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

oBird项目（意为“鸟的外部”）将为几乎所有现存的鸟类创建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如何产生和扩散提供了基线。在过去的几十年里，主要的努力是使博物馆记录数字化，以方便他们的访问和纳入大规模的研究项目。计算机断层扫描（CT）是制作数字标本的一种越来越常见的方法，特别是当标本的内部也被保存时，比如保存在罐子里的整条鱼。然而，对于鸟类，CT扫描将错过羽毛的颜色和排列，这些特征对研究人员非常重要，也受到公众的赞赏。oBird将使用一种名为摄影测量的过程创建3D数字模型。摄影测量使用数百张来自标本各个角度的照片，以创建逼真的交互式3D虚拟模型。oBird的3D模型将在互联网上免费访问，促进对鸟类多样性起源的研究，包括新的颜色和色素。3D模型还将被纳入西方学院新的安德森环境科学中心的生物多样性公共展示以及K-12教育的课程计划中。（OVert TCN），oBird将把OVert扩展到3D摄影测量领域，一种新兴的收藏品数字化方法，将标本的外部特征保留为交互式3D模型。与OVert相比，该项目将使鸟类多样性的属级覆盖率从60%提高到90%。3D摄影测量技术涉及在旋转支架上拍摄数百张完整的干燥鸟类标本的2D照片，然后使用一种新颖的自动计算管道进行处理，以最小的手动监督生成3D模型。oBird将优先对与OVert相同的物种进行成像，以提供跨物种的配对外部和内部解剖结构。3D模型将托管在MorphoSource上，MorphoSource是一个用于存储和存档3D数据的开放访问平台，扩展了对大规模表型数据的访问，以促进OVert研究主题：脊椎动物形态多样性的演变。通过为3D标本提供自然颜色数据，oBird将为羽毛进化研究带来更准确和逼真的颜色分析，特别是在现有鸟类生命树的比较背景下。新的问题，将启用包括鸟类羽毛颜色和形态新奇的喙尺寸和翅膀形状的起源和进化的研究，使这些重要的生态形态特征的比较进化研究。oBird将与一个强大的本科生研究计划相结合，在一个小型文科学院进行大型鸟类自然历史收藏，提供数字技术和效果，生物多样性信息学和博物馆收藏方面的培训。该奖项反映了NSF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。

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.