SPARX, a new environment for Cryo-EM image processing.
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.
Hohn
Michael
M
Lawrence Berkeley National Laboratory, Physical Bioscience Division, Berkeley, CA 94720, USA.
Tang
Grant
G
Goodyear
Grant
G
Baldwin
P R
PR
Huang
Zhong
Z
Penczek
Pawel A
PA
Yang
Chao
C
Glaeser
Robert M
RM
Adams
Paul D
PD
Ludtke
Steven J
SJ
D019295:Computational Biology; D020285:Cryoelectron Microscopy / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D012984:Software; D012985:Software Design; D018511:Systems Integration