Panel A shows histology images with spatial annotations of thymic tissue, highlighting capsule, cortex, corticomedullary junction, and medulla regions across samples. Panel B shows dotplot, x-axis shows marker genes and y-axis shows thymic regions, dot size represents fraction of spots and color represents scaled gene expression. Panel C shows dotplot, x-axis shows Hassall corpuscle marker genes IVL KRT1 KRT10 and y-axis shows samples, dot size represents fraction of spots and color represents scaled expression.
Annotation of thymic tissue regions and validation by marker gene expression. (A) H&E stainings, pixel-based annotations, and spot-based annotations of all thymic samples used in this study. Tissue regions were annotated by combining gene expression–based information from Visium with manual annotation of the H&E image. Visium spots were assigned to anatomically defined regions: capsular, cortex, CMJ, and medulla. The color of spots indicates region identity. (B) Dotplot showing the expression of marker genes in annotated regions. The expression of each gene is scaled using min-max scaling, where the blue color indicates low relative expression, and the red color indicates high relative expression. (C) Dotplot showing the expression of Hassall’s corpuscle marker genes IVL, KRT1, and KRT10 in medullary spots. Scaled gene expression is shown, with blue indicating low relative expression and red indicating high relative expression. H&E, hematoxylin and eosin.