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Convergent beam electron diffraction is routinely applied for studying deformation and local strain in thick crystals by matching the crystal structure to the observed intensity distributions. Recently, it has been demonstrated that CBED can be applied for imaging two-dimensional (2D) crystals where a direct reconstruction is possible and three-dimensional crystal deformations at a nanometre resolution can be retrieved. Here, we demonstrate that second-order effects allow for further information to be obtained regarding stacking arrang