OVert: Open Exploration of Vertebrate Diversity in 3D: Difference between revisions

OVert: Open Exploration of Vertebrate Diversity in 3D (view source)

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 ''Principal Investigators:'' [mailto:maisano@mail.utexas.edu Jessica Maisano] (PI), David Blackburn (co-PI)
+===CryptoVert - Digitizing small-bodied cryptobenthic fishes for the oVertTCN===
+The Open Vertebrate thematic collections network (oVert) aims to create a digital resource of computed tomography (CT) scans across the vertebrate Tree of Life. This digital database allows researchers to quickly and efficiently study morphological patterns across all vertebrate groups. One of the most apparent differences among vertebrates is their body size, with some species obtaining large body sizes, while others remain very small even as mature adults. This Partner to Existing Networks (PEN) award will link the Natural History Museum of Los Angeles County with oVert to create a digital repository of data focusing on some of the world?s smallest vertebrates: cryptobenthic fishes. Fishes represent approximately half of the total vertebrate diversity, yet many groups remain understudied. Cryptobenthic fishes, which are small marine fishes that live in a variety of habitats, are one of these understudied groups and their importance in marine ecosystems is only beginning to be understood. This project will complement oVert taxonomically by focusing on an understudied vertebrate group, and methodologically by developing best practices for scanning very small organisms for both bony and soft-tissue anatomy. In addition to their research utility, these scans will be an excellent educational resource that will be incorporated into public museum displays and K-12 classroom lesson plans. Furthermore, processing of CT scans will train undergraduate students in skills that are used in a variety of professional disciplines.
+Studying very small organisms comes with inherent challenges, and previous attempts to describe the internal anatomy of small vertebrates was only possible using destructive approaches. This project will focus on 17 different fish families that comprise the majority of cryptobenthic fishes using traditional CT scans to document the skeletal system and contrast-enhanced CT scans to reveal soft-tissue anatomy such as muscle, nervous, and circulatory systems. Cryptobenthic fishes fill a variety of functional ecosystem roles, and the bony and soft-tissue scans associated with this project will create the raw data necessary for researchers to understand how these minute fishes have adapted in different ways to their environment without damaging valuable museum specimens. In combination with CT scans completed by oVert and oVert partners, the products of this project will also be useful for researchers to identify general trends in vertebrate anatomical evolution associated with body size and will be a valuable resource for the development of new questions and hypotheses in a variety of scientific disciplines. Data will be shared with and made available through iDigBio.org and MorphoSource.org.
+''Project Sponsor'': [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001443 Los Angeles County Museum of Natural History Foundation (NSF Award #2001443)]
+''Principal Investigators'': [mailto:wbludt@gmail.com Willian Ludt] (PI)
+===GalapaGateway: Unlocking Model Evolutionary Systems for Research and Education===
+The California Academy of Sciences (CAS) is home to the largest and most complete collection of scientific research specimens from the Galápagos Islands, the majority of which can only be accessed by a small number of researchers able to visit the museum. GalapaGateway is a Partnership to Existing Networks (PEN) award that compliments the Open Vertebrate Thematic Collections Network (oVert TCN). This PEN will produce and disseminate high resolution three-dimensional (3D) imagery of approximately 1300 vertebrate specimens of reptiles, birds, and mammals from the Galápagos Islands, thereby increasing accessibility to these historical specimens. Resulting 3D scans will be available free of charge on multiple platforms, including iDigBio, MorphoSource, SketchFab, and a dedicated CAS portal that links scans to specimen data, fieldnotes, and images. Physical 3D models of selected specimens, such as giant tortoises and Darwin?s finches, will be printed for use in education and public outreach at the CAS and at the Charles Darwin Foundation in the Galápagos Islands.
+While the oVert TCN aims to scan a single representative of each vertebrate genus, this PEN will image multiple specimens per species to capture within-species variation. Variation within species of Galapagos animals was central to Darwin?s theory of evolution by natural selection and continues to serve as a textbook example for explaining these foundational concepts to students and the general public. Through a combination of computed tomography (CT) and structured light surface scanning, the GalapaGateway project will create morphological data and 3D models of multiple series of closely related taxa from across the Galápagos Archipelago, allowing for in-depth analysis of vertebrate morphology, variation, adaptation, and speciation. 3D surface scanning will be used on specimens too large for traditional CT-scanning machines. Producing these scans of iconic historical specimens from the Galápagos will facilitate a wide variety of academic inquiries, including research into morphology and allometry, development, taxonomy, and adaptive ecology and evolution.
+''Project Sponsor'': [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001435 California Academy of Sciences (NSF Award #2001435)]
+''Principal Investigators'': [mailto:lscheinberg@calacademy.org Lauren Scheinberg] (PI), David Blackburn, Maureen Flannery (co-PIs)
+===oBird: 3D Photogrammetry of Museum Specimens for Phenomics across the Avian Tree of Life===
+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.
+''Project Sponsor'': [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001652 Occidental Collect (NSF Award #2001652)]
+''Principal Investigators'': [mailto:mccormack@oxy.edu John McCormack] (PI)