Appion Main Page¶

Overview¶

Appion is a "pipeline" for semi-automated three-dimensional electron microscopy starting from raw images to complete three-dimensional models.

It consists of a web based user interface linked to a set of python scripts that control several underlying processing packages. These include EMAN, Spider, findem, ACE, and Chimera. All data input and output is managed by MySQL databases. The ultimate goal is to have all control of the processing pipeline managed from the web based user interface and all output from the processing presented using web based viewing tools. These notes are provided as a rough guide to using the pipeline but are not guaranteed to be up to date or accurate.

View an overview of the Appion code base found in the "myami" repository.

Software Availability and Licensing Information¶

Appion is released under the Apache License, Version 2.0

Software Installation:¶

see Complete Appion Installation

User Guide:¶

see Appion User Guide

Publications:¶

Primary Publication to Cite:¶

• Lander, G.C.; Stagg, S.M., Voss, N.R., Cheng, A., Fellmann, D., Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P.W., et al. (2009). "Appion: an integrated, database-driven pipeline to facilitate EM image processing.". Journal of Structural Biology 166: 95-102. PMID 19263523.

Additional References:¶

• Voss, N.R.; Lyumkis D, Cheng A, Lau PW, Mulder A, Lander GC, et al. (2010). "A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.". Journal of Structural Biology 169 (3): 389-98. PMID 20018246.

Contact information:¶

appion@scripps.edu

Youtube videos:¶

• An Introduction to Appion
• TiltPicker Demonstration

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