Automating 3DED data processing at eBIC

Three-dimensional electron diffraction (3DED) is an emerging and useful technique for solving molecular structures of small and biological macro-molecules from nanometre-sized crystals. We present our automated data processing workflow for 3DED datasets collected at Diamond Light Sources electron Bio-Imaging Centre (eBIC). For this purpose, we developed a package called AutoED. The processing pipeline includes data collection, analysis of the beam position, metadata gathering, file conversion, and finally data processing using xia2 (which supports both DIALS and XDS). The processing results are captured in a summary report produced by AutoED. Our main goal is to reduce the workload of electron diffraction scientists, but also to enforce good standards already used in macromolecular crystallography (MX). All the collected 3DED datasets are automatically converted into NeXus data format which is considered a Gold Standard for MX. This standardized data format allows for all the relevant metadata about the experiment to be kept together with diffraction images. We also discuss the methods used in AutoED to determine the electron beam position on diffraction images.