Extended Data Fig. 5: Ovrlpy’s unsupervised vertical doublet filtering enhances cell-type separation in gene expression space.
From: Identifying 3D signal overlaps in spatial transcriptomics data with ovrlpy
a–d, UMAP embeddings of gene expression data from Xenium mouse brain cell segments colored by (a) mean vertical signal integrity (VSI), (b) singlets and vertical doublets (VSI threshold of 0.7; 162,033 cell segments of which 36,846 are vertical doublets), (c) MapMyCells cell type annotations, (d) MapMyCells cell type annotations (UMAP embedding after excluding vertical doublets). Same as a-d for e–h, the Xenium mouse brain with only nuclear transcripts (162,018 nuclei of which 36,831 are vertical doublets), and i–l, the nuclear segmented MERSCOPE mouse brain (83,505 nuclei of which 15,780 are vertical doublets).
