Creating a stem cell state map from pluripotency through cardiomyocyte differentiation The Allen Institute for Cell Science is creating a dynamic visual model of cell organization from hiPSCs to differentiated cells with a collection of fluorescent-tagged clonal hiPSC lines. Our approach utilizes CRISPR/Cas9 to fluorescently tag proteins that localize to the major organelles of the cell. Live cell imaging, image analysis, modeling and visualization, and open distribution to the scientific community define our endeavor. To date we have generated fluorescently tagged hiPSC clonal lines for ~40 major cellular structures and performed key genetic, cell biological, and stem cell validation. We will demonstrate the utility of these cell lines for generating image-based integrated models of cell organization and dynamics. We will present imaging data demonstrating the epithelial organization of the undifferentiated hiPS cells, dynamics of major organelles during cell division and early mesoderm differentiation, and the organization of the sarcomere in hiPSC-derived cardiomyocytes. We will describe the use of these high-resolution, 3D live images for quantitative analysis and development of integrative cell models. We will also present our on-going work to develop a state space of structural and gene expression changes during differentiation using a multi-dimensional approach. This approach integrates quantitative image-based readouts of gene expression, transcript localization, and cellular organization co-measured in single cells and leads to a better understanding of cell behaviors and cell states. Our cell lines, plasmids, 3D images, various analysis and visualization tools, integrated cell models, and biological findings are available to the research community (www.allencell.org).