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Organelle structure has been studied and visualized for decades; however, publicly available databases that use improved high-throughput microscopy of gene-edited cell lines have recently revolutionized the amount and quality of information now available for use in undergraduate classes. This lesson demonstrates how the use of high-throughput (HT) microscopy has generated data describing organelle structure and variability. Students access, analyze, and evaluate cell structure images using the Allen Institute for Cell Science's Allen Cell Explorer. Students synthesize the information to make recommendations and propose a future experiment. Using web-based tools and a realistic scenario that merges antimicrobial drug screens with eukaryotic cell perturbations and structure, this case study provides a guided tour of the powerful applications of high-throughput microscopy.