SpatialLeiden - Spatially-aware Leiden clustering

Clustering can identify the natural structure that is inherent to measured data. For single-cell omics, clustering finds cells with similar molecular phenotype after which cell types are annotated. Leiden clustering is the algorithm of choice in the single-cell community. However, in the field of spatial omics, Leiden has been considered a non-spatial clustering method. Here, we show that by integrating spatial embeddings Leiden clustering is rendered into a computationally highly performant, spatially aware clustering method that compares well with state-of-the art clustering methods.