Interrogating fundamental cell biology principles that govern tissue
morphogenesis is critical to better understanding of developmental biology and
engineering novel multicellular systems. Recently, functional micro-tissues
derived from pluripotent embryonic stem cell (ESC) aggregates have provided
novel platforms for experimental investigation; however elucidating the factors
directing emergent spatial phenotypic patterns remains a significant challenge.
Computational modelling techniques offer a unique complementary approach to
probe mechanisms regulating morphogenic processes and provide a wealth of
spatio-temporal data, but quantitative analysis of simulations and comparison to
experimental data is extremely difficult. Quantitative descriptions of spatial
phenomena across multiple systems and scales would enable unprecedented
comparisons of computational simulations with experimental systems, thereby
leveraging the inherent power of computational methods to interrogate the
mechanisms governing emergent properties of multicellular biology. To address
these challenges, we developed a portable pattern recognition pipeline
consisting of: the conversion of cellular images into networks, extraction of
novel features via network analysis, and generation of morphogenic trajectories.
This novel methodology enabled the quantitative description of morphogenic
pattern trajectories that could be compared across diverse systems:
computational modelling of multicellular structures, differentiation of stem
cell aggregates, and gastrulation of cichlid fish. Moreover, this method
identified novel spatio-temporal features associated with different stages of
embryo gastrulation, and elucidated a complex paracrine mechanism capable of
explaining spatiotemporal pattern kinetic differences in ESC aggregates of
different sizes.