Index

A

add_scale_bar() (in module visualize) Affine_GD() (in module CAST_Stack) affine_reg_params() (in module CAST_Stack) affine_trans_t() (in module CAST_Stack) alpha (models.model_GCNII.CCA_SSG attribute) (models.model_GCNII.GCNII attribute) alpha_basis (CAST_Stack.reg_params attribute)

alpha_basis_bs (CAST_Stack.reg_params attribute) alpha_init() (in module CAST_Stack) Args (class in models.model_GCNII) attention_params (CAST_Stack.reg_params attribute) attention_params_bs (CAST_Stack.reg_params attribute) attention_region (CAST_Stack.reg_params attribute) average_dist() (in module CAST_Projection)

B

B_matrix() (in module CAST_Stack) backbone (models.model_GCNII.CCA_SSG attribute) bleeding (CAST_Stack.reg_params attribute)

BSpline_GD() (in module CAST_Stack) BSpline_GD_preparation() (in module CAST_Stack) BSpline_GD_uv_ij_calculate() (in module CAST_Stack) BSpline_renew_coords() (in module CAST_Stack)

C

CAST module CAST_Mark module CAST_MARK() (in module CAST) CAST_PROJECT() (in module CAST) CAST_Projection module CAST_Stack module CAST_STACK() (in module CAST) CAST_STACK_rough() (in module CAST_Stack)

CCA_SSG (class in models.model_GCNII) cdist_check() (in module CAST_Projection) cdist_hist() (in module CAST_Projection) cell_select() (in module utils) confusion_mat_plot() (in module CAST_Projection) coords2adjacentmat() (in module utils) coords_minus_mean() (in module CAST_Stack) coords_minus_min() (in module CAST_Stack) coords_minus_min_t() (in module CAST_Stack) corr_dist() (in module CAST_Stack) corr_heat() (in module CAST_Stack) cosine_IDW() (in module CAST_Projection)

D

d_list (CAST_Stack.reg_params attribute) dataname (CAST_Stack.reg_params attribute) (models.model_GCNII.Args attribute) delaunay_dgl() (in module CAST_Mark) delta_cell_cal() (in module utils) delta_exp_cal() (in module utils) delta_exp_sigplot() (in module utils) delta_exp_statistics() (in module utils) der (models.model_GCNII.Args attribute) detect_highly_variable_genes() (in module utils)

device (CAST_Stack.reg_params attribute) (models.model_GCNII.Args attribute) dfr (models.model_GCNII.Args attribute) diff_step (CAST_Stack.reg_params attribute) dist_penalty1 (CAST_Stack.reg_params attribute) dist_penalty2 (CAST_Stack.reg_params attribute) dJ_dt_cal() (in module CAST_Stack) dJ_dtheta_cal() (in module CAST_Stack) drop_feature() (in module models.aug) dsplot() (in module visualize)

E

Encoder (class in models.model_GCNII) encoder_dim (models.model_GCNII.Args attribute) (models.model_GCNII.CCA_SSG attribute) (models.model_GCNII.Encoder attribute) (models.model_GCNII.GCN attribute) (models.model_GCNII.GCNII attribute)

epochs (models.model_GCNII.Args attribute) evaluation_project() (in module CAST_Projection) extract_coords_exp() (in module utils)

F

FFD_Bspline_apply_t() (in module CAST_Stack) forward() (models.model_GCNII.CCA_SSG method) (models.model_GCNII.Encoder method) (models.model_GCNII.GCN method) (models.model_GCNII.GCNII method)

G

GCN (class in models.model_GCNII) GCNII (class in models.model_GCNII) get_dxy_ffd() (in module CAST_Stack) get_embedding() (models.model_GCNII.CCA_SSG method)

get_neighborhood_rad() (in module utils) get_range() (in module CAST_Stack) gpu (CAST_Stack.reg_params attribute) (models.model_GCNII.Args attribute) group_shift() (in module CAST_Projection)

H

Harmony_integration() (in module utils)

hv_cutoff() (in module utils)

I

IDW() (in module CAST_Projection) ifrigid (CAST_Stack.reg_params attribute) img_size_bs (CAST_Stack.reg_params attribute) in_dim (models.model_GCNII.CCA_SSG attribute) (models.model_GCNII.Encoder attribute) (models.model_GCNII.GCN attribute) (models.model_GCNII.GCNII attribute)

iterations (CAST_Stack.reg_params attribute) iterations_bs (CAST_Stack.reg_params attribute)

J

J_cal() (in module CAST_Stack)

K

kmeans_plot_multiple() (in module visualize)

L

lambd (models.model_GCNII.Args attribute) lambda_ (models.model_GCNII.CCA_SSG attribute) (models.model_GCNII.GCNII attribute)

link_plot() (in module visualize) link_plot_3d() (in module CAST_Projection) lr1 (models.model_GCNII.Args attribute)

M

mask_edge() (in module models.aug) max_minus_value() (in module CAST_Stack) max_minus_value_t() (in module CAST_Stack) mean_q (CAST_Stack.reg_params attribute) mean_r (CAST_Stack.reg_params attribute) mesh_plot() (in module CAST_Stack) mesh_trans_list (CAST_Stack.reg_params attribute) mesh_weight (CAST_Stack.reg_params attribute) meshsize (CAST_Stack.reg_params attribute) min_qr2 (CAST_Stack.reg_params attribute) mirror_t (CAST_Stack.reg_params attribute) models.aug module

models.model_GCNII module module CAST CAST_Mark CAST_Projection CAST_Stack models.aug models.model_GCNII utils visualize

N

n_layers (models.model_GCNII.Args attribute) (models.model_GCNII.CCA_SSG attribute) (models.model_GCNII.GCN attribute) (models.model_GCNII.GCNII attribute)

nearest_neighbors_idx() (in module utils) non_zero_center_scale() (in module utils)

P

PaddingRate_bs (CAST_Stack.reg_params attribute) physical_dist_priority_project() (in module CAST_Projection) plot_mid() (in module CAST_Stack) (in module visualize)

plot_mid_v2() (in module visualize) prelocate() (in module CAST_Stack) prelocate_loss_plot() (in module CAST_Stack) preprocess_fast() (in module utils)

R

random_aug() (in module models.aug) random_sample() (in module utils) reg_params (class in CAST_Stack)

reg_total_t() (in module CAST_Stack) region_detect() (in module CAST_Stack) register_result() (in module CAST_Stack) rescale_coords() (in module CAST_Stack)

S

space_project() (in module CAST_Projection) sparse_mask() (in module CAST_Projection)

standardize() (in module models.model_GCNII) sub_data_extract() (in module utils) sub_node_sum() (in module utils)

T

theta_r1 (CAST_Stack.reg_params attribute) theta_r2 (CAST_Stack.reg_params attribute) theta_renew() (in module CAST_Stack)

torch_Bspline() (in module CAST_Stack) train_seq() (in module CAST_Mark) translation_params (CAST_Stack.reg_params attribute)

U

use_encoder (models.model_GCNII.Args attribute) (models.model_GCNII.CCA_SSG attribute) (models.model_GCNII.GCN attribute) (models.model_GCNII.GCNII attribute)

utils module

V

visualize module

W

wd1 (models.model_GCNII.Args attribute)