Appion: An integrated, database-driven pipeline to facilitate EM image processing

Gabriel C. Lander, Scott M. Stagg, Neil R. Voss, Anchi Cheng, Denis Fellmann, James Pulokas, Craig Yoshioka, Christopher Irving, Anke Mulder, Pick Wei Lau, Dmitry Lyumkis, Clinton S. Potter, Bridget Carragher

Research output: Contribution to journalArticlepeer-review

592 Scopus citations


The use of cryoEM and three-dimensional image reconstruction is becoming increasingly common. Our vision for this technique is to provide a straightforward manner in which users can proceed from raw data to a reliable 3D reconstruction through a pipeline that both facilitates management of the processing steps and makes the results at each step more transparent. Tightly integrated with a relational SQL database, Appion is a modular and transparent pipeline that extends existing software applications and procedures. The user manages and controls the software modules via web-based forms, and all results are similarly available using web-based viewers directly linked to the underlying database, enabling even naive users to quickly deduce the quality of their results. The Appion API was designed with the principle that applications should be compatible with a broad range of specimens and that libraries and routines are modular and extensible. Presented here is a description of the design and architecture of the working Appion pipeline prototype and some results of its use.

Original languageEnglish (US)
Pages (from-to)95-102
Number of pages8
JournalJournal of Structural Biology
Issue number1
StatePublished - Apr 2009
Externally publishedYes


  • 3D reconstruction
  • Automated CryoEM
  • Automation
  • CryoEM
  • CryoEM pipeline
  • EM
  • Image processing
  • Single particle analysis
  • TEM

ASJC Scopus subject areas

  • Structural Biology


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