Collecting large datasets of rotational electron diffraction with ParallEM and SerialEM

Kiyofumi Takaba, Saori Maki-Yonekura, Koji Yonekura

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15 Citations (Scopus)


A semi-automated protocol has been developed for rotational data collection of electron diffraction patterns by combined use of SerialEM and ParallEM, where SerialEM is used for positioning of sample crystals and ParallEM for rotational data collection. ParallEM calls standard camera control software through an AutoIt script, which adapts to software operational changes and to new GUI programs guiding other cameras. Development included periodic flashing and pausing of data collection during overnight or day-long recording with a cold field-emission beam. The protocol proved to be efficient and accurate in data collection of large-scale rotational series from two JEOL electron microscopes, a general-purpose JEM-2100 and a high-end CRYO ARM 300. Efficiency resulted from simpler steps and task specialization. It is possible to collect 12–20 rotational series from ~−68° to ~68° at a rotation speed of 1°/s in one hour without human supervision.

Original languageEnglish
Article number107549
JournalJournal of Structural Biology
Issue number2
Publication statusPublished - 2020 Aug 1


  • 3D ED/MicroED
  • Automated data collection
  • Electron 3D crystallography
  • Electron diffraction
  • ParallEM


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