title: Appion: an integrated, database-driven pipeline to facilitate EM image processing.
abstract: 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.
authors.affiliation: National Resource for Automated Molecular Microscopy, The Scripps Research Institute, CB 129, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA.
authors.forename: Gabriel C
authors.initials: GC
authors.lastname: Lander
authors.forename: Scott M
authors.initials: SM
authors.lastname: Stagg
authors.forename: Neil R
authors.initials: NR
authors.lastname: Voss
authors.forename: Anchi
authors.initials: A
authors.lastname: Cheng
authors.forename: Denis
authors.initials: D
authors.lastname: Fellmann
authors.forename: James
authors.initials: J
authors.lastname: Pulokas
authors.forename: Craig
authors.initials: C
authors.lastname: Yoshioka
authors.forename: Christopher
authors.initials: C
authors.lastname: Irving
authors.forename: Anke
authors.initials: A
authors.lastname: Mulder
authors.forename: Pick-Wei
authors.initials: PW
authors.lastname: Lau
authors.forename: Dmitry
authors.initials: D
authors.lastname: Lyumkis
authors.forename: Clinton S
authors.initials: CS
authors.lastname: Potter
authors.forename: Bridget
authors.initials: B
authors.lastname: Carragher
mesh_terms: D018834:Chaperonin 60 / Q000737:chemistry; D020285:Cryoelectron Microscopy / Q000379:methods; D016208:Databases, Factual; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods; D020407:Internet; D008854:Microscopy, Electron / Q000379:methods*; D046529:Microscopy, Electron, Transmission / Q000379:methods; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface
chemical_list: D018834:Chaperonin 60