Forum 09/04/2008

“Appion: an integrated, database-driven pipeline for lucid EM image processing”

Gabe Lander – The Department of Cell Biology, The Scripps Research Institute, La Jolla, CA
The use of cryo-EM and three-dimensional image reconstruction is becoming increasingly common. Our vision for this technique is to provide a straightforward manner in which, provided a suitable specimen, users can proceed from raw data to a reliable 3D reconstruction. Tightly integrated with a relational SQL database, Appion is a modular and transparent pipeline that makes use of existing software applications and procedures, guiding users through the data processing via web-based viewers. The ease of viewing the results of each procedure from a web-browser enables even naive users to quickly deduce the quality of their results. In addition to a generally directed method of reconstruction, we also wish to maintain Appion’s ability to integrate new routines, methods and software. Presented here is a working prototype of the APPION pipeline and some results of its use in the processing of the bacteriophage P22 infection machinery.