Fig. 2: Tangram maps cells with high-resolution MERFISH measurements and expands them to genome scale.
From: Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram
a, Probabilistic mapping of snRNA-seq data on MERFISH data. Probability of mapping (color bar) of each cell subset (gray label) in each of three major categories. Bottom right, schematic of key layers. b, Deterministic mapping. MERFISH slide with segmented cells (dot) colored by the cell-type annotation of the most likely snRNA-seq profile mapped on that position by Tangram (legend). c,d, Predicted expression of test genes. c, Measured (top) and Tangram-predicted (bottom) expression (color bar signifies fluorescence at top and normalized mRNA counts at bottom, see Methods) of select test gene (gray labels) with different extents of spatial correlation (bottom arrow, %) between measured and predicted patterns. d, Cumulative distribution function (CDF) of spatial correlation (x axis) between predicted and measured patterns for test genes. Dashed line: 75% of test genes are predicted with spatial correlation >40%. e, Predicted expression of test genes. Tangram-predicted (bottom) expression (top; color bar, normalized mRNA counts, see Methods) and corresponding ISH images from the Allen Brain Atlas (bottom) for 11 genes not measured by MERFISH. f, Correction of low-quality spatial measurements. MERIFSH measured (top), Tangram-predicted (middle) and Allen Brain Atlas ISH, for genes where predicted patterns differ from MERFISH measurement but match direct inspection of Allen ISH images (color bar, normalized mRNA counts, see Methods).
