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The ability to manipulate particles has always been a fundamental aspect for developing and improving scattering and microscopy techniques used for material investigations. So far, microscopy applications have mostly relied on a classical treatment of the electron-matter interaction. However, exploiting a particle's quantum nature can reveal novel information not accessible with conventional schemes. Here, after describing recent methods for coherent wave function engineering, we discuss how quantum manipulation of electrons, He ions, and nuclei can be used to implement low-dose imaging methods, to explore correlated quantum state dynamics in condensed matter, and to modulate nuclear reactions for energy-related applications and gamma-ray lasers.