Figure 3.

External validation of pipeline results

(A) Comparison of predicted gene expression by Tangram with measured expression of the same gene by smFISH (top six correlating genes shown). Each column corresponds to a gene, with the Tangram predicted expression above and the measured smFISH expression below. Pearson correlation coefficient is printed below each.

(B) Correlation of MERFISH counts with bulk RNA-seq FPKM values.

(C) Comparison of spatial distribution of four genes found in the targeted ISS dataset by the pipeline with reference expression of the same genes in a similar brain slice from the Allen Brain Atlas. In the top row, each yellow dot represents a transcript, while the image underneath is the DAPI stain of the sample; in the bottom row, blue dots represent low expression, while more red dots represent higher expression (no color map provided by Allen Brain Atlas), while the image underneath is the Nissl stain of the sample.