An in-house developed python script automatically processed the MicroED data via three steps using available software: (1) the raw MicroED data in MRC format were automatically converted to SMV format using mrc2smv software (); (2) the converted data were processed in XDS and (3) data sets were merged using XSCALE. XDS used a few typical settings in input: the detector distance is not refined together with the unit cell refinement due to the flatness of the Ewald's sphere, DELPHI was set to 30°, maximum errors was set to 10 and 3 for spot and spindle respectively, and occasionally we used MINIMUM_FRACTION_OF_INDEXED_SPOTS equals 0.1 to include weak data. (See "XDS.INP template", Supplementary Information). The script evaluates different settings in XDS input for STRONG_PIXEL, SIGNAL_PIXEL, MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT, OFFSET, DATA_RANGE, SPOT_RANGE. The best merged data was found by evaluating all combinations of data sets to a certain maximal number of data sets included and the solutions were scored using statistics from XSCALE. The structures were solved using SHELXT and refined with SHELXL .