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对环境的适应、进化历史及其系统关系的重要线索。对生物体形状和功能的形态测量（定量）研究通常在自然历史博物馆通过直接测量标本进行。高分辨率 3D 成像技术（例如微型计算机断层扫描）使我们能够以前所未有的细节捕获生物样本的内部和外部解剖结构。同样，在线虚拟“馆藏”（例如 MorphoSource）提供了对这些数据集的便捷访问，而无需科学家前往不同的博物馆来收集数据。然而，这些 3D 数据集的复杂性使得大多数研究人员难以对其进行分析。在这个项目中，我们建议开发一款开源软件，用于从在线博物馆检索和可视化 3D 生物标本。我们还将开发工具，供科学家更轻松地测量和分析解剖结构。几何形态计量学方法 (GMM) 是一套定量分析技术，依靠地标来捕获生物体的形状和形态。该项目建议为开源 3D-Slicer (Slicer) 可视化软件开发 GMM 模块作为集成工具包，以解决研究人员在处理 3D 解剖数据时面临的挑战。除了地标的手动注释之外，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，以便为不同的研究设计提供通用的密集空间采样。带注释的地标数据可以使用广义 Procrustes 分析 (GPA) 在 GMM 模块中进行分析。与 GPA 相关的形状变化可以分解为主扭曲，并且可以以全 3D 形式可视化。 Toolkit 还将提供一个数据聚合器 (SpecMart)，它将通过分类（和其他标记）查询在线 3D 样本存储库 MorphoSource，在 Slicer 中检索和可视化数据。我们将培训学生 3D 图像分割、分析和可视化的理论和应用，因为它适用于非医学体积成像数据集，以促进此类数据集的可重复和高通量分析。该工具包将使用开源工具链和软件开发平台（例如 git）开发为 Slicer 的附加包。该模块的稳定版本将通过 Slicer 的扩展管理器（及其在线门户）分发，文档将托管在其网站上。这种开发的开源性质以及对 Slicer 社区现有基础设施的使用（该基础设施已经存在超过 15 年来分发和支持该工具包）意味着该软件将在未来许多年内广泛使用并得到支持（该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

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