Fig. 2: Multicellular neighbourhood analysis of the intestine.

a, Twenty unique intestinal multicellular neighbourhoods were defined by enriched cell types as compared to the overall percentage of cell types in the samples. b, An example in which neighbourhoods mapped back to the tissue show overall tissue structures. Scale bar, 0.5 mm. c, The percentage of Neuroendocrine-Enriched neighbourhood of all of the neighbourhoods as determined by individually characterizing cellular neighbourhoods by region. n = 8 donors. The box plots show the median (centre line), 25th to 75th percentile (box limits), minimum and maximum values (whiskers), and outliers (points outside 1.5× the interquartile range). d,e, Quantification of the same-cell density for neuroendocrine cells compared across the small bowel and colon (n = 32 tissue sections) (d) or the epithelial neighbourhoods as determined by individually characterizing cellular neighbourhoods by region (n = 64 tissue sections) (e). Avg., average; max., maximum. f, A subset of epithelial neighbourhoods mapped back to a representative magnified region (n = 8 donors) of the mucosa of a transverse colon section. Scale bar, 250 µm. g,h, The approach to calculate concentric increasing neighbourhoods around a Paneth cell (g) to generate cellular neighbourhoods for Paneth cells at increasing radii (h). i,j, Schematic (i) and CODEX fluorescence data illustrating a representative (1 of 32 sections from 8 donors) magnified portion of the proximal jejunum depicting colocalization of Paneth cells (DEFA5, green) and CD8⁺ T cells (CD8, cyan) and CD4⁺ T cells (CD4, yellow) in the intestinal crypt environment (j). Scale bar, 50 µm.