Mantis: high-throughput 4D imaging and analysis of the molecular and physical architecture of cells.

High-throughput dynamic imaging of cells and organelles is important for parsing complex cellular responses. We report a high-throughput 4D microscope, named Mantis, that combines two complementary, gentle, live-imaging technologies: remote-refocus label-free microscopy and oblique light-sheet fluorescence microscopy. We also report open-source software for automated acquisition, registration, and reconstruction, and virtual staining software for single-cell segmentation and phenotyping. Mantis enabled high-content correlative imaging of molecular components and the physical architecture of 20 cell lines every 15 minutes over 7.5 hours, and also detailed measurements of the impacts of viral infection on the architecture of host cells and host proteins. The Mantis platform can enable high-throughput profiling of intracellular dynamics, long-term imaging and analysis of cellular responses to stress, and live cell optical screens to dissect gene regulatory networks.