COLLABORATIVE PROPOSAL:ABI DEVELOPMENT: AN INTEGRATED PLATFORM FOR RETRIEVAL, VISUALIZATION AND ANALYSIS OF 3D MORPHOLOGY FROM DIGITAL BIOLOGICAL COLLECTIONS

合作提案：ABI 开发：数字生物馆藏 3D 形态检索、可视化和分析的综合平台

• 批准号: 1759839
• 负责人: Douglas Boyer
• 金额: $ 32.53万
• 依托单位: Duke University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-01 至 2023-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1759839&HistoricalAwards=false
• 关键词: COLLABORATIVE; PROPOSAL; ABI; DEVELOPMENT; INTEGRATED

The anatomical structure of an organism can provide important clues about its adaptation to its environment, its evolutionary history and its systematic relationships. The morphometric (quantitative) study of the organism?s shape and function is typically conducted at natural history museums, by measuring the specimen directly. High-resolution 3D imaging techniques (e.g., micro computed tomography) provide us to capture the internal and external anatomy of biological specimens in unprecedented detail. Likewise, online virtual "collections" (e.g., MorphoSource) provide a convenient access to these datasets, without requiring scientists to travel to different museums to collect their data. However, the complex nature of these 3D datasets makes them challenging to analyze for most researchers. In this project, we propose to develop an open-source software to retrieve and visualize 3D biological specimens from online museums. We will also develop tools for the scientists to measure and analyze the anatomy more easily. Geometric Morphometrics Methods (GMM) are a set of quantitative analytical techniques that rely on landmarks to capture organismal shape and form. This project proposes to develop a GMM module for open-source 3D-Slicer (Slicer) visualization software as an integrated toolkit to address challenges researchers face working with 3D anatomical data. In addition to manual annotation of landmarks, the toolkit will provide two distinct (user-guided and automated) types of semi-landmarking methods to enable general purpose dense spatial sampling for different study designs. Annotated landmark data can be analyzed in the GMM module using the Generalized Procrustes Analysis (GPA). Shape variation associated with GPA can be decomposed as principal warps and can be visualized in full 3D. Toolkit will also provide a data aggregator (SpecMart) that will query online 3D specimen repository MorphoSource by taxonomy (and other tokens), retrieve and visualize data within Slicer. We will train students in theory and application of 3D image segmentation, analysis and visualization as it applies to nonmedical volumetric imaging datasets to facilitate reproducible and high-throughput analysis of such datasets. The toolkit will be developed as an add-on package to Slicer using open-source toolchains and software development platforms (such as git). The stable versions of the module will be distributed through Extension Manager of Slicer (and its online portal) and documentation will be hosted on their site. The open-source nature of this development and use of the Slicer community's existing infrastructure that has been in existence more than 15 years to distribute and support the toolkit will mean that the software will be widely available for many years to come and can be supported (and potentially expanded) by the user community.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

生物体的解剖结构可以提供有关其适应环境，进化史和系统关系的重要线索。生物体形状和功能的形态计量学（定量）研究通常在自然历史博物馆直接测量样品。高分辨率3D成像技术（例如，微计算机断层扫描）为我们提供了前所未有的细节来捕获生物标本的内部和外部解剖结构。同样，在线虚拟“收藏”（例如，Morphosource）提供了方便地访问这些数据集的，而无需科学家前往不同的博物馆收集数据。但是，这些3D数据集的复杂性使它们在分析大多数研究人员方面具有挑战性。在这个项目中，我们建议开发一种开源软件，以检索和可视化在线博物馆中的3D生物标本。我们还将为科学家开发工具，以更轻松地测量和分析解剖结构。几何形态计量方法（GMM）是一组定量分析技术，依靠地标捕获有机形状和形式。该项目建议为开源3D-Slicer（Slicer）可视化软件开发一个GMM模块，作为一种集成工具包，以解决研究人员面临的挑战，面对使用3D解剖学数据。除了对地标的手动注释外，该工具包还将提供两种不同的（用户引导和自动化）类型的半地标方法，以实现用于不同研究设计的通用空间采样。可以使用广义Procrustes分析（GPA）在GMM模块中分析带注释的地标数据。与GPA相关的形状变化可以分解为主要扭曲，并且可以完整3D可视化。 Toolkit还将提供一个数据聚合器（Specmart），该数据聚合器将在线查询3D标本存储库形态（以及分类学和其他令牌），检索和可视化Slicer中的数据。我们将培训学生的3D图像分割，分析和可视化的理论和应用，以适用于非医学体积成像数据集，以促进此类数据集的可再现和高通量分析。该工具包将使用开源工具链和软件开发平台（例如GIT）作为Slicer的附加软件包开发。该模块的稳定版本将通过Slicer（及其在线门户网站）的扩展管理器分发，并且文档将在其网站上托管。 The open-source nature of this development and use of the Slicer community's existing infrastructure that has been in existence more than 15 years to distribute and support the toolkit will mean that the software will be widely available for many years to come and can be supported (and potentially expanded) by the user community.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review 标准。

项目成果

SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology

• DOI: 10.1111/2041-210x.13669
• 发表时间: 2021-07-22
• 期刊: METHODS IN ECOLOGY AND EVOLUTION
• 影响因子: 6.6
• 作者: Rolfe, Sara;Pieper, Steve;Maga, A. Murat
• 通讯作者: Maga, A. Murat

ariaDNE: A robustly implemented algorithm for Dirichlet energy of the normal

ariaDNE：一种稳健实现的法线狄利克雷能量算法

• DOI: 10.1111/2041-210x.13148
• 发表时间: 2019
• 期刊: Methods in Ecology and Evolution
• 影响因子: 6.6
• 作者: Shan, Shan;Kovalsky, Shahar Z.;Winchester, Julie M.;Boyer, Doug M.;Daubechies, Ingrid;Cooper, ed., Natalie
• 通讯作者: Cooper, ed., Natalie