title: SPARX, a new environment for Cryo-EM image processing.
abstract: SPARX (single particle analysis for resolution extension) is a new image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a graphical user interface that provides a complete graphical programming environment with a novel data/process-flow infrastructure, an extensive library of Python scripts that perform specific TEM-related computational tasks, and a core library of fundamental C++ image processing functions. In addition, SPARX relies on the EMAN2 library and cctbx, the open-source computational crystallography library from PHENIX. The design of the system is such that future inclusion of other image processing libraries is a straightforward task. The SPARX infrastructure intelligently handles retention of intermediate values, even those inside programming structures such as loops and function calls. SPARX and all dependencies are free for academic use and available with complete source.
authors.affiliation: Lawrence Berkeley National Laboratory, Physical Bioscience Division, Berkeley, CA 94720, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Hohn
authors.forename: Grant
authors.initials: G
authors.lastname: Tang
authors.forename: Grant
authors.initials: G
authors.lastname: Goodyear
authors.forename: P R
authors.initials: PR
authors.lastname: Baldwin
authors.forename: Zhong
authors.initials: Z
authors.lastname: Huang
authors.forename: Pawel A
authors.initials: PA
authors.lastname: Penczek
authors.forename: Chao
authors.initials: C
authors.lastname: Yang
authors.forename: Robert M
authors.initials: RM
authors.lastname: Glaeser
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Ludtke
mesh_terms: D019295:Computational Biology; D020285:Cryoelectron Microscopy / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D012984:Software; D012985:Software Design; D018511:Systems Integration