Fig. 4
From: Image guided construction of a common coordinate framework for spatial transcriptome data
Evaluation of STaCker in aligning digitally warped spatial transcriptome slices of mouse brain. (a) The reference is a mouse sagittal posterior brain slice profiled by 10 × Genomics Visium platform. It was digitally warped using Simplex noises to a low (noise amplitude = 5, NCC of the deformed image = 0.61), medium (noise amplitude = 10, NCC of the deformed image = 0.57), or high (noise amplitude = 15, NCC of the deformed image = 0.54 level to generate a series of moving slices (noise frequency remains 1 for all warping). (b) The discordance between the spatial coordinates of the spots in each moving slice and those in the reference slice is quantified by the MSE (Methods) shown in the bar plots. STaCker, together with previously published methods STUtility, PASTE, and GPSA, was applied to align each of the moving spatial transcriptome slices to the reference. The spots’ coordinates before (blue crosses) or after the alignment (red crosses) are displayed together with the reference spot coordinates (gray dots) to aid the visual comparison. The post-alignment MSEs from each method are illustrated in the bar plots. Value from STaCker is the mean over five runs, shown together with the standard errors as error bars. STaCker’s MSE is significantly lower than that of all other programs (one sample t-test p-values < = 1e-3).
