The cuboctahedron_3D_clustering_and_alignment.m is a matlab file that will do the 3D clustering, template alignment and decoding for 3D DNA origami cuboctahedron picks.

To run the code, download cuboctahedron_3D_clustering_and_alignment.m and the HDF5 file of 0(1)_cuboctahedron_DNA-PAINT.hdf5 and 0(1)_cuboctahedron_DNA-PAINT.yaml. Place them in the same folder. Then open the .m file. Run in Matlab. The code has been tested with Matlab R2022a and R2019 with phased_array_system_toolbox, signal_blocks, signal_toolbox and statistics_toolbox installed. The output files are also provided (Output.rar) which can be downloaded from https://bit.ly/output_cuboctahedron. The result is presented in Figure 5D and 5E.

The cuboctahedron_3D_clustering_and_alignment.m code runs the 0(1)_cuboctahedron_DNA-PAINT.hdf5 that contains 210 picks within 38 minutes on an Alienware Desktop Computer with an Intel Core i7-6800K CPU, 32 GB RAM, and NVIDIA GeForce GTX 1080 graphics card. The code should also run in normal desktop with expected longer time than mentioned above. No additional non-standard hardware is required.