Fig. 8
From: Image guided construction of a common coordinate framework for spatial transcriptome data
Alignment of ISH-based spatial transcriptome slices. (a) MERFISH slices from three mouse brain samples, illustrated using the DAPI staining images. (b) Superimposed spatial coordinates of cells in the three slices before and after alignment by different methods. Cells are color-coded by their niches, defined based on the gene profiling of the cells (see Methods). (c) Quantitative evaluation of tissue domain consistency across the three slices before and after alignment, using Spatial Coherence Score and Mean Pairwise Adjusted Rand Index. STUtility and STalign do not offer de novo alignments so their values are averaged over three alignments each with a different slice as the fixed template, with standard errors shown as error bars. (d) Spatial patterns of four representative genes before and after alignment by STaCker, STUtility and STalign. The displayed expression is after the natural logarithm transformation of the normalized UMI count (104 total UMI counts per cell). (e) Comparison of Moran’s I autocorrelation (left panel) and Gene Coherence Score (right panel) of the four representative genes from the slices aligned by STaCker, STUtility or STalign. Values from STUtility and STalign are the average over three alignments each using a different slice as the fixed template, with standard errors shown as error bars. (f) Boxplots of the Moran’s I autocorrelation (left panel) and Gene Coherence Score (right panel) of all non-randomly distributed genes (Moran’s I p-value < = 0.01) over the slices aligned by STaCker, STUtility or STalign. The top and bottom edges of the box represent the 3rd and 1st quantiles, with the horizontal line inside denoting the median. The ends of the whisker mark the 1.5 times interquartile range, calculated as the difference between the 3rd and 1st quartiles, from the box edges. Data points beyond the whisker range are represented as dots. STalign was executed using the same parameters applied to the same MERFISH dataset in the original publication. (g) Comparison of the spatial coherence in gene expressions after the alignment by STaCker and STalign. Genes that show significantly higher Moran’s I correlation (left panel) or Gene Coherence Score (GCS, right panel) after alignment with STaCker are marked with orange dots, while genes with significantly elevated values for these metrics following STalign alignment are indicated by blue dots. The dashed line represents the significance cutoff (0.05) for the two-sided Student’s t-test p-value.
