Direct observation of Cu in Cu-chabazite (CHA) zeolite has been achieved by electron ptychography using the Wigner distribution deconvolution. The imaging properties of ptychographically reconstructed images were evaluated by comparing the intensities of six-membered-ring columns of the zeolite with and without Cu using simulated ptychography images. It was concluded that although false contrast may appear at Cu-free columns for some acquisition conditions, ptychography can discriminate columns with and without Cu. Experimental observation of CHA with and without Cu was performed. Images obtained from the Cu-containing sample showed contrast at the six-membered-rings, while no contrast was observed for the Cu-free sample. The results show that ptychography is a promising technique for visualizing the atomic structures of beam-sensitive materials.