Extended Data Fig. 2: Multicellular neighbourhood analysis of CODEX imaging data indicates conserved cellular structures across the intestine.

A) Neighbourhood analysis was done by taking a window across cell type maps and vectorizing the number of cell types in each window, clustering windows, and assigning clusters as cellular neighbourhoods of the intestine. B-D) Neighbourhood percentages from CODEX data averaged normalized by B) stromal, C) immune, and D) epithelial compartments. Asterix indicates p-value less than 0.05 difference in cell type percentage from the small bowel (SB) to the colon (CL) by two-sided T test. E) Stromal multicellular neighbourhood percentages either as a percent of all neighbourhoods restricted to the Muscularis Externa tissue unit (* p value< 0.05, *** p value < 0.001, n = 8 donors, by two-sided T test,). F) Quantification of the same-cell density for just smooth muscle cells within different smooth muscle multicellular neighbourhoods (x axis) (n = 32 tissue sections). G-H) Cell type maps for a region of the small intestine (one of 64 tissue sections imaged from 8 donors) with G) all cell types plotted for the whole tissue (scale bar = 500 µm), H) cells contained within the plasma cell neighbourhood (scale bar = 500 µm), and a magnified area of denoted by rectangle showing subset of cell types (scale bar = 50 µm). I) CODEX fluorescent imaging with subset of fluorescent markers overlaid for the same tissue as G (Hoechst=Blue, CD4=Green, CD68=magenta, CD38=yellow, CD206=cyan, CD138=grey), (scale bar = 500 µm with magnified insert scale bar = 100 µm).