Beyond structure: spectroscopic imaging in cryogenic electron microscopy

Cryogenic electron microscopy (cryo-EM) has transformed structural biology by enabling near-atomic resolution imaging of macromolecules and the direct visualization of molecular architectures in native cellular environments. However, conventional cryo-EM, although outstanding at elucidating molecular density and morphology, provides little direct information about chemical composition or molecular state. Here, we review recent advances in scanning-based and spectroscopic electron microscopy that extend cryo-EM beyond phase contrast, including Z-contrast imaging, energy-dispersive X-ray spectroscopy, and electron energy-loss spectroscopy. We highlight how these techniques enable label-free mapping of elemental distributions and chemical states in beam-sensitive biological specimens, and we discuss emerging workflows that integrate spectroscopy with cryogenic sample preparation and correlative imaging. Together, these developments position spectroscopic cryo-EM as a powerful approach for linking structure, composition, and function across molecular and cellular scales.