a t-SNE map of all segmented cells expressing at least one of the markers included in the panel (cut-off = 0.1 MFI). Nine phenotypically distinct clusters are manually selected and annotated based on their expression profile as in (c) and depicted in a color-coded fashion (fibroblasts in pink, endothelial cells in magenta, progenitor cells in green, plasma cells in yellow, B cells in red, myeloid cells in brown, HLA-DR+ T cells in cyan, T cells in blue and ILCs in black). Each dot represents one cell. b Heat-map representation of the mean relative expression levels for the 48 markers analyzed in every cluster as in (a). c Region of interest (ROI) shown as an overlay of fluorescence images of relevant markers for ILC characterization. White arrows indicate ILCs. CD3 (red), CD127 (green), and DAPI (blue) are shown in the upper left panel. CD14 (red), CD19 (green), and CD141 (blue) are shown in the upper middle panel. CD161 (red), CD127 (green) and CD141 (blue) are shown in the upper right. ICOS (red), CXCR3 (green), and CCR6 (blue) are shown in the bottom left panel. CD45RA (red), CD45RO (green), and CD69 (blue) are shown in the bottom middle panel. Fibronectin (red), Collagen IV (green), and CD31 (blue) are shown in the bottom left panel. Scale bar 20 µm. a–c (n = 2).