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Although atom probe tomography (APT) reconstructions do not directly influence the local elemental analysis, any structural inferences from APT volumes demand a reliable reconstruction of the point cloud. Accurate estimation of the reconstruction parameters is crucial to obtain reliable spatial scaling. In the current work, a new automated approach of calibrating atom probe reconstructions is developed using only one correlative projection electron microscopy (EM) image. We employed an algorithm that implements a 2D cross-correlation of microstructural features observed in both the APT reconstructions and the corresponding EM image. We apply this protocol to calibrate reconstructions in a Cu(In,Ga)Se2-based semiconductor and in a Co-based superalloy. This work enables us to couple chemical precision to structural information with relative ease.