API

Core

Cellina(adata[, n_hidden, n_latent, ...])	Cellina model with dual encoders for counts and spatial data.
CellinaGCN(adata[, n_hidden, n_latent, ...])	Cellina model with dual encoders for counts (MLP) and spatial context (GCN).

Utilities

compute_spatial_features(adata[, ...])	Compute spatial neighbourhood features and store them in adata.obsm.
make_counterfactual_adata(adata, ...[, ...])	Create a counterfactual AnnData keeping everything from the original except .obsm[spatial_column], which is replaced with counterfactual spatial neighbourhood features.
make_neighbor_perturbation(adata, perturbations)	Apply Node perturbations to neighbour expression and re-aggregate.
make_perturbed_expression(adata[, ...])	Apply Node perturbations to counts and store the result as a layer.
spatial_neighbors(adata[, bandwidth, ...])	Generate spatial connectivity weights using Euclidean distance.