Index

A

adapted_rand_error() (in module gala.evaluate) add_nats_to_plot() (in module gala.viz) add_opts_to_plot() (in module gala.viz) adj_rand_index() (in module gala.evaluate) agglomerate() (gala.agglo.Rag method)

agglomerate_count() (gala.agglo.Rag method) agglomerate_ladder() (gala.agglo.Rag method) apply_segmentation_map() (in module gala.imio) approximate_boundary_mean() (in module gala.agglo) at_volume_boundary() (gala.agglo.Rag method)

B

best_possible_segmentation() (in module gala.agglo) bin_values() (in module gala.evaluate) boundary_overlap_threshold() (in module gala.classify) build_boundary_map() (gala.agglo.Rag method)

build_graph_from_watershed() (gala.agglo.Rag method) build_merge_queue() (gala.agglo.Rag method) build_volume() (gala.agglo.Rag method)

C

cluster_by_labels() (gala.agglo.Rag method) compute_feature_caches() (gala.agglo.Rag method) compute_local_rand_change() (in module gala.agglo) compute_local_vi_change() (in module gala.agglo) compute_orphans() (gala.agglo.Rag method) compute_sp_to_body_map() (in module gala.imio)

compute_true_delta_rand() (in module gala.agglo) compute_W() (gala.agglo.Rag method) concatenate_data_elements() (in module gala.classify) conditional_countdown() (in module gala.agglo) contingency_table() (in module gala.evaluate) copy() (gala.agglo.Rag method)

D

damify() (in module gala.morpho) default_classifier_extension() (in module gala.classify) display_3d_segmentations() (in module gala.viz)

divide_columns() (in module gala.evaluate) divide_rows() (in module gala.evaluate) draw_seg() (in module gala.viz)

E

edit_distance() (in module gala.evaluate)

extract_segments() (in module gala.imio)

F

fm_index() (in module gala.evaluate)

G

gala.agglo (module) gala.classify (module) gala.evaluate (module) gala.features (module) gala.imio (module) gala.morpho (module)

gala.viz (module) get_classifier() (in module gala.classify) get_edge_coordinates() (gala.agglo.Rag method) (in module gala.agglo) get_neighbor_idxs() (in module gala.morpho) get_segmentation() (gala.agglo.Rag method) get_stratified_sample() (in module gala.evaluate)

H

hminima() (in module gala.morpho)

hollowed() (in module gala.morpho)

I

imhmin() (in module gala.morpho) impose_minima() (in module gala.morpho) imshow_grey() (in module gala.viz)

imshow_jet() (in module gala.viz) imshow_rand() (in module gala.viz) is_traversed_by_node() (gala.agglo.Rag method)

L

label_merges() (in module gala.classify) learn_agglomerate() (gala.agglo.Rag method) learn_edge() (gala.agglo.Rag method)

learn_epoch() (gala.agglo.Rag method) learn_flat() (gala.agglo.Rag method) load_classifier() (in module gala.classify)

M

make_synaptic_functions() (in module gala.evaluate) make_synaptic_vi() (in module gala.evaluate) make_thresholded_boundary_overlap_loss() (in module gala.classify) manual_split() (in module gala.morpho) merge_edge_properties() (gala.agglo.Rag method)

merge_nodes() (gala.agglo.Rag method) merge_subgraph() (gala.agglo.Rag method) minimum_seeds() (in module gala.morpho) morphological_reconstruction() (in module gala.morpho)

N

ncut() (gala.agglo.Rag method) non_traversing_bodies() (gala.agglo.Rag method)

non_traversing_segments() (in module gala.morpho)

O

orphans() (gala.agglo.Rag method) (in module gala.morpho)

P

pil_to_numpy() (in module gala.imio) pixel_wise_boundary_precision_recall() (in module gala.evaluate) plot_split_vi() (in module gala.viz)

plot_vi() (in module gala.viz) plot_vi_breakdown() (in module gala.viz) plot_vi_breakdown_panel() (in module gala.viz)

R

Rag (class in gala.agglo) rand_by_threshold() (in module gala.evaluate) rand_index() (in module gala.evaluate) rand_values() (in module gala.evaluate) raveled_steps_to_neighbors() (in module gala.morpho) raveler_body_annotations() (gala.agglo.Rag method) (in module gala.imio) raveler_output_shortcut() (in module gala.imio) raveler_rgba_to_int() (in module gala.imio) raveler_serial_section_map() (in module gala.imio) raveler_to_labeled_volume() (in module gala.imio) raw_edit_distance() (in module gala.evaluate) read_h5_stack() (in module gala.imio) read_image_stack() (in module gala.imio) read_mapped_segmentation() (in module gala.imio) read_mapped_segmentation_raw() (in module gala.imio) read_multi_page_tif() (in module gala.imio)

read_multi_page_tif_libtiff() (in module gala.imio) read_prediction_from_ilastik_batch() (in module gala.imio) read_vtk() (in module gala.imio) real_edges() (gala.agglo.Rag method) real_edges_iter() (gala.agglo.Rag method) rebuild_merge_queue() (gala.agglo.Rag method) reduce_vi() (in module gala.evaluate) refined_seeding() (in module gala.morpho) regional_minima() (in module gala.morpho) relabel_connected() (in module gala.morpho) relabel_from_one() (in module gala.evaluate) remove_inclusions() (gala.agglo.Rag method) remove_merged_boundaries() (in module gala.morpho) remove_obvious_inclusions() (gala.agglo.Rag method) rename_node() (gala.agglo.Rag method) replay_merge_history() (gala.agglo.Rag method)

S

sample_training_data() (in module gala.classify) save_classifier() (in module gala.classify) seg_to_bdry() (in module gala.morpho) segs_to_raveler() (in module gala.imio) sem() (in module gala.evaluate) serial_section_map() (in module gala.imio) set_exclusions() (gala.agglo.Rag method) set_feature_manager() (gala.agglo.Rag method) set_ground_truth() (gala.agglo.Rag method) set_orientations() (gala.agglo.Rag method) set_probabilities() (gala.agglo.Rag method)

set_watershed() (gala.agglo.Rag method) sorted_vi_components() (in module gala.evaluate) sparse_csr_row_max() (in module gala.evaluate) sparse_max() (in module gala.evaluate) sparse_min() (in module gala.evaluate) special_points_evaluate() (in module gala.evaluate) split_components() (in module gala.evaluate) split_exclusions() (in module gala.morpho) split_node() (gala.agglo.Rag method) split_vi() (in module gala.evaluate) split_vi_threshold() (in module gala.evaluate)

T

traversing_bodies() (gala.agglo.Rag method)

U

ucm_to_raveler() (in module gala.imio) undam() (in module gala.morpho)

update_merge_queue() (gala.agglo.Rag method)

V

vi() (in module gala.evaluate) vi_by_threshold() (in module gala.evaluate) vi_pairwise_matrix() (in module gala.evaluate)

vi_statistics() (in module gala.evaluate) vi_tables() (in module gala.evaluate)

W

watershed() (in module gala.morpho) watershed_sequence() (in module gala.morpho) wiggle_room_precision_recall() (in module gala.evaluate) write_h5_stack() (in module gala.imio) write_ilastik_batch_volume() (in module gala.imio) write_ilastik_project() (in module gala.imio) write_image_stack() (in module gala.imio)

write_json() (in module gala.imio) write_mapped_segmentation() (in module gala.imio) write_plaza_json() (gala.agglo.Rag method) write_png_image_stack() (in module gala.imio) write_to_raveler() (in module gala.imio) write_vtk() (in module gala.imio)

X

xlogx() (in module gala.evaluate)