Fig. 3: MAGIC-seq enables spatial mapping of mouse brain at cellular resolution.

a, Schematic representation of spatial profiling of mouse brain tissue at a 15 μm resolution. Two sections from a mouse brain were mounted to a splicing-grid chip and a single-grid chip with a spatial resolution of 15 μm. The splicing-grid chip covered the entire brain hemisphere, while the single-grid chip could merely cover an area of the hippocampus. b, Unsupervised clustering of spots (left) and spatial visualization of deconvolved cell types (right) from the mouse hemibrain section by MAGIC-seq. The white dashed lines showed the gaps between the subgrids of splicing chip that have been interpolated using nearest-neighbor interpolation. Spots and cells are colored by their annotation. Scale bar, 1 mm. c, Bottom left, bar plot showing the proportion of the number of cell types assigned per spot. Top right, pie plot showing the proportion of spots for each cell type defined by scRNA-seq data. d, Spatial mapping of selected cell types in hippocampus regions for the single-grid or splicing-grid chip. The plot shows estimated cell abundances (color intensity) of hippocampal neuron types (Ext_Hpc subtypes) and a thalamic habenular neuron type (Inh_6). e, Spatial mapping of hippocampus marker genes in the single-grid chip (top) and the splicing-grid chip (bottom). f, Correlation analysis of gene expression between the single- and splicing-grid chips in the hippocampus region. g, Measurement of cell type clustering/dispersion using Ripley’s L statistics with increasing distance. h, Spatial mapping of oligodendrocytes (Oligo_1 and Oligo_2) in the mouse brain hemisphere. HPC region was marked with dashed box. i, Spatial expression of the oligodendrocyte marker (Mbp) in the mouse brain hemisphere. Oligo, oligodendrocyte; Ext, excitatory neuron; Thal, thalamus; Endo, endothelia cell; Inh, inhibitory neuron; HPC, hippocampus; DG, dentate gyrus; Micro, microglia; Astro, astrocyte.