X-ray spectroscopy has nanometer spa-tial resolution,long penetration depth and excellent elemental specificity.The power of synchrotron-based X-ray mi-croscopy(XRM)has been demonstrated in assessing the structure and function of cells at the subcellular level[1].How-ever,currently available contrast agents or probes for XRM,such as metal or semi-conductor nanoparticles,generally lack specificity and biocompatibility and thus limit its utility[2].Newly developed ge-netic tags for electron microscopy(EM)provide EM contrast in cellular com-partments in situ and enable intracellu-lar specific protein imaging and spatially resolved proteomic mapping[3,4],but use of EM for whole cell imaging remains challenging because of low penetration capability.