Fig. 2: Multiscale analysis.

a, Pictogram depicting the hierarchy of multiple biological scales. b, Sankey plot showing the hierarchical relationships between different spatial units in Giotto Suite. c, Spatial plots showing raw transcript locations (top) and corresponding DAPI image (bottom). d, Spatial plots illustrating annotations at different scales, including nucleus (top left), cell (top right), neighborhood (bottom left) and domain (bottom right). Highlighted annotations correspond with selection in b. e,f, UMAP and spatial plot showing Leiden clusters for cellular (e) and nuclear (f) segmentations. g, Sankey plot showing the Leiden cluster relationships between count aggregation results from cellular (e) and nuclear (f) segmentations. h, Overlay of multiscale annotations of a MERFISH dataset, depicting nuclear lumen and cytoplasmic enriched transcripts for all genes in GSEA terms related to ‘nuclear lumen’ (magenta) and ‘COPII-coated ER to Golgi transport vesicle’ (cyan), respectively. The nuclear boundary is defined with a yellow border, and the cell body is filled in with dark green. i, Overlay of multiscale annotations of a MERFISH dataset, depicting chromosome centromeric region (magenta) and collagen-containing extracellular matrix (cyan) transcripts. j,k, Waterfall plot depicting the log fold enrichment changes for all transcripts, nuclear versus cytoplasm (j) and within versus outside of the cell (k). l,m, GSEA plots showing results for nuclear versus cytoplasm (l) and inside versus outside cells (m). ER, endoplasmic reticulum; FC, fold change; MHC, major histocompatibility complex.