Increasing the impact of vertebrate scientific collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network

Abstract

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.

Keywords: comparative anatomy; computed tomography (CT); data sharing; light scanning; natural history collections; photogrammetry.

Figure 1.

Diversity of extractable data and analyses resulting from traditional computed tomography (CT), diffusible iodine-based contrast-enhanced CT (diceCT), and photogrammetry (https://doi.org/10.17602/M2/M535781) of a formalin-fixed, ethanol-stored lizard specimen. Traditional CT scanning (https://doi.org/10.17602/M2/M359089) generates tomograms (left center) that can be used to reconstruct and isolate (a) the bony skeleton with osteoderms (teal), (b) isolated cranium segmented into individual and labeled bones, including (c) the braincase and (d) endocranial space representing the inner ear (with associated stapes), as well as (e) conducting Finite Element Analyses such as evaluating the distribution of stresses in the lower jaw when forces are applied (the red arrows) or (f) wall thickness analyses such as of cranial osteoderms or (g) to 3D print models. DiceCT scans (https://doi.org/10.17602/M2/M456707) generate tomograms that can be used to evaluate anatomy of soft tissue anatomy such as (h) skeletal muscles, (i) nervous system, (j) cardiovascular system, and (k) gastrointestinal tract, as well as revealing valuable natural history such as (l) gut contents (coleopteran elytra and carapace), (m) glands (such as the femoral glands [blue] and associated pores, in red), and (n) reproductive tract with eggs. Finally, the overlap between CT and diceCT data sets can be directly compared (o). All data sets are based on UF: Herp:191433 of the cordylid lizard Ouroborus cataphractus, except panel (l), which is from CAS: Herp:199384 of the closely related Karusasaurus polyzonus.

Figure 2.

Simplified workflow diagram of the initial oVert project. Following specimen selection at participating institutions, specimens were CT scanned at participating scanning sites, and the resulting data were deposited in institutional repositories and MorphoSource, such that they became widely available for different communities interested in research, education, art, and more. An example of specimens, data, and resulting models is provided as an inset for Sphenodon punctatus (FMNH: Amphibians and Reptiles:11115).

Figure 3.

Infographic summarizing key aspects of data generation and use during the oVert Project. The data on downloads and users of media are based on data files generated by MorphoSource for media files hosted in that repository for the oVert project and associated PENs (as of 1 November 2023); we cleaned these data to remove downloads and users that appear to be nonhuman automated requests “bots”. Publication data are based on curated information from Google Scholar. The top downloaded data set of the fish Piaractus (ANSP: Fish:166685, https://doi.org/10.17602/M2/M27533) was suggested as a reference data set for users of 3D Slicer by Buser and colleagues (2020).

Figure 4.

Examples of non-research uses of CT scans downloaded from MorphoSource. These data have been used in museum exhibits, including (a) large format prints (from Inner Beauty exhibit at Florida Museum of Natural History [FLMNH], 2021–2023) and (b) manipulatable 3D models on touchscreens (arrow; from Fantastic Fossils exhibit at FLMNH, 2022); for education, including (c) 3D prints used in teaching comparative anatomy (photograph: Christopher Sheil), (d) learning activities posted on QUBESHub, and (e) multipart digital models hosted on Sketchfab; and by artists, such as (f) a sculptural work titled “frog” (sculpture: Margaret Honda, 2019, Carnegie Museum of Art: A. W. Mellon Acquisition Endowment Fund, 2019.71; photograph: Bryan Conley; inspired by Conraua goliath, UF: Herp:64720, https://doi.org/10.17602/M2/M39477, and Pelophylax ridibunda, CAS: Herp:217695, https://doi.org/10.17602/M2/M49916), and (g) digital art of a bushmaster Lachesis muta (art: Erwin van der Minne, based on FMNH: Amphibians and Reptiles:31178, ark:/87,602/m4/M115937).