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Quantum gases in optical lattices offer an opportunity to experimentally realize and explore condensed matter models in a clean, tunable system. We used single atom–single lattice site imaging to investigate the Bose-Hubbard model on a microscopic level. Our technique enables space- and time-resolved characterization of the number statistics across the superfluid–Mott insulator quantum phase transition. Site-resolved probing of fluctuations provides us with a sensitive local thermometer, allows us to identify microscopic heterostructures of low-entropy Mott domains, and enables us to measure local quantum dynamics, revealing surprisingly fast transition time scales. Our results may serve as a benchmark for theoretical studies of quantum dynamics, and may guide the engineering of low-entropy phases in a lattice.