SPIDER, WEB, AND GENERAL IMAGE PROCESSING DEVELOPMENT

蜘蛛、网络和通用图像处理开发

• 批准号: 8172274
• 负责人: Ardean Leith
• 金额: $ 5.41万
• 依托单位: WADSWORTH CENTER
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-04-07 至 2011-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8172274
• 关键词: Back; Biological; Classification; Communities; Computer Retrieval of Information on Scientific Projects Database; Computer software; Data; Data Analyses; Data Set; Development; Documentation; Electron Microscopy; Electrons; Fourier Transform; Funding; Grant; Image; Institution; Internet; Java; Linux; Maintenance; Methods; Nature; Paper; Procedures; Protocols documentation; Publishing; Reporting; Research; Research Personnel; Resources; Running; Series; Source; Speed; Spiders; Time; United States National Institutes of Health; Work; abstracting; base; cluster computing; design; electron tomography; image processing; improved; macromolecule; open source; operation; particle; reconstruction; tool; web site

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: http://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.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 抽象的： SPIDER 是一款功能丰富的图像处理软件包，专为电子显微镜中的 3D 重建而设计。 自 20 世纪 70 年代末以来，Frank 博士的实验室一直在不断发展它，并包含用于单粒子重建、分类分析、电子断层扫描和体积分割的适当工具。 当前的分布包括： + SPIDER 快速命令行和程序计算引擎 + 用于图像交互的 Web 点击式 GUI + JWeb 用于图像交互的基于 Java 的点击式 GUI + SPIRE 用于运行 SPIDER 程序的点击式 GUI + 用于在计算集群上分配工作的 PubSub 脚本化机制 自 2005 年以开源方式发布以来，该软件已被知名注册用户下载了 1500 多次。 SPIDER 的网站是：http://www.wadsworth.org/spider_doc/spider/docs/spider.html。 目前，SPIDER 100% 依赖 RVBC 资金进行维护、开发和分发。 ArDean Leith 博士主要负责 SPIDER 的维护、分发和支持，但 Bill Baxter 和 Tapu Shaikh 为下述的一些项目做出了贡献。 过去报告期的活动： 一般图像处理和 SPIDER 软件增强功能 1. Linux 和 Altix 的 SPIDER 可执行文件现在使用 FFTW3。在大多数情况下，这提高了傅里叶变换的速度。 2. 通过使用三角值的预先计算、傅里叶步长中的 FFTW3 和更好的数据流，大量使用的对齐操作“AP SH”和“AP REF”的速度得到了显着提高。 3. 模体搜索使用：RAMOS 模体签名搜索得到简化和加速。 4. 添加了新操作“AP SCC”，可快速计算实验图像/体积与一系列参考图像/体积之间的平移差异。 5. 研究了通过将计算密集型部分移动到图形板上（使用 NVIDIA 的 CUDA 协议）来加速对齐操作的方法。 6. SPIDER 反投影操作中使用的 MPI 并行性得到改进和简化。 7. 开发了“扭曲”电子断层扫描数据集的方法，以在成像过程中基准粒子移动时恢复信息。 8. 包含新的文档，用于使用多元数据分析和分类进行单粒子、基于参考的重建的粒子验证。本文档源自今年发表的以下论文： + Shaikh, T.R.、Trujillo, R.、LeBarron, J.S.、Baxter, W.T. 和 Frank, J. (2008) 使用多元数据分析和分类对单粒子、基于参考的重建进行粒子验证。 J.结构。生物。 164：41-48。 PMCID 2577219。 9. 安装了使用非均匀傅里叶变换（“网格化”）的投影和反投影的新操作。 10. 花费了大量时间向内部和外部 SPIDER 社区提供建议和支持。 发表了以下论文： + Shaikh, T.R.、Gao, H.、Baxter, W.、Asturias, F. Boisset, N.、Leith, A. 和 Frank, J. (2008) 用于从电子单粒子重建生物大分子的 SPIDER 图像处理显微照片。 自然协议。 3：1941-74。 PMCID 2737740。