biostudies-literatureWang LH2020 Marie Sklodowska-Curie ActionsVetenskapsraådetKnut och Alice Wallenbergs StiftelseCancerfonden105-115https://www.ebi.ac.uk/biostudies/studies/S-EPMC12809502biostudies-literatureUnknown13(Pt 1)Three-dimensional electron diffraction (3D ED), also known as microcrystal electron diffraction (microED), is an emerging method for determining structures from submicron-sized crystals. With the development of rapid and convenient data collection protocols, acquiring dozens of datasets in a single 3D ED/microED session has become routine. A fast and automated workflow for processing, scaling and merging a large number of 3D ED/microED datasets can significantly accelerate the structure determination process. Herein, we present an XDS-based pipeline with a graphical user interface for automated real-time and offline batch 3D ED/microED data processing (AutoLEI). We demonstrate the functionality and applications of the pipeline through four examples, using both offline and real-time data processing capabilities. The samples include small organic molecules, metal-organic frameworks (MOFs) and proteins, showcasing the versatility and efficiency of AutoLEI in various applications.IUCrJAutoLEI: An XDS-based pipeline with graphical user interface for automated real-time and offline batch 3D ED/microED data processing.PMC128095022019.012424-3848-Pj2022-035962022-036812019-00815956099Zou XHofer GStenmark PHutchinson ESChen YXu HWang LfalseAutoLEI: An XDS-based pipeline with graphical user interface for automated real-time and offline batch 3D ED/microED data processing.Three-dimensional electron diffraction (3D ED), also known as microcrystal electron diffraction (microED), is an emerging method for determining structures from submicron-sized crystals. With the development of rapid and convenient data collection protocols, acquiring dozens of datasets in a single 3D ED/microED session has become routine. A fast and automated workflow for processing, scaling and merging a large number of 3D ED/microED datasets can significantly accelerate the structure determination process. Herein, we present an XDS-based pipeline with a graphical user interface for automated real-time and offline batch 3D ED/microED data processing (AutoLEI). We demonstrate the functionality and applications of the pipeline through four examples, using both offline and real-time data processing capabilities. The samples include small organic molecules, metal-organic frameworks (MOFs) and proteins, showcasing the versatility and efficiency of AutoLEI in various applications.2026-01-01T00:00:00Z2026 Jan2026-06-06T16:05:51.486Z2026-06-02T03:12:17.203ZS-EPMC128095024143144310.1107/S2052252525010784