Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

J Struct Biol. 2016 Jul;195(1):93-9. doi: 10.1016/j.jsb.2016.04.010. Epub 2016 Apr 20.


In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. One of the central players in this wide-reaching change is the continuous development of image processing software. Here we present Scipion, a software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. Scipion is an open-source project that can be downloaded from

Keywords: Electron microscopy; Image processing; Reproducibility; Single particle analysis; Software package; Workflows.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Image Processing, Computer-Assisted / methods*
  • Imaging, Three-Dimensional / instrumentation*
  • Imaging, Three-Dimensional / methods
  • Microscopy, Electron / methods*
  • Reproducibility of Results
  • Workflow