Point cloud surface fitting, skeletons, and φ simulations. (A) Example of a point cloud of Sec61β. (B) Point cloud in A and a surface generated from that point cloud. (C) The surface alone. The surface is composed of triangles, which are joined by shared edges. We refer to the points where multiple edges meet as vertices and use their locations to calculate the local density of Rtn4. (A–C) Scale bars represent 50 nm. (D) Two-color 3D SMLM data of Rtn4 (green), Sec61β (magenta), and a 3D surface based on the Sec61β point cloud (cyan). (E) As in D but with the 3D surface removed and the skeleton (white) added. (F) Skeleton (white) is shown with data simulated randomly in circular rings (red) around it. (D–F) Scale bars represent 1 μm.