Fig. 5. Discovery of age-related spatial domains.

A MENDER-UMAP of the MERFISH aging dataset, colored by the expert annotation from the original publication (left) and MENDER results (right). B The ARI and NMI before and after MENDER sub-clustering. Each point is a slice (the number of slices in total is 31). The green line indicates improved performance after sub-clustering and the orange line indicates decreased performance after sub-clustering. The original annotation and MENDER’s annotation were plotted on the three stages, 4 weeks (C), 24 weeks (D), and 20 months (E), respectively. The aging stage labels are annotated on the MENDER-UMAP plot both on a single plot (F) and separately (G). H The stage distribution across different domains from the original annotation (top) and MENDER (bottom), respectively. I The domain distribution across different slices from 4-week-old mice. J Spatial distribution of MENDER-annotated domains across different aging stages. Different colors indicate different spatial domains. K The spatial signature analysis of MENDER-annotated domains across slices from all aging stages. Each row is a feature of MENDER-computed context representation. The cell states are indicated by different colors, and the ranges are indicated by the number beside the cell state label. Each column shows the spatial signature of an identified domain. The values of the context representation matrix are reflected by the size and colors of the dots. Source data are provided as a Source Data file.