Fig. 4: Cell Mapping across technologies and resolutions.

a Mapping of Stereo-seq mouse embryo cells onto seqFISH mouse embryo cells shows that Vesalius recovers expected tissue structures across technologies. b Alluvial plot demonstrating where each mapped cell type in the query (Stereo-seq) maps to in the reference (seqFISH). c Mapping VisiumHD mouse brain onto Visium mouse brain with the tissue territories detected by Vesalius in the reference, the query, as well as the mapped cells with a jitter added to the coordinates. We recover the overall structure of the mouse brain, including the Dentate gyrus and the Cornus Amonis fields (CA1 & CA2 – annotated on figure). d The mapped p-values after performing a Chi-squared test between cell type frequencies in Visium (after cell type deconvolution) and the mapped cell types taken from VisiumHD. A discretized p-value map shows that only a few spots exhibit a statistically different cell type frequency between spots and mapped cells (p-value < 0.05). e JI of mapped cell labels between Visium and VisiumHD. 50% of cells have a JI score above 0.32. The orange vertical line represents the 25th percentile. The light blue line represents the 50th percentile. The green line represents the 75th percentile. Source data are provided as a Source Data file.