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

Occidental College, Los Angeles CA

Investigators

Abstract

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.