Development and Maintenance of SPIDER Software for Electron Microscopy Imaging

电子显微镜成像 SPIDER 软件的开发和维护

• 批准号: 7847200
• 负责人: Ardean Leith
• 金额: $ 45.2万
• 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: 2010-09-30 至 2013-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7847200
• 关键词: Abnormal Cell; Algorithms; Area; Back; Biological; Biological Process; Cell model; Code; Communities; Complex; Computer software; Data; Data Set; Development; Electron Microscope; Electron Microscopy; Electrons; Feedback; Grant; Image; Image Analysis; Knowledge; Laboratories; Libraries; Maintenance; Maps; Methods; Mission; Molecular Motors; Nuclear Pore; Phase; Procedures; Process; Published Comment; Reference Standards; Research; Research Personnel; Research Project Grants; Resolution; Ribosomes; Roentgen Rays; Sampling; Site; Solutions; Speed; Spiders; Structural Biologist; Structure; System; Techniques; Testing; Time; United States National Institutes of Health; Virus; base; cell behavior; cluster computing; density; flexibility; graphical user interface; image processing; improved; interoperability; molecular assembly/self assembly; open source; operation; particle; programs; public health relevance; reconstruction; software development; software systems; trend

DESCRIPTION (provided by applicant): Single-particle reconstruction from cryo-electron micrographs has proven to be a powerful technique for studying structure and function of biological macro-molecules. Many of these studies are not feasible by any other technique. SPIDER (System for Processing Image Data in Electron microscopy and Related fields) has been the foremost software system for carrying out such a reconstruction, especially for non-symmetrical objects. Developed in the laboratory of Dr. Joachim Frank, SPIDER software is currently providing 6.8 Angstrom reconstructions of non-symmetrical objects such as ribosomes and efforts are underway to push the resolution toward the atomic range (<3.5 A). SPIDER has been available to the electron microscopy community for more than 30 years and for almost 4 years as 'Free Open Source Software'. In 2008 alone there were 678 downloads by registered sites. The standard reference for the system has more than 800 methodological citations. Single-particle reconstruction software is unique in the scale of image sizes that it handles, the diversity of image processing techniques used, and the great computational load of many of the processing steps. Aims: 1: Increase speed/accuracy of single-particle reconstruction by implementing new alignment and back-projection methods, off-loading computations to GPUs, and adding parallel MPI I/O. 2: Develop efficient methods for handling large datasets with more than one million 500x500 pixel images, and for phase-plate imaging. 3: Further develop JWeb and SPIRE's graphical user interfaces, and better integrate them with SPIDER. 4: Collaborate with other developers to integrate outside solutions for alignment, heterogeneous samples, and interoperability into SPIDER. 5: Maintain SPIDER to take advantage of new hardware and compiler capabilities and distribute compiled, tested executables to users. PUBLIC HEALTH RELEVANCE: The SPIDER software developed and distributed by this grant is being used by a sizable community of structural biologists in research projects to increase our understanding of the structure and mechanism of action of large biological molecules and molecular assemblies. Used to analyze images from electron microscopes, SPIDER allows creation of density maps and, through fitting of X-ray structures, models of cellular objects including ribosomes, nuclear pores, molecular motors, transport molecules, viruses, and large enzymatic complexes. Such basic structural knowledge is crucial to the understanding of the processes in normal and abnormal cell behavior. As such the knowledge is directly relevant to the core mission of the NIH.

描述（由申请人提供）：冷冻电子显微照片的单粒子重建已被证明是研究生物大分子结构和功能的强大技术。其中许多研究无法通过任何其他技术实现。 SPIDER（电子显微镜及相关领域图像数据处理系统）是执行此类重建的最重要的软件系统，特别是对于非对称物体。 SPIDER 软件由 Joachim Frank 博士的实验室开发，目前可提供核糖体等非对称物体的 6.8 埃重建，并且正在努力将分辨率推向原子范围（<3.5 A）。 SPIDER 已向电子显微镜社区提供了 30 多年的历史，并且作为“免费开源软件”已有近 4 年的历史。仅 2008 年，注册网站就有 678 次下载。该系统的标准参考文献有超过 800 条方法论引用。单粒子重建软件的独特之处在于它处理的图像尺寸的规模、所使用的图像处理技术的多样性以及许多处理步骤的巨大计算负荷。 目标：1：通过实施新的对齐和反投影方法、将计算卸载到 GPU 以及添加并行 MPI I/O，提高单粒子重建的速度/准确性。 2：开发有效的方法来处理具有超过一百万个 500x500 像素图像的大型数据集以及相位板成像。 3：进一步开发JWeb和SPIRE的图形用户界面，并与SPIDER更好地集成。 4：与其他开发人员合作，将用于对齐、异构样本和互操作性的外部解决方案集成到 SPIDER 中。 5：维护 SPIDER，以利用新的硬件和编译器功能，并将编译后的、经过测试的可执行文件分发给用户。 公共健康相关性：由这笔资助开发和分发的 SPIDER 软件正在被相当大的结构生物学家社区在研究项目中使用，以增进我们对大型生物分子和分子组装体的结构和作用机制的理解。 SPIDER 用于分析电子显微镜图像，可以创建密度图，并通过拟合 X 射线结构，创建细胞物体模型，包括核糖体、核孔、分子马达、运输分子、病毒和大型酶复合物。这些基本的结构知识对于理解正常和异常细胞行为的过程至关重要。因此，这些知识与 NIH 的核心使命直接相关。