TY - JOUR T1 - Particle-verification for single-particle, reference-based reconstruction using multivariate data analysis and classification. JF - J Struct Biol Y1 - 2008 A1 - Shaikh, Tanvir R A1 - Trujillo, Ramon A1 - LeBarron, Jamie A1 - Baxter, Bill A1 - Frank, Joachim KW - Algorithms KW - Artificial Intelligence KW - Classification KW - Image Enhancement KW - Image Processing, Computer-Assisted KW - Microscopy, Electron KW - Multivariate Analysis KW - Ribosomes AB -

As collection of electron microscopy data for single-particle reconstruction becomes more efficient, due to electronic image capture, one of the principal limiting steps in a reconstruction remains particle-verification, which is especially costly in terms of user input. Recently, some algorithms have been developed to window particles automatically, but the resulting particle sets typically need to be verified manually. Here we describe a procedure to speed up verification of windowed particles using multivariate data analysis and classification. In this procedure, the particle set is subjected to multi-reference alignment before the verification. The aligned particles are first binned according to orientation and are binned further by K-means classification. Rather than selection of particles individually, an entire class of particles can be selected, with an option to remove outliers. Since particles in the same class present the same view, distinction between good and bad images becomes more straightforward. We have also developed a graphical interface, written in Python/Tkinter, to facilitate this implementation of particle-verification. For the demonstration of the particle-verification scheme presented here, electron micrographs of ribosomes are used.

VL - 164 UR - http://www.ncbi.nlm.nih.gov/pubmed/18619547 IS - 1 ER - TY - JOUR T1 - SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. JF - Nat Protoc Y1 - 2008 A1 - Shaikh, Tanvir R A1 - Gao, Haixiao A1 - Baxter, Bill A1 - Asturias, Francisco J A1 - Boisset, Nicolas A1 - Leith, ArDean A1 - Frank, Joachim KW - Image Processing, Computer-Assisted KW - Microscopy, Electron KW - Models, Molecular KW - Molecular Structure KW - Software KW - User-Computer Interface AB -

This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Computation here is performed using the image-processing software SPIDER and can be managed using a graphical user interface, termed the SPIDER Reconstruction Engine. Two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines. Once an existing model is available, reference-based alignment can be used, a procedure that can be iterated. Also described is supervised classification, a method to look for homogeneous subsets when multiple known conformations of the molecule may coexist.

VL - 3 UR - http://www.ncbi.nlm.nih.gov/pubmed/19180078 IS - 12 ER -