Fig. 2: SSAM improves astrocyte and ventricle detection in the mouse SSp region.

A Gene expression heatmap showing cell-type-specific expression of marker genes (8,252 vectors). Rows show z-scored gene expression and columns show the gene expression patterns of filtered local maxima vectors. The top annotation shows the cell types and coloring based on the best correlating segmentation-based cell-type signature from Codeluppi et al. The colors of the top annotation correspond to the cell type legend in Fig. 2B; B A t-SNE map of cell-type signatures with distinct expression. Cell-type clusters are visualized as a 2D t-SNE embedding of filtered local maxima vectors. Cell-type annotation and coloring are based on the best correlating segmentation-based cell-type signature from Codeluppi et al (Supplementary Fig. 4C, D). The cell-type legend is grouped by cell-type classes labels shown in the t-SNE plot, and is based on groupings by Codeluppi et al.; C The SSAM de novo cell-type map showing the spatial organization of the cell types signatures in the gene expression vector field. Inset shows a zoom-in of the highlighted tissue region. The colors of the cell types correspond to the cell-type legend in B; D SSAM improves the reconstruction of the ventricle. The upper left two panels show the DAPI and Poly-A signal around the ventricle area, showing tightly packed cells (occlusion) and lower signal in the ventricle structure compared to surrounding cells. The lower-left two panels show the KDE gene expression signature for Foxj1 (the marker for ependymal cells) and Ttr (the marker for choroid plexus cells). The bottom right two panels show the reconstructions of only the ependymal (yellow) and choroid plexus (teal) cell types by SSAM and Codeluppi et al.; E The far-left upper and lower panels show DAPI and Poly-A signals. The middle left upper and lower panels show the overlap of the Mfge8 signal with DAPI and Poly-A signals. The top right two panels show the cell-type signals for Mfge8 expressing astrocytes by SSAM and Codeluppi et al. The bottom right two panels show the overlay of the Mfge8 signal with the cell-type calls by SSAM and Codeluppi et al.