Fig. 4: Transcriptome inference and high-resolution label transfer identifies spatial expression patterns in the brain. | Nature Communications

Fig. 4: Transcriptome inference and high-resolution label transfer identifies spatial expression patterns in the brain.

From: Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection

Fig. 4

a Stacked MERFISH images of oligodendrocyte populations identified according to dominant cell type predicted by scProjection across anterior to posterior slices from Moffitt et al. Images are ordered by Bregma value. b Heatmap visualizing the gene-specific spatial expression patterns within the oligodendrocytes of imputed (top) and measured (bottom) genes. c MERFISH image of a single slice of the mouse cortex from Zhang et al., replicated four times to highlight neurons from different layers. Six examples of statistically significant spatial motifs (recurring neighborhoods) are illustrated in the circle plots. Spatial motifs were identified by first categorizing each individual cell (‘query’, squares) in the MERFISH dataset into a neighborhood type based on the number and cell types of neighboring cells (‘neighbor’, circles) within a radius around the query, then using permutation tests to determine whether there are specific neighborhood types that occur more frequently than expected by chance.

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