Alignment and integration of spatial transcriptomics data | Nature Methods

PASTE aligns and integrates spatial transcriptomics data generated from adjacent tissue slices by leveraging their transcriptomic similarity and spatial coordinates, which ultimately increases the power for downstream analysis.

Subjects Data integration Genome informatics Abstract Spatial transcriptomics (ST) measures mRNA expression across thousands of spots from a tissue slice while recording the two-dimensional (2D) coordinates of each spot. We introduce probabilistic alignment of ST experiments (PASTE), a method to align and integrate ST data from multiple adjacent tissue slices. PASTE computes pairwise alignments of slices using an optimal transport formulation that models both transcriptional similarity and physical distances between spots. PASTE further combines pairwise alignments to construct a stacked 3D al

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