Fig. 5: Projection of single cells from the normal thymus to spatial coordinates.

a The strategy of TSO-hismap for projecting single cells onto spatial transcriptomics (ST) slices. Details of the full algorithm can be found in the “Methods” section. b Boxplots showing the performance of SrtCT, CellTrek, CARD, and TSO-hismap. Various noise levels (5%, 10%, and 15%) were introduced to evaluate the accuracy of assigning individual cells to the correct spot in simulated ST datasets. Median value, interquartile range (IQR) as bounds of the box and whiskers that extends from the box to upper/lower quartile ± IQR × 1.5. P-values were obtained using the two-sided t-tests. c Projection of thymic single cells to ST coordinates using TSO-hismap. Examples include Thy5, Thy6 and Thy7. Each dot represents a single cell from the normal thymus, with cell types color-coded. An enlarged lobule with a medullary center of ATAGTTCCACCCACTC-1 is shown. d Sankey plot showing the proportion of single cells of each cell type projected onto the medullary, cortical, and Medulla-Cortex (M-C) boundary regions of ST slices using TSO-hismap. The thickness of the lines indicates the proportion of one cell type projecting to that region. e Bubble plot showing a panoramic view of thymocytes in the cortical, medullary, and M-C boundary regions inferred by TSO-hismap, based on eight pediatric ST sections. The size of the dots indicates the proportion of that cell type in a particular region, and the color shade represents the average distance of that cell type from the medullary centers. f Single-cell resolved distribution of B_memory, CD8aa, DC, and Mono in ST slices (left: Thy5, right: Thy7). Each dot represents an individual cell. B_memory: Memory B cells, DC: Dendritic cells, Mono: Monocytes. The cell type icons in Fig. 5a 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.