QuantumProbe will devise a novel microscope to probe and fully control the intriguing properties of quantum systems, formed by neutral atoms trapped in optical lattices. This includes in particular the possibility of in-depth quantum state characterization as well as engineering arbitrary quantum correlations. The microscope’s achievements will go far beyond standard state-of-the-art detection and manipulation capabilities in both, top-down approaches using large quantum gas systems, and bottom-up approaches with single particles.For this purpose, single or few well controlled neutral atoms will be immersed as “quantum-probes” into a quantum target system, a Mott-insulating state of another atomic species. Hence, QuantumProbe extends the concept of scanning microscopy to a single atom based coherent microscope, capable of parallel multi-tip operation with more than one probe atom. The fundamental measurement mechanism of this microscope is the entanglement between probe and target atoms, induced by coherent inter-species interaction, and subsequent detection of the probe atom’s state. QuantumProbe will thereby enable local, quantum non-demolition measurements of atom number or spin state as well as local, coherent manipulations such as spin flips and controlled-NOT quantum gates within the Mott-insulator.QuantumProbe will pave the way for break-throughs in various fields of research and practice: It will introduce local, fundamental quantum gates in scalable many-body systems, highly relevant for implementations of quantum information processing and quantum computing strategies; help elucidating the classification and quantification of multi-particle entanglement, which is even theoretically not fully clear; allow local coherent spin state engineering and read-out, opening the route for studies of quantum magnetism and related quantum simulations with single atom resolution; and devise tools for the studies of impurity physics in a well controlled environment.