Technological advances have made it possible to measure spatially resolved gene 
expression at high throughput. However, methods to analyze these data are not 
established. Here we describe SpatialDE, a statistical test to identify genes 
with spatial patterns of expression variation from multiplexed imaging or 
spatial RNA-sequencing data. SpatialDE also implements 'automatic expression 
histology', a spatial gene-clustering approach that enables expression-based 
tissue histology.