The properties of nanoparticles are known to critically depend on their local chemistry but characterizing three-dimensional (3D) elemental segregation at the nanometer scale is highly challenging. Scanning transmission electron microscope (STEM) tomographic imaging is one of the few techniques able to measure local chemistry for inorganic nanoparticles but conventional methodologies often fail due to the high electron dose imparted. Here, we demonstrate realization of a new spectroscopic single particle reconstruction approach built on a method developed by structural biologists. We apply this technique to the imaging of PtNi nanocatalysts and find new evidence of a complex inhomogeneous alloying with a Pt-rich core, a Ni-rich hollow octahedral intermediate shell and a Pt-rich rhombic dodecahedral skeleton framework with less Pt at ⟨100⟩ vertices. The ability to gain evidence of local surface enrichment that varies with the crystallographic orientation of facets and vertices is expected to provide significant insight toward the development of nanoparticles for sensing, medical imaging, and catalysis.