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Scipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED data.

Viktor E G Bengtsson1, Laura Pacoste1, José Miguel de la Rosa-Trevin2

  • 1Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden.

Journal of Applied Crystallography
|June 20, 2022
PubMed
Summary
This summary is machine-generated.

Scipion-ED offers a graphical interface for processing 3D electron diffraction (3D ED) and MicroED data, simplifying complex terminal-based workflows. This tool facilitates data merging strategies, improving the resolution of structural features in electrostatic potential maps.

Keywords:
3D EDMicroEDcomputer programsdata processingelectron diffraction

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Area of Science:

  • Crystallography and Structural Biology
  • Electron Microscopy and Diffraction

Background:

  • Three-dimensional electron diffraction (3D ED) and microcrystal electron diffraction (MicroED) are increasingly utilized techniques.
  • Current data processing for 3D ED/MicroED often relies on command-line interfaces or scripting, posing a barrier for some researchers.
  • A need exists for user-friendly software to streamline the analysis of 3D ED/MicroED data.

Purpose of the Study:

  • To introduce Scipion-ED, a novel graphical user interface (GUI) and framework for processing 3D ED/MicroED data.
  • To demonstrate the utility of Scipion-ED by processing experimental data of tetragonal lysozyme.
  • To compare different data merging strategies for their effectiveness in resolving structural features.

Main Methods:

  • Development and implementation of the Scipion-ED software with an extendable framework.
  • Processing of multiple 3D ED/MicroED datasets from tetragonal lysozyme using Scipion-ED.
  • Integration and utilization of the DIALS software package within the Scipion-ED GUI.
  • Comparative analysis of three data merging strategies to assess their impact on electrostatic potential maps.

Main Results:

  • Scipion-ED successfully provided a GUI for processing 3D ED/MicroED data, simplifying the workflow.
  • The processing of lysozyme datasets demonstrated the practical application of Scipion-ED and DIALS.
  • Comparison of merging strategies revealed differences in the ability to resolve unmodelled features in the electrostatic potential map.

Conclusions:

  • Scipion-ED offers an accessible and efficient platform for 3D ED/MicroED data analysis.
  • The software framework supports various data processing strategies, including different merging approaches.
  • Scipion-ED facilitates advanced structural analysis by enabling detailed comparison of data processing outcomes.