Fig. 2: Stamp-seq enables single-nucleus spatial transcriptomics in the mouse brain.

a UMAP embedding of snRNA-seq profiles (WTH1092), with cells color-coded by annotated cell types. CA1 Cornu Ammonis area 1, CA3 Cornu Ammonis area 3, OPCs oligodendrocyte precursor cells. b Stamp-seq enables high-resolution spatial mapping of nuclei in the adult mouse brain, with cells color-coded according to the same rule as in a. The lower image displays the “on-chip” DAPI-stained tissue section, providing a morphological reference for the sequenced region. c Spatial expression patterns of marker genes identified by Stamp-seq are compared against in situ hybridization (ISH) data from the Allen Mouse Brain Atlas⁶⁶. Color scales represent normalized expression levels. d Spatial barcode distribution patterns that define nuclear centers in the adult mouse brain sample WTH1092. Each bin represents a 100 × 100-pixel region. The enlarged plots (right panel) depict three representative distribution patterns of nuclear centers, with the color intensity indicating the density of spatial barcode UMIs within each bin. e Stamp-seq-captured cells are overlaid onto a DAPI image, showing the alignment of nuclear morphology (green arrows) with cell type annotations (endothelial cells). The upper left panel highlights the nuclear shapes on the DAPI image, while the upper right panel depicts the spatial distribution and cell types of all the captured cells. The lower left panel outlines the nearest nuclei on the DAPI image, color-coded by cell type based on the Stamp-seq data. The lower right panel integrates Stamp-seq nuclear locations, cell type annotations, and the nearest nuclear outlines from the DAPI image. The black dots denote the CellProfiler-extracted centroid positions of all the nuclei. f Spatial distances between nuclear positions determined using Stamp-seq and their nearest counterparts identified by CellProfiler on the DAPI image are quantified. As a control, distances from randomly generated nucleus positions to their nearest DAPI-identified nuclei are compared (right panel). e illustrates part of the nuclei quantified in f. *** denotes P < 0.001 (Wilcoxon test).