Alignment and Integration of Spatial Transcriptomics Data

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2022 May 16

PMID 35577957

Authors

Ron Zeira

Max Land

Alexander Strzalkowski

Benjamin J Raphael

Affiliations

Soon will be listed here.

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 alignment of a tissue. Alternatively, PASTE can integrate multiple ST slices into a single consensus slice. We show that PASTE accurately aligns spots across adjacent slices in both simulated and real ST data, demonstrating the advantages of using both transcriptional similarity and spatial information. We further show that the PASTE integrated slice improves the identification of cell types and differentially expressed genes compared with existing approaches that either analyze single ST slices or ignore spatial information.

Citing Articles

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