Quantitative analysis of PSD nanoblock. (A) A schematic showing the measured 2D gray values in a 40-nm-thick PSD region beneath the postsynaptic membrane across consecutive virtual tomographic slices, which were combined to generate a gray value density map of the entire PSD region. (B) 3D density analysis of the synaptosome PSD region. Top panel: Density plot shows gray values of 40-nm-thick PSD density combined from multiple tomographic slices. Bottom panel: DBSCAN clustering result of 40-nm-thick PSD density projected onto the xz plane. Scale bars: 50 nm. (C) A schematic showing the clustering results of PSD densities produced from 3D synaptosome data. (D) Examples of PSD nanoblocks in 2D tomographic slices and corresponding projected DBSCAN clustering results. Values in each panel indicate the width (nm) of the PSD block. Blue dash lines in DBSCAN clusters indicate the corresponding planes of tomographic slices. Scale bars: 20 nm. (E) Distribution of PSD nanoblock area, width, centroid-to-centroid distance, and edge-to-edge distance of synaptosome, synaptoneurosome, and intact synapse.