Overview of Spatial Integration for Imputation and Deconvolution (SIID). Given Xenium and Visium expression matrices A_X and A_V, respectively, with corresponding gene panels G_X and G_V (with G_X ⊂ G_V), and a Xenium to Visium spatial mapping Γ, SIID finds a NMF decomposition of a latent gene count matrix A_U, with corresponding factorizations of A_X and A_V, into location to latent factor assignment matrix P and the gene expression matrix Q for latent factors. The estimated parameters are used to impute the absent gene expression in Xenium data and predict the cell type mixture proportions for each Visium spot.