Index

A

avg_shape() (in module cajal.utilities)

avg_shape_spt() (in module cajal.utilities)

B

batch_filter_and_preprocess() (in module cajal.swc)

C

cajal.combined_slb_qgw module cajal.qgw module cajal.run_gw.DistanceMatrix (class in src.cajal.run_gw) cajal.run_gw.Distribution (class in src.cajal.run_gw) cajal.sample_mesh.FaceArray (class in src.cajal.sample_mesh) cajal.sample_mesh.VertexArray (class in src.cajal.sample_mesh) cajal.sample_seg module cajal.swc.SWCForest (built-in class) cajal.ugw module

cajal.ugw.UGW (class in cajal.ugw) cell_boundaries() (in module cajal.sample_seg) cell_iterator() (in module cajal.swc) cell_iterator_csv() (in module cajal.run_gw) cell_pair_iterator_csv() (in module cajal.run_gw) CellAligner_Cell (class in cajal.subcellular) combined_slb_quantized_gw() (in module cajal.combined_slb_qgw) combined_slb_quantized_gw_memory() (in module cajal.combined_slb_qgw) compute_gw_distance_matrix() (in module cajal.run_gw) compute_icdm_all() (in module cajal.sample_mesh) (in module cajal.sample_seg) compute_icdm_all_euclidean() (in module cajal.sample_swc) compute_icdm_all_geodesic() (in module cajal.sample_swc)

D

dCellAlignerNetwork (class in cajal.subcellular_dl)

default_name_validate() (in module cajal.swc) discrete_depth() (in module cajal.swc)

E

estimate_distr() (in module cajal.ugw)

extract_embeddings() (in module cajal.subcellular_dl)

F

find_centroid() (in module cajal.subcellular) forest_from_linear() (in module cajal.swc)

fused_gromov_wasserstein() (in module cajal.fused_gw_swc) fused_gromov_wasserstein_parallel() (in module cajal.fused_gw_swc)

G

generate_dataset_split_pairs() (in module cajal.subcellular_dl) geodesic_distance() (in module cajal.sample_swc) get_filenames() (in module cajal.swc) get_sample_pts_euclidean() (in module cajal.sample_swc)

get_sample_pts_geodesic() (in module cajal.sample_swc) gw_mapped_ot_pairwise_parallel() (in module cajal.subcellular) gw_pairwise_parallel() (in module cajal.run_gw) (in module cajal.subcellular)

I

icdm_csv_validate() (in module cajal.run_gw)

icdm_euclidean() (in module cajal.sample_swc) icdm_geodesic() (in module cajal.sample_swc)

K

keep_only_eu() (in module cajal.swc)

L

laplacian_scores() (in module cajal.laplacian_score) leiden_clustering() (in module cajal.utilities)

linearize() (in module cajal.swc) load_dCellAligner_model() (in module cajal.subcellular_dl) louvain_clustering() (in module cajal.utilities)

M

make_NN_training_data() (in module cajal.subcellular_dl) map_cell_to_cell() (in module cajal.subcellular) map_to_anchor_cell() (in module cajal.subcellular) mass_lower_bound() (in module cajal.ugw) Modality (class in cajal.wnn) module cajal.combined_slb_qgw cajal.qgw cajal.sample_seg cajal.ugw src.cajal.run_gw src.cajal.sample_mesh

N

NeuronNode (class in cajal.swc) NeuronTree (class in cajal.swc)

node_type_counts_forest() (in module cajal.swc) node_type_counts_tree() (in module cajal.swc) num_nodes() (in module cajal.swc)

P

PairedDataset (class in cajal.subcellular_dl) plot_cell_image() (in module cajal.subcellular) plot_distance_predictions() (in module cajal.subcellular_dl) plot_reconstruction_comparison() (in module cajal.subcellular_dl)

predict_distances() (in module cajal.subcellular_dl) preprocessor_eu() (in module cajal.swc) preprocessor_geo() (in module cajal.swc) pretrain_model() (in module cajal.subcellular_dl) process_image() (in module cajal.subcellular)

Q

quantized_gw_parallel() (in module cajal.qgw)

quantized_icdm (class in cajal.qgw)

R

RandomHorizontalRescale (class in cajal.subcellular_dl) read_obj() (in module cajal.sample_mesh)

read_preprocess_save() (in module cajal.swc) read_swc() (in module cajal.swc) rho_of() (in module cajal.ugw)

S

slb_parallel() (in module cajal.qgw) slb_parallel_memory() (in module cajal.qgw) src.cajal.run_gw module

src.cajal.sample_mesh module

T

ternary_distance_clusters() (in module cajal.ternary)

total_length() (in module cajal.swc) train_dCellAligner() (in module cajal.subcellular_dl)

U

ugw_armijo() (in module cajal.ugw.UGW) ugw_armijo_euclidean() (in module cajal.ugw.UGW)

ugw_armijo_pairwise() (in module cajal.ugw.UGW) ugw_armijo_pairwise_increasing() (in module cajal.ugw.UGW) ugw_bound() (in module cajal.ugw)

W

weighted_depth() (in module cajal.swc) WeightedTree_of() (in module cajal.weighted_tree) WeightedTreeChild (class in cajal.weighted_tree)

WeightedTreeRoot (class in cajal.weighted_tree) wnn() (in module cajal.wnn) write_swc() (in module cajal.swc)