Fig. 9

Alignment across different spatial transcriptome platforms. (a) Two mouse brain hemispheres profiled using 10 × Genomics Visium and Xenium, shown as the acquired H&E and DAPI images, respectively. (b) Superimposed spatial coordinates of spots (red circles, Visium slice) or cells (blue crosses, Xenium slice) before and after alignment by different methods. (c) Spatial patterns of the representative genes before and after alignment by STaCker, STUtility or STalign. The positions of the spots in the Visium slice (red) and the 55-micron × 55-micron pseudo-spots in the Xenium slice (blue) are displayed. At each spot or pseudo-spot, the expression of a gene is divided by the maximum expression of that gene on the slice, converting it to a value within 0 and 1. The scaled gene expressions are comparable across platforms and thus used for visualization and quantitative evaluation. (d) Moran’s I autocorrelation (upper panel) and the Gene Coherence Score (lower panel) of the representative genes from the slices aligned by STaCker, STUtility or STalign. Values for STUtility and STalign that do not offer de novo alignment are the average over alignments each using one of the slices as the reference, with the standard errors shown as error bars. (e) Boxplots of the Moran’s I autocorrelation score (upper panel) and the Gene Coherence Score (lower panel) of all non-randomly distributed genes (Moran’s I p-value < = 0.01) over the slices aligned by STaCker, STUtility or STalign. For both metrics, the mean of the distribution in STaCker is significantly higher than that in STalign (two-sided student t-test p-value < = 6e-5) and in STUtility (two-sided student t-test p-value < = 2e-3). In all boxplots, the top and bottom edges of the box represent the 3rd and 1st quantiles with the horizontal line inside to denote the median. The whiskers extend to 1.5 times the interquartile range (IQR), which is the difference between the 3rd and 1st quantiles, from the box edges. Data points outside the whisker range are displayed as dots. (f) Comparison of spatial coherence in gene expressions following alignment using STaCker and STalign. Genes exhibiting significantly higher Moran’s I correlation (left panel) or Gene Coherence Score (right panel) after alignment with STaCker are depicted with orange dots. Genes with significantly increased values for the two metrics after alignment with STalign are shown with blue dots. The dashed line indicates the significance cutoff (0.05) for the two-sided Student’s t-test p-value.