Deep manifold learning reveals hidden developmental dynamics of a human embryo model

Abstract

In this study, postimplantation human epiblast and amnion development are modeled using a stem cell–based embryoid system. A dataset of 3697 fluorescent images, along with tissue, cavity, and cell masks, is generated from experimental data. A computational pipeline analyzes morphological and marker expression features, revealing key developmental processes such as tissue growth, cavity expansion, and cell differentiation. To uncover hidden developmental dynamics, a deep manifold learning framework is introduced. This framework uses an autoencoder to project embryoid images into a twenty-dimensional (20D) latent space and models the dynamics using a mean-reverting stochastic process of mixed Gaussians. The approach accurately captures phenotypic changes observed at discrete experimental time points. Moreover, it enables the generation of artificial yet realistic embryoid images at finer temporal resolutions, providing deeper insights into the progression of early human development.