3d images

Researchers use micro-CT scanners to upload 3D images of specimens

Behind the exhibits held at the University of Colorado Museum of Natural History are rows and rows of preserved specimens.

“We have thousands and thousands of specimens,” said Cameron Pittman, a graduate collection assistant at the University of Colorado Museum of Natural History, as he browsed the aisles of jars.

It is not a place that the public can generally access. These preserved snakes and lizards are for research and traditionally had to be sent by regular mail to other researchers for scientific purposes.

“Researchers all over the world, people all over the world want to see this stuff and they don’t get the chance,” Pittman said. He is part of a network of people working to change that.

“The goal here is to create this high resolution digital anatomical data that can be used in research, but can also be used in the classroom and by the public in general audiences for other purposes,” David Blackburn, the curator of amphibians and reptiles at the Florida Museum of Natural History, said.

Blackburn has helped spearhead this project with other institutions across the United States over the past five years. Their goal is to create 3D models of specimens and upload them to several websites, such as an online repository called MorphoSource, which scientists use, and Sketchfab where the public can manipulate 3D files.

“Our data has been viewed over a million times in this data repository and downloaded hundreds of thousands of times for research purposes,” Blackburn said.

In their final form, they might look like a multi-layered x-ray or a perfect scan of a creature. In some cases, they are transformed into 3D models.

“We rely primarily on micro CT scans, similar to CT scans you might get from the doctor,” Blackburn explained. Its online collection shows what it can become online – for example, models of skulls with each part colorized to highlight different parts.

“For a smaller number of them, there are these dynamic 3D models that are really more geared towards educators and students,” he said.

“From the mom and dad who want to show their kids cool specimens to the person who wants to draw a snake and needs a realistic setting,” Pittman said.

The process is tedious and begins with sample selection. Each micro-CT scan can take up to 10 hours.

“The goal is to digitize literally everything we have in our collection,” Pittman said. Everything is then put online.

“When we put them online, it’s a way of preserving them,” he said.

In this museum, the team focuses on the diversity of Mesoamerican herpetofauna, and the project is called oMeso for short.

This helps make collections like these – and the rare or endangered species that may exist here – more accessible to people around the world.

“We protect them by finding ways to share them, because the more people who know about these specimens, the more people there would be who would be interested in keeping these specimens,” Pittman said.

Blackburn said the goal of the project is to put at least one example of every living vertebrate genus online. So far, approximately 12,000 specimens have been imaged using computed tomography, photogrammetry or light-based scanning. This may have its limits.

“There’s no giant whale preserved in liquid that we can fit into a scanner, so there are some things that are out of reach,” Blackburn said.

The project is funded by the National Science Foundation.