Issue: Volume 36 Issue 3: (Mar/Apr 2013)

Digital Specimens


Josh O’Dell

Whether intentional or not, the study of natural history has almost always been exclusionary, limited to those who have access to the rare specimens collected by museums and research institutions.

But what if researchers, teachers, and students could use remote computers to closely examine rare species and artifacts?

Democratizing and Demystifying

Since 2003, the Idaho Virtualization Laboratory (IVL) in Pocatello, Idaho, has been facilitating exactly these types of learning and research opportunities. Under the guidance of Lab Director Dr. Herb Maschner, IVL’s mission is to apply 3D imaging for the benefit of science and education. In large part, this means working to democratize science. “We want to take this closed world and open it up, put it in the hands of everyone,” says Lab Manager Robert Schlader. “Demystify it. Play with it.”

IVL’s expanding 3D imaging capabilities are advancing research, improving collaboration, encouraging education and outreach, and helping archivists better preserve history collections.

With IVL’s help, museums, researchers, and scientists can easily archive and share accurate virtual 3D copies of valuable collections for easy retrieval, teaching purposes, research, and posterity, all the while preserving the often-fragile original artifacts.

IVL has made the collection of the Idaho Museum of Natural History available to anyone with a computer anywhere in the world. Maschner and his team also have an agreement with the Smithsonian Institution to help capture whale skeletons and other artifacts and convert them into 3D images.

Menagerie of Artifacts

In its laboratory space on the Idaho State University campus, IVL houses seven laser surface scanners and Geomagic Studio software, which allow researchers to sample and process digital shapes rapidly and efficiently without sacrificing accuracy.

The 3D technological tool set is used to scan a vast range of skeletal remains into 3D – birds, walruses, sea lions, otters, bears, camels, even a prehistoric helicorpion – along with artifacts, such as arrowheads and primitive tools.

It’s all part of a project that Maschner has championed for the past decade, starting with his 3D Virtual Zooarchaeology of the Arctic Project (VZAP). Beyond VZAP, the Idaho Virtualization Laboratory’s projects include the Virtual Museum of Idaho, Virtual Museum of the Arctic, and Whales of the World, all of which can be accessed at IVL’s website (ivl.imnh.isu.edu).

“VZAP has been a real help training students in basic sorting and identification of faunal specimens,” says Dr. Anne Jensen, the general manager and senior scientist at UIC Science in Barrow, Alaska.

Jensen, an arctic archaeologist, works with local high school and junior college students who have no prior experience in faunal analysis. Her students use VZAP’s images in lieu of short-term, cumbersome physical collections to classify the specimens they unearth.

“Recently,” Jensen adds, “we have been using it to narrow the range of species that we need to compare specimens with, both to target loan requests better and to make sure we take the appropriate specimens to the repository.”

Tale of the Sitka Whale

One of the lab’s more ambitious assignments came about after a juvenile orca whale washed ashore on Kruzof Island near Sitka, Alaska, in 2011. After the University of Alaska scientists finished processing the whale skeleton, the IVL team journeyed to Sitka to digitize the remains.

Where typical jobs involve 3D scanning only certain animal bones, the Kruzof whale skeleton had to be completely digitized. In the course of a seven-day process, IVL technicians scanned skeletal data into Geomagic Studio to rapidly create quality 3D images. In only the second undertaking of its kind, scientists were able to take the captured 3D data, build 3D models, and articulate an intricate, entire skeleton in digital space.

Capturing Fine Details

The job of creating 3D models of each bone falls on the lab’s regular four-technician staff. The effort is led by Schlader, one of the region’s most skilled 3D technicians and a self-proclaimed “computer guy” who helped to build the lab from the ground up.

At this point, the team has developed a streamlined 3D scanning process that begins with data compilation and photography of each specimen. The photographs become part of the IVL’s archive and aid in the digital modeling process.

After photography, depending on the article to be scanned – its size, detail and morphology – the team selects from a range of scanners, including two FARO Technologies Edge scanners and one FARO Focus3D, Minolta VIVID 9i, NextEngine 3D scanner HD, Cyberware Model Shop, and Cyberware Desktop.

Each object is scanned in several positions to capture a complete 3D model. Scanning small specimens, such as birds, can be particularly challenging. IVL’s team has gotten creative to overcome some of the challenges, often dusting specimens with talcum powder. Because the grains are smaller than the scanner resolution, talcum helps the scanner pick up the surfaces, and it doesn’t damage the specimen.

From Real to Virtual

IVL technicians use Geomagic Studio for the preliminary editing of the resultant polygon meshes to remove any unnecessary artifacts from the scan. The software automates the process of filling remaining holes, removing intersecting polygons, and clearing vertex color data.

Using Geomagic Studio, technicians create two 3D model files: one at full resolution and one at roughly 1,000-polygon resolution. The two files are needed because full-resolution 3D models often contain anywhere from several hundred thousand to several million polygons – too large for most computers to process within a reasonable timeframe.

Geomagic Studio enables technicians to subdivide the low-resolution image and superimpose it onto the full-resolution image. The result is a clean topological surface and a flexible file that can be displayed in one of several layers of resolution depending on the capabilities of the user’s computer.

Finally, technicians use the photographs taken in the opening stage to overlay a texture map and color data onto each 3D model. This final version is rendered into a U3D file that is then converted into a PDF file.

The resultant PDF is viewable via Adobe Acrobat and allows users to take measurements, view in full 3D, and conduct comparisons. IVL also makes the Euclidian geometry of the image available, so it is possible to extrapolate dimensional data required for casting, machining, or rapid prototyping.

Teachers and Researchers

By bridging the real and virtual worlds, IVL is fulfilling its mission to democratize science one scan at a time. It’s a sometimes painstaking process, but a challenge that the IVL staff undertakes contentedly, knowing that its work is helping students and researchers in countries throughout the globe.

“Biologists teaching high school kids in Alaska, teachers of faunal analysis of skeletal material, osteology researchers and teachers, and professors studying human and VZAP material,” says Schlader, “they’re all using our images to do it.”

Josh O’Dell is a content creator for Geomagic, whose scanning and design software solutions are used to capture and model 3D content from physical objects, organically sculpt complex shapes, and prepare products for manufacturing.

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