Fig. 2: Deconvolution of simulated ST data.

a Ground truth single-cell resolution MERFISH data of one section of the MPOA partitioned into 100 µm² pixels (black dashed squares). Each dot is a single cell colored by its ground truth cell type label. b Proportions of deconvolved cell types from STdeconvolve represented as pie charts for each simulated pixel. c The ranking of each gene based on its expression level in the deconvolved cell-type transcriptional profiles compared to its gene rank in the matched ground truth cell-type transcriptional profiles. d Heatmap of Pearson’s correlations between the deconvolved and ground truth cell type proportions across simulated pixels. Ground truth cell types are ordered by their frequencies in the ground truth dataset. Matched deconvolved and ground truth cell types are boxed. e Root-mean-square-error (RMSE) of the deconvolved cell-type proportions (n = 3072 pixels) compared to ground truth for STdeconvolve, f for supervised deconvolution approaches using the ideal single cell transcriptomics MERFISH MPOA reference, g for supervised deconvolution approaches using the single cell transcriptomics MERFISH MPOA reference with missing neurons, and h for supervised deconvolution approaches using a brain single-cell RNA-seq reference. Boxplots indicate median (middle line), 25th, 75th percentile (box) and 5th and 95th percentile (whiskers).