Continued Development and Maintenance of a Computational Morphometry Toolkit

计算形态测量工具包的持续开发和维护

• 批准号: 7626623
• 负责人: TORSTEN ROHLFING
• 金额: $ 12.77万
• 依托单位: SRI INTERNATIONAL
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-04-10 至 2011-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7626623
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DESCRIPTION (provided by applicant): Over the past ten years, the PI has developed a flexible set of software tools for accurate computational morphometry, named the Computational Morphometry Toolkit (CMTK), which has been used in numerous studies, ranging from insect brain connection mapping to investigations of effects of alcoholism and aging on the human brain. CMTK's registration tools have also been successfully applied to extra-cranial problems, such as patient motion correction in contrast-enhanced MR breast imaging and CT subtraction angiography. The proposed project will make CMTK publicly available, improve its usability, and ensure its future support and development. The existing software consists of three parts: (1) a library with application-proven implementations of a large number of image processing and analysis algorithms; (2) command line tools for image restoration, registration, segmentation, and statistical modeling; (3) scripts for complex combinations of the elementary registration and segmentation tasks, such as longitudinal and cross-sectional morphometric studies. CMTK has a unique set of features, as it combines robust tools for image registration, segmentation, filtering, and modeling. These tools can be applied to data from different imaging modalities, and are useful for analysis of large, under-analyzed archival data sets. The software is end-user focused and computationally efficient, enabled by state-of-the-art parallel computation techniques. We propose three specific aims: (1) Access. Legacy third-party code in the existing software that prevents open source distribution will be replaced with freely available alternatives. (2) Usability. We will improve and document the pre-defined processing pipelines for complex studies (e.g., longitudinal deformation-based morphometry with a general linear model) and provide a user manual. (3) Maintenance. We will review and complete source code documentation, replace the current configuration and build environment, and set up auto- mated testing and bug tracking with state-of-the-art systems that are publicly available. We will improve interoperability with selected related soft- ware development efforts, which provide complementary functions to CMTK. (4) Enhancement. We will port key algorithms to state-of-the-art high-performance computing hardware. We will also implement an image-relationship database for transformation bookkeeping. By making publicly available a proven software system for morphometric studies, this project will enable any institution with appropriate image data to perform data analysis with efficiency, reliability, and reproducibility. Once released as the result of this project, CMTK will continue to enable new scientific insights in many fields of neuroscience, from human applications to insect science. The state-of-the-art registration tools in CMTK will furthermore continue to support clinically relevant applications such as treatment target delineation and patient motion correction. PUBLIC HEALTH RELEVANCE: Computerized morphometric analysis based on three-dimensional imaging enables high-throughput studies of disease (e.g., alcohol abuse, HIV/AIDS, stroke, dementia, and cancer), normal development, and aging effects on human and animal brain and body structure. Structural differences between diseased and control groups can be used to help identify potential biological causes of such conditions as Alzheimer's disease or schizophrenia. This project will enhance a proven soft- ware system for imaging-based morphometric studies and make it freely avail- able to the scientific community.

描述（由申请人提供）：在过去的十年中，PI开发了一套灵活的软件工具，用于精确的计算形态计量学，称为计算形态计量学工具包（CMTK），该工具已在许多研究中使用，范围从昆虫脑连接映射到对人类大脑的效果和对人类大脑的影响。 CMTK的注册工具也已成功应用于颅外问题，例如在对比增强的MR乳房成像和CT减法血管造影中的患者运动校正。拟议的项目将使CMTK公开可用，提高其可用性，并确保其未来的支持和发展。现有软件包括三个部分：（1）具有大量图像处理和分析算法的应用程序证实实现的库； （2）用于图像恢复，注册，细分和统计建模的命令行工具； （3）基本注册和分割任务的复杂组合的脚本，例如纵向和横截面形态计量学研究。 CMTK具有一组独特的功能，因为它结合了用于图像注册，分割，过滤和建模的强大工具。这些工具可以应用于来自不同成像方式的数据，可用于分析大型，分析不足的档案数据集。该软件是最终用户的重点和计算高效的，由最新的并行计算技术启用。我们提出了三个具体目标：（1）访问。现有软件中的旧版第三方代码防止开源分发替换为免费可用的替代方案。 （2）可用性。我们将改进并记录用于复杂研究的预定义的处理管道（例如，使用一般线性模型基于纵向变形的形态计量学）并提供用户手册。 （3）维护。我们将审查并完成源代码文档，替换当前的配置和构建环境，并使用公开可用的最新系统进行自动测试和错误跟踪。我们将通过选定相关的软件开发工作提高互操作性，这些软件开发工作为CMTK提供了互补的功能。 （4）增强。我们将将密钥算法移植到最新的高性能计算硬件。我们还将实施一个图像关联数据库，以进行转换簿记。通过使公开可用的形态计量学研究成为现实的软件系统，该项目将使任何具有适当图像数据的机构都能以效率，可靠性和可重复性进行数据分析。一旦发布该项目的结果，CMTK将继续在许多神经科学领域，从人类应用到昆虫科学领域的许多领域。 CMTK中最新的注册工具将继续支持临床相关的应用，例如治疗目标描述和患者运动校正。公共卫生相关性：基于三维成像的计算机化形态分析可以使疾病的高通量研究（例如，酗酒，艾滋病毒，艾滋病，中风，痴呆症和癌症），正常发育以及对人体和动物脑结构的衰老影响。患病组和对照组之间的结构差异可用于确定阿尔茨海默氏病或​​精神分裂症等疾病的潜在生物学原因。该项目将增强一个经过验证的软件系统，用于基于成像的形态计量学研究，并可以自由地利用科学界。