Abstract

Highly multiplexed imaging assays allow simultaneous quantification of multiple protein and phosphorylation markers, providing a static snapshots of cell types and states. Pseudo-time techniques can transform these static snapshots of unsynchronized cells into dynamic trajectories, enabling the study of dynamic processes such as development trajectories and the cell cycle. Such ordering also enables training of mathematical models on these data, but technical challenges have hitherto made it difficult to integrate multiple experimental conditions, limiting the predictive power and insights these models can generate. In this work, we propose data processing and model training approaches for integrating multiplexed, multi-condition immunofluorescence data with mathematical modelling. We devise training strategies for mathematical models that are applicable to datasets where cells exhibit oscillatory as well as arrested dynamics and use them to train a cell cycle model on a dataset of MCF-10A mammary epithelial cells exposed to cell-cycle arresting small molecules. We validate the model by investigating predicted growth factor sensitivities and responses to inhibitors of cells at different initial conditions. We anticipate that our framework will generalise to other highly multiplexed measurement techniques such as mass-cytometry, rendering larger bodies of data accessible to dynamic modelling and paving the way to deeper biological insights. ©: © 2025 Cortés-Ríos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.