Fig. 5: NIPMAP generalizes to RNA-based spatial profiling of healthy tissue.
From: NIPMAP: niche-phenotype mapping of multiplex histology data by community ecology
a The cellular and phenotypic architecture of the human developing lung was characterized by in situ RNA sequencing. Data: Sountoulidis et al.44. b The developing lung can be segmented into 5 histological niches. c Each niche has a specific cellular composition suggesting the histological basis of that niche. d Niche-phenotype mapping recovers known spatial associations between niches, such as the epithelial niche separating the smooth muscle niche from ductal/alveolar space. Dots: sites projected on the face of the 5 niches simplex defined by the ductal/alveolar, epithelial and smooth muscle niches. Colored areas: contours of dots density. The sequential organization of the ductal, epithelial, and smooth muscle niches is reflected by a depletion of sites at the ductal-smooth muscle interface relative to the ductal-epithelial interface. Thus, from the ductal/alveolar space, we first encounter the epithelial niche. Beyond the epithelial niche, the smooth muscle niche increases in weight. e Projecting phenotypes onto niches identifies cell types and phenotypes that associate with specific niches. f Arterial cells express JAG1 when located in the arterial niche but not when located in other niches. Dots: arterial cells. Color bar: JAG1 RNA count per cell. Background color: niche segmentation. ASM airway smooth muscle. Source data are provided as a Source Data file.
