Microstructure characterization has become indispensable to the study of complex materials, such as strongly correlated oxides, and can obtain useful information about the origin of their physical properties. Although atomically resolved measurements have long been possible, an important goal in microstructure characterization is to achieve element-selective imaging at atomic resolution. A combination of scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS)1, 2 is a promising technique for atomic-column analysis. However, two-dimensional analysis has not yet been performed owing to several difficulties, such as delocalization in inelastic scattering or instrumentation instabilities. Here we demonstrate atomic-column imaging of a crystal specimen using localized inelastic scattering and a stabilized scanning transmission electron microscope3. The atomic columns of La, Mn and O in the layered manganite La1.2Sr1.8Mn2O7 are visualized as two-dimensional images.