Fig. 5: Cell Mapping across time.

a Mapping Stereo-seq Axolotl brain regeneration datasets (ARTISTA) at 15 days post injury (DPI) to 20DPI using cell, niche, and territory similarity. Blue circle highlights ependymoglial cells and their transition to regenerative intermediate progenitor cells. b Integrated tissue territories of mapped cells and reference cells where tissue territories are recovered using a shared latent space. For visualization purposes, we separate both samples. c Two differentially expressed genes (two-sided Wilcoxon rank sum test – p-value < 0.05 – FDR adjusted) at the zone of injury (territory 8 – dark blue): AMEX60DD048805 and AMEX60DD022398 show expression patterns limited to a small subset of cells involved in cell differentiation and proliferation necessary for wound healing. d Mapping Stereo-seq Mouse embryo (MOSTA) development at stage E11.5 to stage E12.5 using cell, niche, and territory similarity. e Clustering of query brain cells mapped onto the reference brain cells. Brain cells are demarcated into sub-territories, including cells that lie at the interface between brain regions (cluster 2) and the interface between the brain and other tissues (clusters 4). f Differential gene expression (two-sided Wilcoxon rank sum test – p-value < 0.05 – FDR adjusted) between clusters exemplified by Hes5, Stnm2, and Cancng4 as genes highlighting the different spatial sub-structures present in the mouse brain and the accurate mapping of gene expression patterns across time. gCrabp1 – a gene involved in the regulation of stem cell differentiation – shows a spatial-temporal decoupling behavior where the expression shows a spatial demarcation at the earlier developmental stage (E11.5), which is then extinguished at the following developmental stage. Source data are provided as a Source Data file.