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Integration of lineage tracing with WAO-ExM revealed that cell number increases were driven by a few hepatocytes undergoing drastic clonal expansion at the whole-organ scale. Disruption of extracellular matrix laminins decoupled liver shaping from total cell number increases, suggesting independent regulatory control of tissue architecture and cell proliferation. We also utilized WAO-ExM to monitor diseased livers and other adult organs, including heart and pancreas. 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