This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. ABSTRACT: SPIDER is an extensive image-processing software package specifically designed for 3D reconstruction in electron microscopy. It has been evolving in Dr. Frank's Lab since the late 1970's and contains appropriate tools for single particle reconstruction, classification analysis, and electron tomography, and segmentation of volumes. The current distribution consists of: + SPIDER Fast command line and procedural computation engine + Web Point-and-click GUI for image interaction + JWeb Point-and-click Java-based GUI for image interaction + SPIRE Point-and-click GUI for running SPIDER procedures + PubSub Scripted mechanism for distributing work on a compute cluster Since released as open source in 2005 there have been more than 1500 downloads of the software by recognizable registered users. SPIDER's web site is: www.wadsworth.org/spider_doc/spider/docs/spider.html. Currently, SPIDER is 100% dependent on RVBC funding for maintenance, development, and distribution. Dr. ArDean Leith has primary responsibility for SPIDER maintenance, distribution, and support, but Bill Baxter and Tapu Shaikh contributed to some of the projects described below. Activity in past reporting period: General image-processing and SPIDER software enhancements 1. SPIDER executables for Linux and Altix now use FFTW3. This increases speed of Fourier transformation under most circumstances. 2. The speed of the heavily used alignment operations 'AP SH'and 'AP REF'was dramatically increased by using precalculation of trigonometric values, FFTW3 in Fourier steps and better data flow. 3. Motif searching using: RAMOS motif signature search was simplified and speeded up. 4. New operation 'AP SCC'was added which rapidly calculates translational differences between experimental image/volume(s) and a series of reference image/volumes(s). 5. Method for speeding up the alignment operations by moving the compute intensive portions onto a graphics board (using NVIDIA's CUDA protocol) were investigated. 6. The MPI parallelism used in SPIDER's back projection operations was improved and simplified. 7. Methods were developed for 'warping'an electron tomography data set to recover information when fiducial particles move during imaging. 8. New documentation was included for particle verification for single-particle, reference-based reconstruction using multivariate data analysis and classification. This documentation arose from the following paper, published this year: + Shaikh, T.R., Trujillo, R., LeBarron, J.S., Baxter, W.T. and Frank, J. (2008) Particle-verification for single-particle, reference-based reconstruction using multivariate data analysis and classification. J. Struct. Biol. 164: 41-48. PMCID 2577219. 9. New operations for projection and back projection using non-uniform Fourier transforms ('gridding') were installed. 10. A large amount of time was spent providing advice and support to both internal and external SPIDER communities. The following paper was published: + Shaikh, T.R., Gao, H., Baxter, W., Asturias, F. Boisset, N., Leith, A., and Frank, J. (2008) SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nature Protocols. 3:1941-74. PMCID 2737740.
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