Machine learning-assisted imaging analysis of a human epiblast model

Abstract

The human embryo is a complex structure that emerges and develops as a result of cell-level decisions guided by both intrinsic genetic programs and cell–cell interactions. Given limited accessibility and associated ethical constraints of human embryonic tissue samples, researchers have turned to the use of human stem cells to generate embryo models to study specific embryogenic developmental steps. However, to study complex self-organizing developmental events using embryo models, there is a need for computational and imaging tools for detailed characterization of cell-level dynamics at the single cell level. In this work, we obtained live cell imaging data from a human pluripotent stem cell (hPSC)-based epiblast model that can recapitulate the lumenal epiblast cyst formation soon after implantation of the human blastocyst. By processing imaging data with a Python pipeline that incorporates both cell tracking and event recognition with the use of a CNN-LSTM machine learning model, we obtained detailed temporal information of changes in cell state and neighborhood during the dynamic growth and morphogenesis of lumenal hPSC cysts. The use of this tool combined with reporter lines for cell types of interest will drive future mechanistic studies of hPSC fate specification in embryo models and will advance our understanding of how cell-level decisions lead to global organization and emergent phenomena. Insight, innovation, integration: Human pluripotent stem cells (hPSCs) have been successfully used to model and understand cellular events that take place during human embryogenesis. Understanding how cell–cell and cell–environment interactions guide cell actions within a hPSC-based embryo model is a key step in elucidating the mechanisms driving system-level embryonic patterning and growth. In this work, we present a robust video analysis pipeline that incorporates the use of machine learning methods to fully characterize the process of hPSC self-organization into lumenal cysts to mimic the lumenal epiblast cyst formation soon after implantation of the human blastocyst. This pipeline will be a useful tool for understanding cellular mechanisms underlying key embryogenic events in embryo models.

Derivation of human primordial germ cell-like cells in an embryonic-like culture

“…To corroborate this, we conducted live imaging and lineage tracing for the first 3 days of Gel-3D cultures (see “Methods”). In order to track individual cells, live-cell videos were analyzed using a CNN (convolutional neural network)-LSTM (long short-term memory) machine learning classifier [CNN-LSTM] 20 . The hPGCLC or non-hPGCLC identity of cells in Gel-3D cultures at t = 70 h was ascertained by immunostaining for hPGCLC markers TFAP2C and SOX17.…”

“…Live cell video analysis was conducted with a Python pipeline developed by Resto-Irizarry et al 20 . In brief, individual cells in a time point were identified after (1) contrast enhancement, (2) thresholding, and (3) cell cluster segmentation.…”