Direct visualization of electronic-structure symmetry within each crystalline unit cell is a new technique for complex electronic matter research (Lawler et al 2010 Nature 466 347-51, Schmidt et al 2011 New J. Phys. 13 065014, Fujita K et al 2012 J. Phys. Soc. Japan 81 011005). By studying the Bragg peaks in Fourier transforms of electronic structure images and particularly by resolving both the real and imaginary components of the Bragg amplitudes, distinct types of intra-unit-cell symmetry breaking can be studied. However, establishing the precise symmetry point of each unit cell in real space is crucial in defining the phase for such a Bragg-peak Fourier analysis. Exemplary of this challenge is the high-temperature superconductor Bi 2Sr 2CaCu 2O 8+δ for which the surface Bi atom locations are observable, while it is the invisible Cu atoms that define the relevant CuO 2 unit-cell symmetry point. Here we demonstrate, by imaging with picometer precision the electronic impurity states at individual Zn atoms substituted at Cu sites, that the phase established using the Bi lattice produces a ∼2%(2π) error relative to the actual Cu lattice. Such a phase assignment error would not diminish reliability in the determination of intra-unit-cell rotational symmetry breaking at the CuO 2 plane (Lawler et al 2010 Nature 466 347-51, Schmidt et al 2011 New J. Phys. 13 065014, Fujita K et al 2012 J. Phys. Soc. Japan 81 011005). Moreover, this type of impurity atom substitution at the relevant symmetry site can be of general utility in phase determination for the Bragg-peak Fourier analysis of intra-unit-cell symmetry. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.