Repository for the datasets, code, and images underlying figures in the manuscript "Combined expansion and STED microscopy reveals altered fingerprints of postsynaptic nanostructure across brain regions in ASD-related SHANK3-deficiency". The folder structure is organized according to associated figures: Figure_NHSE-EF (Figures 1/S1), Figure_SYNLOC (Figure 2/S2-S3), Figure_REGSHAPE-SH3SHAPE (Figure 3/S4-S8), Figure_SH3STED (Figure 4-5/S9-S14), Figure_S15. In each folder all images, which were used in the figures are also included.