We have made available for download a set of fluctuation electron microscopy data analysis routines for electron nanodiffraction patterns written in MATLAB. Right now, the routines only calculate the variance of annular averages, and they only work for data files in the SER file format created by the TIA software on FEI electron microscopes. The routines implement TEM sample thickness filtering based on an ADF image acquired simultaneously with the nanodiffraction patterns, as described in Jinwoo’s paper. Bug fixes, modifications, and improvements are welcome!