We report direct evidence of Fano resonances in atomic-resolution imaging of a crystalline material using a focused electron beam. Spectroscopic images of DyScO3 that are derived from the Fano resonance in the Dy-N4,5 spectrum can exhibit unexpected atomic-scale contrast, markedly different to non-resonant images. These effects are explained by our theoretical calculations of the inelastic and elastic scattering, and show excellent agreement with the experimental data. The results have significant implications for spectroscopic imaging of rare-earth elements at the atomic scale.