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The files contain the numerical data of the figures of the article "Footprints of atomic-scale features in plasmonic nanoparticles as revealed by Electron Energy Loss Spectroscopy" published in Physical Chemistry Chemical Physics (doi.org/10.1039/D4CP01034E) and written by Mattin Urbieta, Marc Barbry, Peter Koval, Alberto Rivacoba, Daniel Sánchez-Portal, Javier Aizpurua, and Nerea Zabala. The data files are organized in different folders and subfolders corresponding to each of the figures in the paper.