Sladitschek, H. L. et al. Cell 181, 922–935 (2020).

Single-cell RNA sequencing (scRNA-seq) has become a valuable tool for revealing transcriptomic patterns during embryonic development. Yet it is still not an easy task to map single-cell expression profiles onto spatial organization in a developing embryo. Sladitschek et al. examine the optically transparent embryo of Phallusia mammillata, a marine tunicate that recapitulates the embryonic cell diversity of a vertebrate. The researchers describe a scRNA-seq computational framework for identifying cell types and inferring the lineage history of each cell within the embryo. In addition, they use multiview light-sheet microscopy to image the whole embryo and capture the morphology and physical position of each cell, as well as its developmental evolution in the embryo. The integration of scRNA-seq and imaging data yields a digital embryo with spatiotemporally resolved transcriptomic and morphological profiles at single-cell resolution.