Fig. 6: SOTIP recovers differential microenvironments between liver samples.

a Illustration of healthy and fibrotic livers. b Histological images of the healthy (left) and fibrotic (right) liver samples. The red arrows indicate fibrotic niche. The green dashed line indicates the fibrotic boundary. Scale bar: 100 μm. c Spatial single cell map in healthy (left) and fibrotic (right) liver sample paired with Fig. 6b. The red arrows and green dashed line are consistent with those in Fig. 6b. d MEG abstraction. Each node is a cluster of densely connected MECNs. The width of edges can be considered as similarity between nodes (see “Methods”). Each node (i.e., MECN cluster) is assigned an unique color. The size of each node is proportional to the number of MECNs belonging to that MECN cluster. e MECN clusters of the fibrotic liver sample showed in Voronoi diagram. The colors of MECN clusters are consistent with those in Fig. 6d. The green dashed line is consistent with that in Fig. 6b. f Entropy-SHN (EH) plot (see “Methods”). Each node is a MECN cluster with the same color scheme as Fig. 6d, e. The y-axis is the entropy (H_C) of the MECN cluster C. The x-axis is the average SHN values of the MECN cluster. MECN cluster 0, 3, 9, 11, 12, 14, 15 with low entropy and high SHN values lie at the right bottom corner of EH plot. g Left: The same MECN clusters as Fig. 6e, but only MECN cluster 0, 9, 11, 12, 14 in highlight. The red arrows and green dashed line are consistent with those in Fig. 6b. Right: Cell composition of MECN cluster 0, 9, 11, 12, 14, with the same color scheme as Fig. 6c. h Top: The same MECN cluster map as Fig. 6e, but only MECN cluster 3 in highlight. The red arrows and green dashed line are consistent with those in Fig. 6b. Bottom: Cell composition of MECN cluster 3, with the same color scheme as Fig. 6c. i Similar with Fig. 6h but using MECN cluster 15. Source data are provided as a Source Data file. The experiment results in (b, c, d) were similar with three independent repeats.