a The t-SNE map of tonsil single-cell MELC data reveals nine distinct clusters (germinal center B cells in red, B cells in dark brown, myeloid 1 in orange, myeloid 2 in light brown, T cells in blue, fibroblasts in pink, endothelial cells in magenta, plasma cells—PC—in yellow and ILCs in black) that are manually selected and annotated based on the expression profile shown in (b). Each dot represents one cell. b Heat-map representation of MELC data: mean relative expression level of the 52 markers analyzed for every cluster as in (a). c t-SNE map of tonsil single-cell MELC data previously classified into cell-types (B cells in red, T helper cells in light blue, cytotoxic T cells in dark blue, myeloid cells in orange, endothelial cells in magenta, PC in yellow, and ILCs in black), based on fluorescence thresholding of images for the lineage-defining markers. Each dot represents one cell. a–c (n = 5). See also Supplementary Fig.3.