Appion: an integrated, database-driven pipeline to facilitate EM image processing.
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.
Lander
Gabriel C
GC
National Resource for Automated Molecular Microscopy, The Scripps Research Institute, CB 129, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA.
Stagg
Scott M
SM
Voss
Neil R
NR
Cheng
Anchi
A
Fellmann
Denis
D
Pulokas
James
J
Yoshioka
Craig
C
Irving
Christopher
C
Mulder
Anke
A
Lau
Pick-Wei
PW
Lyumkis
Dmitry
D
Potter
Clinton S
CS
Carragher
Bridget
B
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
D018834:Chaperonin 60