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We demonstrate tomographic reconstruction of the phase space distribution of atoms oscillating in a harmonic trap with weak potential corrugation caused by nanoscale imperfections in an atom chip. We find that deformations in these distributions are highly sensitive to anharmonic components of the potential. They are explained in terms of angular velocity dispersion of isoenergetic phase space trajectories. We show that the method is applicable for probing classical and quantum dynamics of cold atoms, and we note its importance for future technological applications.

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