Digitization PEN: oBird: 3D Photogrammetry of Museum Specimens for Phenomics across the Avian Tree of Life

数字化 PEN：oBird：博物馆标本 3D 摄影测量，研究鸟类生命树的表型组学

• 批准号: 2001652
• 负责人: John McCormack
• 金额: $ 17.25万
• 依托单位: Occidental College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-15 至 2023-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001652&HistoricalAwards=false
• 关键词: Digitization; PEN; oBird; 3D; Photogrammetry

The oBird project (for “outside of the bird”) will create 3D digital models for nearly all living bird species for research and education. Preserved specimens in museum research collections are a record of Earth’s biodiversity and provide a baseline for assessing past and future environmental changes, planetary health, and for understanding how biodiversity arose and proliferated. Major efforts over the last several decades have sought to make museum records digital to facilitate their access and inclusion in large-scale research projects. Computerized tomography (CT) scans are an increasingly common way to make digital specimens, especially when the insides of the specimen have also been preserved, as with whole fish preserved in jars. However, with birds, CT scans will miss the color and arrangement of feathers, features of great importance to researchers and also appreciated by the public. oBird will create 3D digital models using a process called photogrammetry. Photogrammetry uses hundreds of photographs from all angles of a specimen to create realistic, interactive 3D virtual models in full, natural color. The 3D models from oBird will be free to access on the internet, facilitating research on the origins of bird diversity, including novel colors and pigments. The 3D models will also be incorporated into public displays on biodiversity in the new Anderson Center for Environmental Sciences at Occidental College as well as lesson plans for K-12 education.As a partner project to the Open Vertebrate Thematic Collections Network (OVert TCN), oBird will extend OVert into the world of 3D photogrammetry, an emerging method in collections digitization that preserves the external features of specimens as interactive, 3D models. The project will increase genus-level coverage of avian diversity compared to OVert from 60% to 90%. The 3D photogrammetry technique involves taking hundreds of 2D photos of a whole, dried bird specimen on a rotating stand followed by processing with a novel, automated computational pipeline that generates a 3D model with minimal manual oversight. oBird will prioritize imaging the same species as OVert to provide paired external and internal anatomy across species. The 3D models will be hosted on MorphoSource, an open-access platform for storing and archiving 3D data, extending access to large-scale phenomic data in furtherance of the OVert research theme: the evolution of vertebrate morphological diversity. By providing natural-color data for 3D specimens, oBird will thus bring more accurate and realistic color analysis to research on plumage evolution, especially in the comparative context of an existing bird tree of life. New questions that will be enabled include research into the origins and evolution of bird plumage color and morphological novelty in beak dimensions and wing shape, enabling comparative evolutionary study of these important ecomorphological traits. oBird will integrate with a strong undergraduate research program in a large bird natural history collection at a small liberal arts college, providing training in digital technology and effects, biodiversity informatics, and museum collections.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.

bird项目（意为“鸟的外部”）将为几乎所有现存鸟类创建3D数字模型，用于研究和教育。博物馆研究藏品中保存的标本是地球生物多样性的记录，为评估过去和未来的环境变化、地球健康以及了解生物多样性是如何产生和增殖的提供了基线。在过去的几十年里，人们一直在努力将博物馆的记录数字化，以便于在大型研究项目中获取和纳入这些记录。计算机断层扫描（CT）是制作数字标本的一种越来越普遍的方法，特别是当标本的内部也被保存下来时，比如整条鱼被保存在罐子里。然而，对于鸟类，CT扫描将错过羽毛的颜色和排列，这对研究人员来说非常重要，也是公众所欣赏的特征。bird将使用一种称为摄影测量的过程来创建3D数字模型。Photogrammetry使用数百张照片从标本的各个角度来创建逼真的，互动式3D虚拟模型，具有完整的自然色彩。来自bird的3D模型将在互联网上免费访问，促进鸟类多样性起源的研究，包括新的颜色和颜料。这些3D模型还将被纳入西方学院新建的安德森环境科学中心的生物多样性公开展示，以及K-12教育课程计划中。作为开放脊椎动物专题收藏网络（OVert TCN）的合作伙伴项目，obbird将把OVert扩展到3D摄影测量领域。3D摄影测量是收藏数字化的一种新兴方法，它将标本的外部特征保存为交互式3D模型。与OVert相比，该项目将把鸟类多样性的属级覆盖率从60%提高到90%。3D摄影测量技术包括在旋转支架上拍摄数百张整个干燥鸟类标本的2D照片，然后用一种新颖的自动化计算管道进行处理，以最小的人工监督生成3D模型。oBird将优先考虑与OVert相同物种的成像，以提供跨物种的配对外部和内部解剖。3D模型将托管在MorphoSource上，这是一个用于存储和归档3D数据的开放访问平台，扩展了对大规模现象数据的访问，以进一步推进OVert研究主题：脊椎动物形态多样性的进化。通过提供三维标本的自然颜色数据，obbird将为羽毛进化研究带来更准确和真实的颜色分析，特别是在现有鸟类生命树的比较背景下。新的问题将包括研究鸟类羽毛颜色的起源和进化，以及喙尺寸和翅膀形状的形态学新颖性，使这些重要的生态形态学特征的比较进化研究成为可能。bird将与一所小型文理学院的大型鸟类自然历史馆藏的一个强大的本科研究项目相结合，提供数字技术和效果、生物多样性信息学和博物馆藏品方面的培训。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。