A toolkit for mapping cell identities in relation to neighbours reveals Notch-dependent heterogeneity within neuromesodermal progenitor populations

Patterning of cell fates is central to embryonic development, tissue homeostasis, and disease. Quantitative analysis of patterning reveals the logic by which cell-cell interactions orchestrate changes in cell fate. However, it is challenging to quantify patterning when graded changes in identity occur over complex 4D trajectories, or where different cell states are intermingled. Furthermore, comparing patterns across multiple individual embryos, tissues, or organoids is difficult because these often vary in shape and size.

Here we present a toolkit of computational approaches to tackle these problems. These strategies are based on measuring properties of each cell in relation to the properties of its neighbours to quantify patterning, and on using embryonic landmarks in order to compare these patterns between embryos. We use this toolkit to characterise patterning of cell identities within the caudal lateral epiblast of E8.5 embryos, revealing local patterning in emergence of early mesoderm cells that is sensitive to inhibition of Notch activity.