Polytope: High-resolution epitope barcoding for in vivo spatial fate-mapping

Tracing the fate of individual cells and their progeny remains a challenging task. While imaging-based fate-mapping provides spatial information, it generally lacks complexity due to limited label diversity, resulting in diminished capture of comprehensive lineages and fate maps. Here, we introduce Polytope, an epitope barcoding system capable of generating up to 512 unique color codes. Comprising nine epitope tag cassettes flanked by loxP sites, Polytope allows random excision via Cre recombinase, creating unique color codes detectable through multiplexed imaging. Using an engineered Polytope mouse, we traced the fate of hundreds of clones across tissues in vivo, from embryonic development until adulthood. Together, Polytope enables high-resolution imaging-based fate-mapping through endogenous epitope barcoding, comprehensively capturing the spatial organization of complex clonal dynamics in situ. One-Sentence SummaryPolytope is an imaging-based barcoding system to trace lineages at clonal and spatial resolution in living organisms using a diverse set of color-coded markers.