Morphosource: Archiving and Sharing 3-D Digital Specimen Data

Abstract

Advancement of understanding in paleontology and biology has always been hindered by difficulty in accessing comparative data. With current and burgeoning technology, the severity of this hindrance can be substantially reduced. Researchers and museum personnel generating three-dimensional (3-D) digital models of museum specimens can archive them using internet repositories that can then be explored and utilized by other researchers and private individuals without a museum trip. We focus on MorphoSource, the largest web archive for 3-D museum data at present. We describe the site, how to use it most effectively in its current form, and best practices for file formats and metadata inclusion to aid the growing community wishing to utilize it for distributing 3-D digital data. The potential rewards of successfully crowd sourcing the digitization of museum collections from the research community are great, as it should ensure rapid availability of the most important datasets. Challenges include long-term governance (i.e., maintaining site functionality, supporting large amounts of digital storage, and monitoring/updating file to prevent bit rot, which is the slow and random corruption of electronic data over time, and data format obsolescence, which is the problem of data becoming unreadable or ineffective because of the loss of functional software necessary for access), and utilization by the community (i.e., detecting and minimizing user error in creating data records, incentivizing data sharing by researchers and institutions alike, and protecting stakeholder rights to data, while maximizing accessibility and discoverability).MorphoSource serves as a proof-of-concept of how these kinds of challenges can be met. Accordingly, it is generally recognized as the most appropriate repository for large, raw datasets of fossil organisms and/or comparative samples. Its existence has begun to transform data transparency standards because journal reviewers, editors, and grant officers now often suggest or require that 3-D data be made available through this site.

Three‐Dimensional Geometric Morphometric Analysis of Treeshrew (Scandentia) Lower Molars: Insight into Dental Variation and Systematics

“…Treeshrew mandibles ( n = 43; all specimens are listed in Table ) from a mixed sample of males and females were micro‐CT scanned in a Nikon XT H 225 ST High Resolution X‐ray CT Scanner at the Shared Materials Instrumentation Facility at Duke University or were downloaded from MorphoSource (Boyer et al, ) and range in voxel dimensions from 11 to 29 μm. The sample consists of 15 species from both treeshrew families, representing three of four currently recognized genera, excluding only Anathana .…”

A Statistical Pipeline for Identifying Physical Features that Differentiate Classes of 3D Shapes

“…Landmark-based approaches have two major shortcomings. First, many modern datasets are not defined by landmarks; instead, they consist of 3D CT scans [8,9]. Second, reducing these detailed mesh data to simple landmarks often results in a great deal of information loss.…”

“…For example, in a dataset of fruit fly wings, some mutants may have extra lobes of veins [15]; or, in a dataset of brain arteries, many of the arteries cannot be continuously mapped to each other [16]. Indeed, in large databases such as the MorphoSource [9], the CT scans of skulls across many clades are not diffeomorphic. Thus, there is a real need for 3D image analysis methods that do not require correspondences.…”

3-D FOSSILS FOR K–12 EDUCATION: A CASE EXAMPLE USING THE GIANT EXTINCT SHARKCARCHAROCLES MEGALODON

“…There are several resources nationwide in the process of sharing 3-D raw data, including those of paleontological relevance. These initiatives have great potential to allow students to develop deeper understanding of morphological changes demonstrated in specimens (Boyer et al, 2017). This is an enormous shift in how science can be taught.…”

“…For instance, specimens in the past were analyzed in large part through standard, 2-D photographs (Lauridsen et al, 2016). Thanks to 3-D data available today, not only do scientists have the opportunity to produce high fidelity descriptions, but K-12 students can also learn complex concepts, e.g., evolution and extinction, by visually analyzing changes that occur over time (Boyer et al, 2017).…”