Fig. 6: Spatial co-localization and characterization of thymic cell types.

a Atlas of thymic cell types coexisting in spatial transcriptomics (ST) slices. Each vertex represents a cell type and the thickness of the edges indicates the strength of the J-index (see “Methods”). Edges with J-index values below 0.3 are not shown, those with values less than 0.6 are gray, and those above 0.6 are highlighted by the color code of the specific cell type. In addition, Ery was not considered due to contamination in ST slices. b In combination with the ST images (Thy5 and Thy7 as examples), the spatial co-localization of the cell types is visualized. cTEC vs. DP_re (top) and CD8aa vs. B_memory vs. Mono vs. DC (bottom). Each dot represents a cell projected onto spatial coordinates by TSO-hismap, with cell types color-coded. c Immunofluorescence staining showing the expression patterns of GNG4 (CD8aa), IgA (B_memory), and CD14 (Mono) in the thymus (5 months old). Scale bars: 100 um (middle panel) and 50 um (bottom panel; magnified slices) (n = 3 technical replicates). d Schematic representation of the spatial co-localization of thymic cell types at different stages of human T cell development, from the distal cortex to the inner medulla. Ery: Erythrocytes, B_memory: Memory B cells, cTEC: Cortical thymic epithelial cells, Mono: Monocytes, DC: Dendritic cells, DP_re: Double positive rearrangement cells. The thymus, lobule, and cell type icons in Fig. 6d were created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license. Source data are provided as a Source Data file.