SuperSpot: Coarse Graining Spatial Transcriptomic Data into Metaspots

Abstract

SummarySpatial Transcriptomics is revolutionizing our ability to phenotypically characterize complex biological tissues and decipher cellular niches. As of today, thousands of genes can be detected across hundreds of thousands of spots. Akin to standard single-cell RNA-Seq data, spatial transcriptomic data are very sparse due to the limited amount of RNA within each spot. Building upon the metacell concept, we present a workflow, called SuperSpot, to combine adjacent and transcriptionally similar spots into “metaspots”. The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptional similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution. We demonstrate that metaspots can be used to reduce the size of spatial transcriptomic data and remove some of the dropout noise.Availability and implementationSuperSpot is an R package available athttps://github.com/GfellerLab/SuperSpot.