Fig. 5: Integration of spatial and single-nuclei data.

a Visualization of pericentral (top) and periportal (bottom) cell type proportions across spatial positions of sections generated by 10X Visium protocol. Pericentral cell type proportions are shown in red and periportal cell type proportions in blue. Green and gray boxes highlight smaller regions of opposite cell type compositions in salivary gland lysate control (SGC) and infected sections, respectively. The scale bars indicate 500 µm. b Loess-smoothed pericentral and periportal cell type proportions along a distance between 0 and 800 µm originating at computationally annotated central (top) or portal (bottom) veins. Periportal hepatocyte proportions are shown in blue and pericentral cell type proportions in red. Ribbons around the curve indicate the standard error of the mean (SEM). c Change in cell type proportions (Δ) of cell types (Loess-smoothed) with significant (p ≤ 0.05) negative (inflammatory hepatocytes, pericentral hepatocytes) or positive (B cells, periportal hepatocytes) correlation between the distance of 0 to 800 µm to parasite neighborhoods. Ribbons around the curve indicate the standard error of the mean (SEM). Conditions are indicated by colors (12 h infected = red, 24 h infected = green, 38 h infected = blue). Correlation values (r) are indicated for each condition in the respective color. d Change in cell type proportions (Δ) of cell types (Loess-smoothed) with significant (p ≤ 0.05) positive (pericentral hepatocytes) or negative (mesothelial & mesenchymal cells, T & NK cells, and monocytes & DCs) correlation between the distance of 0 and 800 µm to IHS neighborhoods (methods for details) where IHSs were present (12, 24, and 38 hpi as well as 24 and 38 h after salivary gland challenge (control)). Correlations were calculated jointly for all time points and ribbons around the curve indicate the standard error of the mean (SEM). e Composite image of immunofluorescent staining of CD4+ and CD8+ cells (left), CD27+, F4/80+ (middle), and CD11b+ and CD11c+ (right) cells in IHSs of tissue sections at 12 hpi (n = 12). DNA is stained using DAPI. Individual images and quantification are shown in Supplementary Fig. 20). The scale bars indicate 50 µm. f Composite image of immunofluorescent staining of CD4+ and CD8+ cells (left), CD27+, F4/80+ (middle), and CD11b+ and CD11c+ (right) cells in IHSs of SGC tissue sections at 38 h post challenge (n = 8). DNA is stained using DAPI. Individual images and quantification are shown in Supplementary Fig. 22). The scale bars indicate 50 µm.