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Use of SPIDER and SPIRE in image reconstruction
Leith, A., Baxter, W. and Frank, J.  International Tables for Crystallography (2012). Vol. F, ch. 19.8, pp. 620-623 [ doi:10.1107/97809553602060000874 ]
... Use of SPIDER and SPIRE in image reconstruction SPIDER is a comprehensive command-operated suite of programs for image processing in ... 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. 19.8.1. Introduction SPIDER (System for Processing Image ...

Implementation of single-particle reconstruction in SPIRE
Leith, A., Baxter, W. and Frank, J.  International Tables for Crystallography (2012). Vol. F, Section 19.8.4, p. 623 [ doi:10.1107/97809553602060000874 ]
... the SPIDER reconstruction engine) is an interactive GUI for managing a SPIDER reconstruction (Baxter et al., 2007). A project of single-particle reconstruction may involve dozens of procedure ... thousands of files may be generated during the course of a project. SPIRE was developed to manage the numerous procedures ...

Level 2: procedures
Leith, A., Baxter, W. and Frank, J.  International Tables for Crystallography (2012). Vol. F, Section 19.8.3.2, pp. 622-623 [ doi:10.1107/97809553602060000874 ]
... procedures and can request input during an interactive SPIDER session. A single-particle reconstruction project requires the application of many complex operations on perhaps several hundred thousand images, in a 30- to 40-step process that involves branching and decision ... in document files. These are keyed sequential text files containing a table of values, and are used to permanently store ...
     [more results from section 19.8.3 in volume F]

Basic philosophy of single-particle reconstruction
Leith, A., Baxter, W. and Frank, J.  International Tables for Crystallography (2012). Vol. F, Section 19.8.2, pp. 620-621 [ doi:10.1107/97809553602060000874 ]
... particle reconstruction' is the term used for the reconstruction of a biological macromolecule from images of a specimen in which the molecule exists in many `copies' in ... that can be reconstructed, except that they must be above a critical size required for accurate alignment. Combined with cryogenic ...

Introduction
Leith, A., Baxter, W. and Frank, J.  International Tables for Crystallography (2012). Vol. F, Section 19.8.1, p. 620 [ doi:10.1107/97809553602060000874 ]
... License (GPL). In its most common usage, SPIDER allows a researcher to create a three-dimensional (3D) reconstruction of a macromolecule from a collection of transmission electron micrographs, interpreted ...

Conclusion
Leith, A., Baxter, W. and Frank, J.  International Tables for Crystallography (2012). Vol. F, Section 19.8.5, p. 623 [ doi:10.1107/97809553602060000874 ]
... 2008), which has been used successfully in many applications (for a recent example, see Fig.19.8.5.1), can be readily changed to meet the challenges of a new project by users who have received a modest amount of training. The same goes for the ...

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