Fig. 2: Spatial transcript analysis of renal compartments in glomerulonephritis.

a, Workflow of the NichePCA algorithm used for automated annotation and spatial mapping of glomeruli. b, Schematic illustration of a glomerulus and its periglomerular niche, defined by expanding the glomerular boundaries to include surrounding regions. c, Representative H&E image showing glomeruli (blue) as defined by NichePCA, their corresponding periglomerular regions (green) and the remaining tubulointerstitial area (orange). d, Representative images highlighting the spatial localization of various kidney and immune cell types. The top panels show the spatial localization of various kidney and immune cells within the glomerular and periglomerular regions, whereas the bottom panels depict the same in tubulointerstitial regions across the four disease conditions. e, Stacked bar plots showing the proportions of different cell types across the four disease conditions within three spatial niches: the glomerular niche (left), periglomerular niche (center) and tubulointerstitial areas (right).