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Supported Applications

Appion

  • Description

    a "pipeline" for processing and analysis of EM images. Appion consists of a web-based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output within Appion is managed using tightly integrated SQL databases.

  • Usage Notes

    Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images or particle stacks using a set of provided tools.

  • Primary Citation*

    G. Lander, S. Stagg, N. Voss, A. Cheng, D. Fellmann, J. Pulokas, C. Yoshioka, C. Irving, A. Mulder, P. Lau, D. Lyumkis, C. Potter, and B. Carragher. 2009. Appion: an integrated, database-driven pipeline to facilitate EM image processing. Journal of Structural Biology. 166(1): 95-102.


    • *Full citation information available through

  • Tales

    Pipeline Dreams

    Pipeline Dreams

    A year ago, Bridget Carragher and Clint Potter’s group broke the so-called three-angstrom barrier for electron microscopy (EM). Prior to their work, so many structures had been solved using EM at 3.4 or 3.5-angstrom resolution that people had started to believe higher resolutions were out of reach with the technology.

    "Our group set out to show that EM could do better,” says Carragher, co-Director of the Simons Electron Microscopy Center (SEMC) at the New York Structural Biology Center (NYSBC). “We did things carefully and in a fully automated fashion and got to 2.8 angstroms. That was the first time anyone was able to see water molecules in an EM structure."


    Water molecules from an EM structure. Campbell MG, Veesler D, Cheng A, Potter CS ...

    Read More.
  • Keywords

    Computational Chemistry

  • Default Versions

    Linux 64:  2.2
    OS X INTEL:  2.2

  • Other Available Versions

      Linux 64:

      2.1.3
    • OS X INTEL:

      2.1.3
  • Developers

    Bridget Carragher, Clint Potter.

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