Fig. 3: Multilevel hierarchical structural description of the small intestine and colon.

a–d, Representation of multiple levels of hierarchical description: cell type (a), multicellular neighbourhood (b), community (based on clustering windows of cell neighbourhoods) (c) and tissue units (based on clustering communities) (d) comparing the small bowel with the colon for two representative tissue sections (from a total of 64 sections from 8 donors). Scale bar, 1 mm. e, Tissue hierarchy graph of the multilevel network of the tissue comprised of the different structures. Shapes correspond to structural level (cell type, neighbourhoods, communities, tissue units); colours represent individual categories as indicated in a–d; the size of shapes represents the percentage of tissue; and the size of connected lines represents the overall contribution to the next level of the structure when moving down the graph in increasing tissue structural hierarchy. The black rectangles highlight a single trajectory highlighted within this Article. The red bracket indicates separation of stromal tissue units from the mucosal tissue units. f, Magnified mucosal area of a colon community map shown within c. Scale bar, 100 µm. g, The spatial-context maps of the colon highlighting relationships of communities across the entire sample. This structure is defined by the number of unique communities required to make up at least 85% in a given window. The circles represent the number of cells represented by a given structure. The green rectangle highlights a structure discussed in this Article and maps this structure back to g. The colours are as indicated in c. h, The cell type percentage of immune cells shown for each community ordered in relative order of general increasing proximity to the lumen on the basis of community spatial-context analysis.