Imaging is central to gaining microscopic insight into physical systems, and new microscopy methods have always led to the discovery of new phenomena and a deeper understanding of them. Ultracold atoms in optical lattices provide a quantum simulation platform, featuring a variety of advanced detection tools including direct optical imaging while pinning the atoms in the lattice1,2. However, this approach suffers from the diffraction limit, high optical density and small depth of focus, limiting it to two-dimensional (2D) systems. Here we introduce an imaging approach where matter wave optics magnifies the density distribution before optical imaging, allowing 2D sub-lattice-spacing resolution in three-dimensional (3D) systems. By combining the site-resolved imaging with magnetic resonance techniques for local addressing of individual lattice sites, we demonstrate full accessibility to 2D local information and manipulation in 3D systems. We employ the high-resolution images for precision thermodynamics of Bose–Einstein condensates in optical lattices as well as studies of thermalization dynamics driven by thermal hopping. The sub-lattice resolution is demonstrated via quench dynamics within the lattice sites. The method opens the path for spatially resolved studies of new quantum many-body regimes, including exotic lattice geometries or sub-wavelength lattices3–6, and paves the way for single-atom-resolved imaging of atomic species, where efficient laser cooling or deep optical traps are not available, but which substantially enrich the toolbox of quantum simulation of many-body systems.

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Ultracold atoms in optical lattices are pristine model systems with a tunability and flexibility that goes beyond solid-state analogies, e.g., dynamical lattice-geometry changes allow tuning a graphene lattice into a boron-nitride lattice. However, a fast modulation of the lattice geometry remains intrinsically difficult. Here we introduce a multi-frequency lattice for fast and flexible lattice-geometry control and demonstrate it for a three-beam lattice, realizing the full dynamical tunability between honeycomb lattice, boron-nitride lattice and triangular lattice. At the same time, the scheme ensures intrinsically high stability of the lattice geometry. We introduce the concept of a geometry phase as the parameter that fully controls the geometry and observe its signature as a staggered flux in a momentum space lattice. Tuning the geometry phase allows to dynamically control the sublattice offset in the boron-nitride lattice. We use a fast sweep of the offset to transfer atoms into higher Bloch bands, and perform a new type of Bloch band spectroscopy by modulating the sublattice offset. Finally, we generalize the geometry phase concept and the multi-frequency lattice to three-dimensional optical lattices and quasi-periodic potentials. This scheme will allow further applications such as novel Floquet and quench protocols to create and probe, e.g., topological properties.