title: A pipeline for comprehensive and automated processing of electron diffraction data in IPLT.
abstract: Electron crystallography of two-dimensional crystals allows the structural study of membrane proteins in their native environment, the lipid bilayer. Determining the structure of a membrane protein at near-atomic resolution by electron crystallography remains, however, a very labor-intense and time-consuming task. To simplify and accelerate the data processing aspect of electron crystallography, we implemented a pipeline for the processing of electron diffraction data using the Image Processing Library and Toolbox (IPLT), which provides a modular, flexible, integrated, and extendable cross-platform, open-source framework for image processing. The diffraction data processing pipeline is organized as several independent modules implemented in Python. The modules can be accessed either from a graphical user interface or through a command line interface, thus meeting the needs of both novice and expert users. The low-level image processing algorithms are implemented in C++ to achieve optimal processing performance, and their interface is exported to Python using a wrapper. For enhanced performance, the Python processing modules are complemented with a central data managing facility that provides a caching infrastructure. The validity of our data processing algorithms was verified by processing a set of aquaporin-0 diffraction patterns with the IPLT pipeline and comparing the resulting merged data set with that obtained by processing the same diffraction patterns with the classical set of MRC programs.
authors.affiliation: Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, USA. andreas_schenk@hms.harvard.edu
authors.forename: Andreas D
authors.initials: AD
authors.lastname: Schenk
authors.forename: Ansgar
authors.initials: A
authors.lastname: Philippsen
authors.forename: Andreas
authors.initials: A
authors.lastname: Engel
authors.forename: Thomas
authors.initials: T
authors.lastname: Walz
mesh_terms: D000465:Algorithms; D020346:Aquaporins / Q000737:chemistry; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008565:Membrane Proteins / Q000737:chemistry*; D046529:Microscopy, Electron, Transmission / Q000379:methods*; D012984:Software
chemical_list: D020346:Aquaporins; D008565:Membrane Proteins