Fig. 3: Xenium-based in situ transcriptomics profiling and FISH validation.

A Overview for CN and Pu sections after segmentation and cell type classification, scale bar 200 µm. Segmented cells are represented as polygons, based on their expanded segmentation masks. For interneurons, polygons are colored based on their assigned subclass, while non-interneuronal cells are outlined in gray. B Stripplot depicting the relative frequency of interneuron subclasses with variance per sample in CN and Pu (N = 4 each). On top, boxplots are overlaid with minimum and maximum values represented by the whiskers’ ends, while percentiles 25, 50, and 75 are defined by the position of the box. C Barplot illustrating the different proportions of interneuron main classes in CN and Pu (N = 4 each). D Heatmap representing the spatial neighborhood enrichment between interneuron populations characterized across the different sections (N = 8). E Representative images for 14 interneuron subclasses, identified in the Xenium experiment, scale bar 10 µm. DAPI staining is shown as a grayscale image. Read detected on each cell are represented as individual dots, colored based on their transcript identity. Expended segmentation masks of the outlined cells are colored based on their assigned interneuron subclass following the colormap specified in Fig. 3A. F Images of various in-situ hybridization experiments illustrating 10 proposed marker genes, asterisks mark autofluorescence due to lipofuscin, scale bars 10 µm.