TY - JOUR T1 - Use of SPIDER and SPIRE in Image Reconstruction. JF - International Tables for Crystallography Y1 - 2012 A1 - Leith, ArDean A1 - Baxter, Bill A1 - Frank, Joachim AB - SPIDER is a comprehensive command-operated suite of programs for image processing in electron microscopy, with special emphasis on single-particle reconstruction. This chapter provides an outline of the way SPIDER and SPIRE, its interactive graphical user interface, may be used to obtain a three-dimensional reconstruction from projections of many randomly oriented realizations of a biological molecule. VL - F UR - http://xrpp.iucr.org/cgi-bin/itr?url_ver=Z39.88-2003&rft_dat=what%3Dchapter%26volid%3DFb%26chnumo%3D19o8%26chvers%3Dv0001 IS - Crystallography of Biological Macromolecules 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 - TY - JOUR T1 - SPIRE: the SPIDER reconstruction engine. JF - J Struct Biol Y1 - 2007 A1 - Baxter, Bill A1 - Leith, ArDean A1 - Frank, Joachim KW - Computational Biology KW - Image Processing, Computer-Assisted KW - Software KW - Software Design AB -

SPIRE is a Python program written to modernize the user interaction with SPIDER, the image processing system for electron microscopical reconstruction projects. SPIRE provides a graphical user interface (GUI) to SPIDER for executing batch files of SPIDER commands. It also lets users quickly view the status of a project by showing the last batch files that were run, as well as the data files that were generated. SPIRE handles the flexibility of the SPIDER programming environment through configuration files: XML-tagged documents that describe the batch files, directory trees, and presentation of the GUI for a given type of reconstruction project. It also provides the capability to connect to a laboratory database, for downloading parameters required by batch files at the start of a project, and uploading reconstruction results at the end of a project.

VL - 157 UR - http://www.ncbi.nlm.nih.gov/pubmed/17055743 IS - 1 ER - TY - JOUR T1 - A scripting language approach to control software for cryo-electron microscopy. JF - Proc IEEE Int. Symp. Biomed. Imag. Y1 - 2002 A1 - Baxter, Bill A1 - Leith, ArDean A1 - Frank, Joachim AB - Cryo-electron microscopy (Cryo-EM) of single particles has developed into a widely used technique for determining the 3-dimensional structure of large molecules and molecular assemblies. The low signal-to-noise ratio of cryo-EM requires thousands of images of single molecules to be averaged together. The field has matured to the point where realization of high-resolution structures is limited primarily by computational constraints. These constraints are at the algorithmic level, as well as the control level, where dozens of complex procedures and thousands of mathematical operations are applied to the raw data. SPIDER is a highly modular and flexible software package for single particle reconstruction. A typical reconstruction project involves dozens of procedure files, which in turn draw on hundreds of available low-level operations. In the present system, it is virtually impossible to rerun the system from selected branching points in the process flow to determine the effects of various parameters values. A Reconstruction Engine (RE) is being developed as a high-level "shell" for controlling processes in the SPIDER software system. The RE allows backtracking, optimization of parameters, and automation of processing flow. The RE is implemented in a scripting language, Python, which provides an overall management capability at the global level of the project. UR - http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=1029253&abstractAccess=no&userType=inst ER -