Fig. 3: Eco-spatial analysis reveals distinct tissue remodeling in autoimmune disease.

a, Side-by-side visualization of tissue sections from BALBc-1 (healthy control) and MRL-8 (MRL/lpr) mice showing (1) the cell-type map (top); (2) the diversity heatmap (middle), with varying shades indicating cellular diversity levels (red representing higher diversity and blue lower diversity); and (3) the map of the diversity hot spots and cold spots (bottom). DC, dendritic cell. b, Quantitative evaluation of MESA diversity metrics, including MDI, GDI and DPI, highlighting statistically significant differences in spatial diversity patterns between healthy (n = 3) and MRL/lpr tissues (n = 6; same sample size for b–d). Standard box plot metrics were used throughout: median (center line), quartiles (box), and whiskers (1.5 × IQR). Each point in b–d corresponds to an individual tissue sample. Healthy tissues show higher values of GDI (P < 0.001) and DPI (P = 0.014), whereas diseased MRL/lpr tissues exhibit a higher value of MDI (P = 0.002). Statistical comparisons were conducted across different tissue samples using two-sided Welch’s t-test. c, Distribution of cell types as a percentage of total cell population in healthy and diseased spleen tissues. Comparisons were conducted using two-sided Welch’s t-test and adjusted for FDR correction using the BH procedure. Notably, the differences in cell frequency between healthy and diseased tissues are more pronounced within the diversity hot spots than within the whole tissue. d, Cohabitation of different cell types in healthy and diseased tissues. Comparisons were conducted using a two-sided Welch’s t-test and adjusted for FDR correction using the BH procedure. As before, the differences are more pronounced within the diversity hot spots than the entire tissue, with lower P values. e, Side-by-side visualization contrasting the cohabitation patterns of CD8⁺ T cells and F4/80⁺ macrophages in healthy and diseased tissues, with the corresponding CODEX images.