Computed Tomography for Non-Destructive Testing in Natural History Museum Collections
November 04, 2016
In a recent CT Science Days event, Dr. Edward Stanley, PhD of herpetology, of the California Academy of Sciences, discussed how ...
In a recent CT Science Days event, Dr. Edward Stanley, PhD of herpetology, of the California Academy of Sciences, discussed how researchers are using computed tomography to study reptiles and amphibians in ways that preserve specimens and facilitate collaboration. The following is an excerpt of his talk from his educational video seminar, held in Hudson, Ohio, USA, in the spring of 2016. Our thanks to Dr. Stanley for his contributions. --Editor's Note
When you think of natural history museums, you probably think of things like dinosaurs rearing up improbably, or dioramas with cave men, or living forests and bio-domes. Or, maybe you think that it's a good place to employ out-of-work actors. There are all kinds of things like this in natural history museums around the world. Education is a massively important role that museums play, but, actually, behind the scenes they're legitimate research institutions, and they play an important role in academic research for a whole range of different fields.
What Do Natural History Museums Do?
Museums employ a lot of scientists like myself to work on the collections. What sets museums aside from a lot of other research institutions is that they have collections of specimens that they've accumulated over decades, or even hundreds of years, that represent a sampling, a physical database of life on our planet. And they continue to do this. So, not only do they have lots of skulls, and furs, dead birds, and fossils, but they also have tissue as well. They keep DNA samples now, too, which is a new capability. They keep records of expeditions throughout the years. They keep locality information, and genetic data as well, and they're continually adding to this body of knowledge every day.
This colossal repository of biological information is a continuously growing source of natural history information. The collected items can be stored and prepared in multiple ways. A lot of insects are dried, then pinned. This is, as one recalls, similar to Darwin's famous collection of butterflies. Often, a lot of the smaller vertebrates and invertebrates are kept in alcohol, to stop them from decomposing in jars. Scientists also collect skeletal material, especially for the bigger specimens. There isn't really a jar big enough to fit an elephant. And even if you could fit an elephant into a jar of alcohol, no one would be willing to take the elephant out of the jar of alcohol to study it, so there's no point in doing it. That's an extreme example of why skeletal information is so important. Thus, different plant and animal groups have varying, special preparation requirements. For example, birds are often prepared as skins, so you can look at the color of the feathers.
Capturing Life On Earth
The basic reason many of these natural history museum collections exist is to gather, safeguard, and share data and information pertaining the world around us, and the universe in general. But specifically for the things that we look at, it really pertains to the "Tree of Life," which consists of plants and animals.
When we study flora and fauna, it is our attempt to capture how everything fits in with each other, how everything is related to each other, and how animals interact or animals and organisms interact with one another. It's a description of biodiversity, what the differences are, what the similarities are, and understanding the history of life on this planet. And so these natural history collections can be pretty mind-blowingly large and diverse. For example, the American Museum of Natural History in New York is not the biggest museum in North America, but it's one of the larger ones. It houses 24 million invertebrates, 24 million invertebrates, over 4.5 million fossils, two million fish, one million birds, and reptiles and amphibians, mammals, ethnographic and archeological objects, and minerals, meteorites. This institution has a massive, diverse range of specimens from all over the world and going back hundreds of years. Today, this includes a rapidly-growing collection of DNA tissues.
What do people use these samples for? As it turns out, they use this data in wide range of ways. Traditionally, museum collections have been used to describe new species, or understand variation within groups of animals, or to look at predation. Scientists also look at morphology, and variation across groups. Sadly, a museum is the only place to find a Passenger Pigeon these days. They were once common, with billions and billions of them in North America, and now they are extinct. Ultimately, researchers come up with really cool, unpredicted applications that no one could have imagined when they were collected.Consider the Chytrid Fungus. This is a disease that is wiping out massive amounts of amphibians around the world. This global amphibian decline is a real problem. We're not sure where it came from or when it started, but going into museum collections, researchers can swab and test for the presence of this fungus on the museum specimens, going back 10, 20, 100 years from all over the world. We can actually test to see where this fungus originated, and how it spread around.
Just Like Jurassic Park?
Museum collections are constantly being used; people come from all over the world to study them, and the specimens get sent out all over the world. This is great, and it's been going on like this for a long time, but with CT scanning we are able to open up a whole new realm of possibilities for Natural History Museum collections.
For example, we came across some 100 million-year-old specimens in amber. We were very excited about it because these are some of the oldest lizards trapped in amber ever, and there were a lot of them, with an awful lot of diversity to them. We looked at them under regular microscopes, and we thought, "Oh that's pretty cool, we can kinda make out some things." Then we thought, "Well, these are probably geckos or...other things."
Then we used Computed Tomography to perform non-destructive testing. CT scanning really allowed us to go in and look and see huge amounts of detail; it allowed us to go in and "dissect" out certain areas, using software. We can look and see sclerotic rings--the rings in the eyes--from a 100 million-year-old animal, which is amazing. It's practically just like the movie Jurassic Park!
CT Enables Collaboration
Using the CT scans, we also created 3D-printed representations of some of these animals to share with other researchers. The applications for sharing this information are pretty huge. CT scanning will allow museums to share information with people digitally and instantaneously. And it also allows massive collaborations around the world so that people could be working on the same animal simultaneously. For each researcher, the 3D model is actually, for all intents and purposes, an exact facsimile of the animal. Added to that, there are a number of websites that are working on online storage for this type of data so it becomes an online resource. This trend will only accelerate as more researchers discover the benefits of computed tomography.
Digital "Dissections" Preserve Specimens
When we work with specimens digitally, what we are doing is sectioning areas of voxels and assigning them to specific regions that then we can treat as independent objects. Then, we can add a density gradient, and change the color associated with density or even change the transparencies. We can create different volumes and articulate them independently of one another. For example, using a fixed specimen, where the jaws were fused shut, we actually articulated the jaw with the software, moving it around to simulate how it would fit with the upper jaw. We did the same with the lizard in amber; when we reconstructed the skull we digitally pieced it all back together again. All of this is doable with CT technology.
Finally, there are the educational applications. Once the specimens have made their way around, you can just imagine what the applications for teaching evolution or biodiversity or all kinds of things might be. For example, if you have access to a specimen as a digital CT reconstruction or as 3D prints made from that, imagine being in a classroom and learning about convergent evolution. With wing evolution, instead of reading it in a book, a student can hold a bird wing and a bat wing and a pterodactyl wing in her hand and be able to compare the homologous bones. It truly is mind-blowing.
To watch the full video seminar about CT for museum collections, click the image below:
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