ShapeWorks in the Cloud

项目摘要 本申请是对NOT-OD-20-073的回应，作为家长奖励的行政补充 R01AR076120标题：“直接从图像进行解剖：通用、可扩展和开源机器 解剖学的形式(或形状)是描述异常更多的临床语言。 与病理功能有关的生理现象。量化这种细微的形态变化需要进行语法分析 将解剖转化为数量描述，这在所讨论的人群中是一致的。不止是 100年来，形态计量学已经成为医学和生物科学中不可或缺的定量工具 研究解剖形态。但其表示能力仅限于线性距离、角度和面积。站台- 组织形状建模(SSM)是对经典形态测量技术的计算扩展 更详细地表现复杂的解剖结构及其在种群内的变异性父母奖广告- 为在fl可扩展环境中广泛采用SSM计算工具铺平现有的障碍 和通用的SSM方法，称为基于粒子的形状建模(PSM)及其相关的开源套件 软件工具，ShapeWorks。ShapeWorks支持通过自动学习种群级别的形状表示 在具有任意拓扑的大体解剖图像分割上密集放置同源地标。 ShapeWorks的实用性已经在一系列生物医学应用中得到了证明。ShapeWorks拥有 有可能改变研究人员处理解剖形态研究的方式，但它的广泛适用性 对医学和生物学的影响受到计算障碍的阻碍，大多数现有的形状建模 包裹面对的是。这项补充奖励的目的是为家长的目标3提供补充支持 奖，以利用软件开发的最佳实践和云计算的进步，使研究人员 使用有限的计算资源和/或大规模的队列来构建和执行定制的SSM WorkflOWS Us- ING远程可扩展计算资源。为了达到这一目标，我们制定了一项计划，以加强 ShapeWorks的设计、实施和云就绪，并扩充了我们的Sciencefic团队， 经验丰富的软件工程师/开发人员，在专业编程、代码方面具有丰富的经验 重构和科学fic计算。这项奖励将为我们的团队提供必要的支持，以(目标1)消除- 将ShapeWorks签署为模块化和可重用服务的集合，(目标2)将ShapeWorks服务与 显式编码的数据源，以及(目标3)重构ShapeWorks以在云上合理地扩展effi。所有软件 开发将遵循软件工程实践和设计原则进行，包括 编码风格、文档和版本控制。拟议的工作将以开源软件的形式发布 以符合可重复研究原则和开放科学实践的方式。我们的长- 学期目标是使ShapeWorks成为医学中形状分析的标准工具，这里提出的工作 此外，家长奖将为实现这一目标奠定基础。

Project Summary This application is submitted in response to NOT-OD-20-073 as an administrative supplement to the parent award R01AR076120 titled: "Anatomy Directly from Imagery: General-purpose, Scalable, and Open-source Machine Learning Approaches." The form (or shape) of anatomies is the clinical language that describes abnormal mor- phologies tied to pathologic functions. Quantifying such subtle morphological shape changes requires parsing the anatomy into a quantitative description that is consistent across the population in question. For more than 100 years, morphometrics has been an indispensable quantitative tool in medical and biological sciences to study anatomical forms. But its representation capacity is limited to linear distances, angles, and areas. Sta- tistical shape modeling (SSM) is the computational extension of classical morphometric techniques to analyze more detailed representations of complex anatomy and their variability within populations The parent award ad- dresses existing roadblocks for the widespread adoption of SSM computational tools in the context of a flexible and general SSM approach termed particle-based shape modeling (PSM) and its associated suite of open-source software tools, ShapeWorks. ShapeWorks enables learning population-level shape representation via automatic dense placement of homologous landmarks on image segmentations of general anatomy with arbitrary topology. The utility of ShapeWorks has been demonstrated in a range of biomedical applications. ShapeWorks has the potential to transform the way researchers approach studies of anatomical forms, but its widespread applicability and impact to medicine and biology are hindered by computational barriers that most existing shape modeling packages face. The goal of this supplement award is to provide supplemental support for Aim 3 of the parent award to leverage best practices in software development and advances in cloud computing to enable researchers with limited computational resources and/or large-scale cohorts to build and execute custom SSM workflows us- ing remote scalable computational resources. To achieve this goal, we have developed a plan to enhance the design, implementation, and cloud-readiness of ShapeWorks and augmented our scientific team to add senior, experienced software engineers/developers who have extensive experience in professional programming, code refactoring, and scientific computing. This award will provide our team with the support necessary to (Aim 1) de- sign ShapeWorks as a collection of modular and reusable services, (Aim 2) decouple ShapeWorks services from explicitly encoded data sources, and (Aim 3) refactor ShapeWorks to scale efficiently on the cloud. All software development will be performed in adherence to software engineering practices and design principles, including coding style, documentation, and version control. The proposed efforts will be released as open-source software in a manner consistent with the principles of reproducible research and the practices of open science. Our long- term goal is to make ShapeWorks a standard tool for shape analyses in medicine, and the work proposed herein in addition to the parent award will establish the groundwork for achieving this goal.