Fig. 4: Mapping snRNA-seq data to Spatial Transcriptomics data (Visium) demonstrates deconvolution and imputation of dropouts.

a, Single-cell deconvolution. Predicted single cells (colored dots, legend) in each Visium voxel (gray circle) based on snRNA-seq data mapped onto a Visium slide. Cell assignment within a voxel is random with respect to the specific segmented cell. b, Probabilistic mapping of snRNA-seq data on the Visium ROI. Probability of mapping (color bar) of each cell subset (gray label) in each of three major categories. c,d, Predicted expression of test and training genes. c, Normalized (that is, unit area) distribution of single-gene spatial correlation coefficients (y axis) between Tangram-predicted and Visium-measured patterns in training (orange) and test (blue) genes. d, Reducing the number of training genes decreases prediction performance. Spatial correlation (y axis, top) for training genes (orange) and test genes (blue), and scaled spatial correlation (y axis, bottom) for test genes (scaled by the correlation averaged across training genes) for Tangram models learned with different fractions of 1,237 input training genes (x axis). e–h, Impact of Visium data sparsity on prediction and correction. e, Tangram-predicted (top) and Visium-measured (bottom) expression (color bar, normalized mRNA counts, see Methods) of six select test genes (gray labels) with different extents of spatial correlation between measured and predicted patterns (top arrow, %) and of Visium data sparsity (bottom arrow, %). f, Spatial correlation of test genes is negatively correlated to sparsity in Visium data. Spatial correlation (y axis) between measured and predicted patterns for test genes (blue dots) and their corresponding measurement sparsity (x axis). Lines delineate three regions according to model performance. g, Few low-sparsity genes are not predicted well. Tangram-predicted (top) and Visium-measured (bottom) expression (color bar, normalized mRNA counts, see Methods) of four genes (gray labels) with low sparsity that are not well-predicted by model (from region (ii) of f). h, Correction of low-quality spatial measurements. Tangram-predicted (left), Visium (middle) and MERFISH (right) measurements (color bar signifies fluorescence for MERFISH figure, normalized mRNA counts for all others, see Methods), of two genes (gray labels) whose predicted patterns differ from Visium measurements but match direct measurement by MERFISH, and are highly sparse in Visium measurements (from region (iii) of f).