ShapeWorksStudio: An Integrative, User-Friendly, and Scalable Suite for Shape Representation and Analysis

ShapeWorksStudio：用于形状表示和分析的集成、用户友好且可扩展的套件

基本信息

批准号：
10646213
负责人：
Shireen Youssef Elhabian
金额：
$ 25.58万
依托单位：
UNIVERSITY OF UTAH
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-09-30 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10646213
关键词：
Address Adoption Anatomic Models Anatomy Applied Research Area Big Data Biological Biological Sciences Biological Testing Biology Biomedical Research Cardiology Clinical Clinical Research Clinical Trials Communities Complex Complex Analysis Computer software Computers Consensus Data Data Set Development Dimensions Electronic Mail Endowment Ensure Exhibits Face Funding Future Goals Image Interdisciplinary Study Laboratory Research Language Learning Licensing Machine Learning Maintenance Manuals Maps Marketing Mathematics Measures Medical Medicine Memory Methods Modeling Modernization Modification Morphology Operative Surgical Procedures Orthopedics Patients Phenotype Population Process Programming Languages Psychology Reconstructive Surgical Procedures Reproducibility Research Research Personnel Scientist Shapes Software Engineering Software Tools Statistical Data Interpretation Supervision Techniques Technology Testing Time Visualization Work anatomic imaging automated segmentation clinical application clinical care clinical investigation cohort commercialization computerized tools cost design efficacy evaluation experience flexibility imaging Segmentation improved innovation interest interoperability medical implant open source open source tool outreach particle permissiveness reconstruction research and development shape analysis software development statistics tool usability user-friendly

Address Adoption Anatomic Models Anatomy Applied Research Area Big Data Biological Biological Sciences Biological Testing Biology Biomedical Research Cardiology Clinical Clinical Research Clinical Trials Communities Complex Complex Analysis Computer software Computers Consensus Data Data Set Development Dimensions Electronic Mail Endowment Ensure Exhibits Face Funding Future Goals Image Interdisciplinary Study Laboratory Research Language Learning Licensing Machine Learning Maintenance Manuals Maps Marketing Mathematics Measures Medical Medicine Memory Methods Modeling Modernization Modification Morphology Operative Surgical Procedures Orthopedics Patients Phenotype Population Process Programming Languages Psychology Reconstructive Surgical Procedures Reproducibility Research Research Personnel Scientist Shapes Software Engineering Software Tools Statistical Data Interpretation Supervision Techniques Technology Testing Time Visualization Work anatomic imaging automated segmentation clinical application clinical care clinical investigation cohort commercialization computerized tools cost design efficacy evaluation experience flexibility imaging Segmentation improved innovation interest interoperability medical implant open source open source tool outreach particle permissiveness reconstruction research and development shape analysis software development statistics tool usability user-friendly

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项目摘要

Project Summary The morphology (or shape) of anatomical structures forms the common language among clinicians, where ab- normalities in anatomical shapes are often tied to deleterious function. While these observations are often quali- tative, ﬁnding subtle, quantitative shape effects requires the application of mathematics, statistics, and computing to parse the anatomy into a numerical representation that will facilitate testing of biologically relevant hypotheses. Particle-based shape modeling (PSM) and its associated suite of software tools, ShapeWorks, enable learning population-level shape representation via automatic dense placement of homologous landmarks on image seg- mentations of general anatomy with arbitrary topology. The utility of ShapeWorks has been demonstrated in a range of biomedical applications. Despite its obvious utility for the research enterprise and highly permissive open-source license, ShapeWorks does not have a viable commercialization path due to the inherent trade-off between development and maintenance costs, and a specialized scientiﬁc and clinical market. ShapeWorks has the potential to transform the way researchers approach studies of anatomical forms, but its widespread ap- plicability to medicine and biology is hindered by several barriers that most existing shape modeling packages face. The most important roadblocks are (1) the complexity and steep learning curve of existing shape modeling pipelines and their increased computational and computer memory requirements; (2) the considerable expertise, time, and effort required to segment anatomies of interest for statistical analyses; and (3) the lack of interoperable implementations that can be readily incorporated into biomedical research laboratories. In this project, we pro- pose ShapeWorksStudio, a software suite that leverages ShapeWorks for the automated population-/patient-level modeling of anatomical shapes, and Seg3D – a widely used open-source tool to visualize and process volumet- ric images – for ﬂexible manual/semiautomatic segmentation and interactive manual correction of segmented anatomy. In Aim 1, we will integrate ShapeWorks and Seg3D in a framework that supports big data cohorts to enable users to transparently proceed from image data to shape models in a straightforward manner. In Aim 2, we will endow Seg3D with a machine learning approach that provides automated segmentations within a statisti- cal framework that combines image data with population-speciﬁc shape priors provided by ShapeWorks. In Aim 3, we will support interoperability with existing open-source software packages and toolkits, and provide bindings to commonly used programming languages in the biomedical research community. To promote reproducibility, we will develop and disseminate standard workﬂows and domain-speciﬁc test cases. This project combines an interdisciplinary research and development team with decades of experience in statistical analysis and image understanding, and application scientists to conﬁrm that the proposed developments have a real impact on the biomedical and clinical research communities. Our long-term goal is to make ShapeWorks a standard tool for shape analyses in medicine, and the work proposed herein will establish the groundwork for achieving this goal.

项目摘要解剖结构的形态（或形状）形成了临床医生的通用语言，其中解剖形状的正常水平通常与有害功能有关。尽管这些观察通常是合理的鉴定微妙的定量形状效应需要数学，统计和计算的应用将解剖结构分解为数值表示，该表示将有助于测试生物学相关的假设。基于粒子的形状建模（PSM）及其相关的软件工具套件，ShapeWorks，使学习能够人口级形状表示通过在图像seg上自动密集地放置同源地标提及与任意拓扑结构的一般解剖结构。 Shapeworks的实用性已在生物医学应用范围。尽管它显然是研究企业的实用性，并且具有很高的允许性开源许可证，由于继承权衡，Shapeworks没有可行的商业化路径在开发和维护成本以及专门的科学和临床市场之间。 Shapeworks拥有改变研究人员处理解剖形式的研究的潜力，但其宽度广泛大多数现有形状建模套件的障碍阻碍了医学和生物学的价格脸。最重要的障碍是（1）现有形状建模的复杂性和钢制学习曲线管道及其计算和计算机内存要求的增加；（2）大量专业知识，为统计分析所需的时间和精力来分割感兴趣的解剖学；（3）缺乏可互操作可以很容易地将其纳入生物医学研究实验室的实施。在这个项目中，我们会 Pose Shapeworksstudio，一个软件套件，它利用ShapeWorks为自动化人群/患者级别解剖形状和SEG3D的建模 - 一种广泛的使用开源工具，可视化和处理量 - RIC图像 - 用于灵活的手动/词素分割和分段的交互式手动校正解剖学。在AIM 1中，我们将在一个支持大数据队列的框架中整合ShapeWorks和Seg3D 使用户能够从图像数据透明地进行以直接的方式塑造模型。在AIM 2中，我们将通过机器学习方法赋予SEG3D Cal框架将图像数据与ShapeWorks提供的特定于人群的先验相结合。目标 3，我们将支持与现有开源软件包和工具包的互操作性，并提供绑定在生物医学研究界的常用编程语言。为了促进繁殖，我们将开发并传播标准工作流和特异性测试用例。这个项目结合了一个跨学科研发团队拥有数十年的统计分析和形象经验理解和应用科学家确认拟议的发展对生物医学和临床研究社区。我们的长期目标是使ShapeWorks成为标准工具医学的形状分析，本文提出的工作将为实现这一目标建立基础。