconn.processing.synapticity (module) syconn.processing.watershed_segmentation (module) syconn.utils.basics (module) syconn.utils.datahandler (module) syconn.utils.segmentationdataset (module) syconn.utils.skeleton (module) syconn.utils.skeleton_utils (module) syn_btw_anno_pair() (in module syconn.processing.mapper) syn_sign_prediction() (in module syconn.processing.synapticity) syn_type_majority_vote() (in module syconn.contactsites) synapse_matrix() (in module syconn.contactsites)

T

to_kzip() (syconn.utils.skeleton.Skeleton method) to_xml_string() (syconn.utils.skeleton.Skeleton method) toNml() (syconn.utils.skeleton.Skeleton method) (syconn.utils.skeleton.SkeletonAnnotation method) (syconn.utils.skeleton.SkeletonNode method)

toSWC() (syconn.utils.skeleton.Skeleton method) translate_dense_tracings() (in module syconn.processing.mapper) tuple_to_string() (in module syconn.utils.basics) type (syconn.utils.segmentationdataset.UltrastructuralDataset attribute) type_sorted_wiring() (in module syconn.conmatrix) type_sorted_wiring_cs() (in module syconn.conmatrix)

U

UltrastructuralDataset (class in syconn.utils.segmentationdataset) unit_normal() (in module syconn.utils.basics) unRoot() (syconn.utils.skeleton.SkeletonAnnotation method) (syconn.utils.skeleton.SkeletonNode method) unRootInternal() (syconn.utils.skeleton.SkeletonAnnotation method) update_axoness_dict() (in module syconn.contactsites) update_dataset() (in module syconn.utils.segmentationdataset)

update_multiple_datasets() (in module syconn.utils.segmentationdataset) update_property_dict() (in module syconn.contactsites) update_property_feat_kzip() (in module syconn.processing.features) update_property_feat_kzip_star() (in module syconn.processing.features) update_single_cs_axoness() (in module syconn.contactsites) update_single_cs_properties() (in module syconn.contactsites) updating_segmentationDatasets_thread() (in module syconn.utils.segmentationdataset)

V

Version (class in syconn.utils.skeleton)

voxels (syconn.utils.segmentationdataset.SegmentationObject attribute)

W

wd (syconn.utils.datahandler.DataHandler attribute) write2kzip() (syconn.processing.mapper.SkeletonMapper method) write2pkl() (syconn.processing.mapper.SkeletonMapper method) write_anno() (in module syconn.utils.skeleton_utils) write_axoness_dicts() (in module syconn.contactsites) write_cs_summary() (in module syconn.contactsites) write_data2kzip() (in module syconn.utils.datahandler)

write_feat2csv() (in module syconn.processing.learning_rfc) write_feats_importance() (in module syconn.processing.cell_types) write_obj2pkl() (in module syconn.utils.datahandler) write_obj_voxel (syconn.processing.mapper.SkeletonMapper attribute) write_property_dict() (in module syconn.contactsites) write_summaries() (in module syconn.contactsites) write_to_cube() (syconn.utils.segmentationdataset.SegmentationObject method) write_to_overlaycube() (syconn.utils.segmentationdataset.SegmentationObject method)