Single-cell RNA-seq, with its capability to align cells of continuously changed status by pseudo-time reconstruction, has greatly revolutionized the understanding of cell fate transition during embryo development (Shapiro et al., 2013; Hoppe et al., 2014). While there is still a lack of single-cell spatial analysis, with the spatial variance contributing to the cell alignment, pseudo-space analysis might be conducted and the cell organization could be inferred as well (Cheng et al., 2019; Nowotschin et al., 2019). However, rather than revealing spatial or developmental trajectory by computational reconstruction, transcriptomic analysis of real time and space provides an authentic benchmark for dissecting the cell organization, molecular architecture, and lineage allocation. The ability to discern spatial gene expression differences in complex biological systems is critical to our understanding of developmental biology and the progression of disease.
