3D Scanning Helps Crabby Scientists Gather Data

In one of my elementary school classrooms, we had a hermit crab for a class pet, and when the time came, we’d all gather around its cage to see which shell it would choose for its next home. Hermit crabs, or Paguroidea, are one of the most diverse superfamilies of sea crustaceans, and one of the most recognizable features is how the hermit crab conceals and protects its pleon, or abdomen, inside a sea shell (or, occasionally, an artistic 3D printed ‘home’).

There are 1,100 recognized species of hermit crabs at the moment, though there are likely many more sitting in museums unidentified – due to their small size and similar, membranous bodies, hermit crab species are hard to identify through shared characteristics.

Taxonomy is the science of defining groups of biological organisms on the basis of these shared characteristics, and then naming the groups. Taxonomists can’t properly identify a species without intense examination and study of the original illustrations and descriptions of a creature, most of which have not yet been digitized. Often, scientists are only left with the option of borrowing valuable samples from museums.

Recently, a study was published in the GigaScience journal by researchers from the University of Cape Town and Stellenbosch University, both in South Africa, that details some of the latest work completed thanks to the newest functionality available to the public through the GigaDB repository. GigaDB now offers 3D visual data, which can be embedded through the use of widgets, about some rare hermit crab specimens and three recently discovered species, thanks to 3D micro computed tomography (CT) scanning technology.

“By making this microCT data publicly available, taxonomists potentially have more time and cost-efficient options for examining and comparing specimens for taxonomic research, as well as providing new opportunities for education and training,” explained GigaScience Executive Editor Scott Edmunds in a blog post. “To ease access to these data, the authors go beyond just describing the data collection and findings by providing downloadable, interactive files of everything in this study.”

3D scanning and micro-CT scanning provides taxonomists, scientists, and researchers with an easier way to examine animals, like the hermit crab, without having to capture one or borrow a sample from a museum’s private collection.

According to a GigaScience study on this method, “Laboratory x-ray micro–computed tomography (micro-CT) is a fast-growing method in scientific research applications that allows for non-destructive imaging of morphological structures.”

GigaDB now provides 3D printable scans, interactive web-based viewers, and video clips that are available for download. For their paper, Jannes Landschoff, Anton Du Plessis, and Charles L. Griffiths used this new functionality to scan seven different hermit crab samples, including one unknown species, three that were recently discovered, and two rare species, including one from a deep-sea habitat.

“This study clearly shows the power of the technique and the magnification allows precise identification of surface textures which are often missed in photographs or even in manual drawings,” said senior author Du Plessis about the advantages that X-ray micro-CT scanning provides in analyzing and visualizing new species.

The physical specimens the researchers utilized in this study now reside at the Smithsonian National Museum of Natural History and the Iziko South Africa Museum. But, because of the new 3D functionality, other researchers can examine the samples to their heart’s content without ever having to leave their living room.

“The 3D model viewer enables CT and MRI images to be interactively explored. This interface development has huge potential for Digital Biology, and enables morphology and in situ gene expression patterns to be explored easily using a desktop, laptop, or mobile device,” explained GigaScience’s Chris Armit, who deployed the new Sketchfab viewer in GigaDB. “We will be extending the visualisation tools to enable exploration of complex image data captured using optical imaging and molecular imaging techniques.”

Thanks to this new functionality, the researchers were able to publish the latest species description of the Diogenes albimanus in the Zootaxa journal.

“MicroCT is still a relatively new technique for taxonomy,” explained first author Landschoff when Giga asked him about the research. “For describing new species of hermit crabs, these data were particularly useful to visualize the calcified hard structures using 3D surface-rendered images. A good taxonomic description of a species is highly dependent on quality illustration of the identification characters of the candidate species.

“Publishing the dataset also makes the scientific hypothesis of a species being new easier to evaluate, not only in the peer-review process but also in later studies. At the same time these downloadable avatars can act as an insurance policy should the type specimens get damaged or lost.

“I think that hermit crabs are a challenging group for CT-scanning, because their pleon is soft, and because they have many fine-scaled soft-tissue ID characters. In my conclusions of my thesis I stated that hermits are maybe the worst possible model organisms within the Decapoda to use CT scanning, yet the scans were valuable. In a nutshell, if hermit crabs can be scanned, other groups like the Brachyura, which are entirely calcified would be very suitable for scanning.”

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