The electron beam propagation (channelling) simulation, HAADF-STEM image simulation, dose rate calculation scripts and plotting scripts used for data analysis are publicly available at GitHub (https://github.com/KleinAtomLab/Mesoscale-atomic-engineering). The DFT and GW calculations were performed using established community software packages that are not publicly redistributable in their modified form. All relevant computational parameters, input settings and methodological details required to reproduce these calculations are provided in the Methods and the Supplementary Information. The quantitative analysis procedures for the ALO approach are described in detail in the Supplementary Information and ref. 53. A comprehensive discussion of the SLO algorithm and its positioning precision will be presented in a dedicated follow-up study. At the time of publication, the code underlying this work, specifically the custom software developed by the authors for beam positioning, lattice walking without lattice jumps, directional scanning and the automated experimental workflow used in this study, is not available for peer review or public release because of ongoing intellectual property protection and provisional patent filings. The algorithms and implementations are considered proprietary and are subject to confidentiality constraints at this stage. J.K. and F.M.R. acknowledge support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division...