The 3D Alligator: A new anatomical resource for education & research

Alligators are everywhere. They’re team mascots, Transformer toys, actors in Lubriderm commercials (and CSI: Miami), unwanted golfing partners, and even expensive cowboy boots. What might be a surprise is that they’re also “model animals” for scientists, meaning that there are dozens, if not hundreds, of published technical articles on all things gatorly. They’re also commonly used in K-12 and undergraduate classrooms. WitmerLab has been working on American alligators for years, because crocodilians are one of just two living groups (birds are the other) of that great tribe known as archosaurs that includes dinosaurs and pterosaurs. Now, we’re joining with Casey Holliday’s lab at the University of Missouri to present the 3D Alligator, two parallel, complementary, and growing websites that present alligator anatomy in all its 3D digital glory. In both cases, we’re starting with the skull, although we include a few soft-tissue systems that are active areas of research for us (brain, inner ear, sinuses, etc.). Casey’s team presents an adult skull, and we present a wee gatorling, a “day-0” hatchling that was stillborn on its birthday. Sad perhaps, but this little guy is now immortal, because we’re releasing him to the tubes of the interwebz. We also present some of our 3D alligator work on an adult done “way back” in 2008. Check out the WitmerLab 3D Alligator site and the Holliday Lab 3D Alligator site.

Just what is the 3D Alligator?
The 3D Alligator is intended to be a resource that will serve both the educational and research communities. The goal is to provide a highly interactive, freely available, and easily downloadable set of tools for understanding—or just playing with—alligator anatomy. Alligator anatomy, specifically skull structure, is a very common component of most undergraduate comparative anatomy classes and even some public school biology curricula, and so the 3D Alligator addresses STEM objectives as set forth by the US National Research Council. Likewise, many researchers in crocodilian, archosaur, dinosaur, or reptilian evolution can benefit by the detailed interactivity provided. Both the WitmerLab and Holliday Lab 3D Alligator sites use a mixture of 3D PDFs and QuickTime movies. Ultimately, the goal is to put the user in control of what aspects of alligator anatomy they want to see…and then let the user manipulate that anatomy as they see fit.

3D PDF of the WitmerLab day-0 gatorling. Clicking this image will open a 7.5 MB ("medium-sized") 3D PDF in this window. Once its loaded, click to activate. Other 3D PDFs are on the main 3D Alligator sites.

The wonder of 3D PDFs
To me, the heart of the 3D Alligator comprises the 3D PDFs. First, they require nothing of the user other than the ability to open a PDF. Even the free Acrobat Reader will do just fine. The beauty of 3D PDFs is that they provide any user with the high-end capabilities that we enjoy with our expensive software: the skull can be spun around in all directions and zoomed in and out; individual bones or soft tissues can be turned on or off, made transparent, or viewed individually or in combination with other bones; the lighting and background can be changed, etc. We provide each 3D PDF in three sizes so that users can match their interest and computer’s graphical power with our offerings. Download the small size to check it out, or download the large size to really get to work. We’ve been hosting 3D PDFs since 2007 with our work on the dinosaur Majungasaurus, where we even came up with a little 3D PDF tutorial (we’ve got a new one in the works).

Our wee day-0 gatorling (OUVC 10606) perched within the bony nostril of the skull (OUVC 9634) of a 12-foot alligator.

The WitmerLab 3D gatorling
Way back in 1990, while still a doctoral student, I made multiple trips to the Rockefeller Wildlife Refuge in southern Louisiana to work with Ruth Elsey to obtain alligator heads for my research. I also was able to return with complete growth series of embryos up through yearlings, which were fixed in formalin and stored in ethanol. Most were “cleared and stained,” but some just sat in our collection. A few of the latter were still in the egg and about to hatch…but never did. In July 2009, WitmerLab doctoral student Dave Dufeau ran one of these “day-0” gatorlings through the OUµCT scanner and, unwittingly, started the 3D Alligator project. OUVC 10606 was scanned for 5 hours and 12 minutes at a voxel size of 45 µm, 80 kV, 450 µA, 1200 views at 400 ms (Dave keeps meticulous notes!). The scan data were beautiful, and Dave used Avizo to digitally extract and isolate all the bones of the braincase, as well as the soft-tissue cavities within, including the air sinuses that comprise his dissertation (we’ll include the sinuses in the 3D Alligator when he’s done). Later, doctoral student Jason Bourke finished the job of “segmenting” the skull and assembled the QuickTime videos. Dave and Jason’s excellent work was picked up by doctoral students Ashley Morhardt and William Porter who made the 3D PDFs using Right Hemisphere’s Deep Exploration and Adobe Acrobat Pro. Ryan Ridgely and I helped and kibitzed throughout, and, of course, we did the work (with some labeling help from Jason later) on the adult alligator for the 2008 Anatomical Record article.

Team 3D Alligator: WitmerLab doctoral students (from left) Dave Dufeau, Ashley Morhardt, William Porter, and Jason Bourke. Dave is holding the day-0 hatchling that forms the basis for much of our 3D Alligator offerings. (Yes, the inspiration for this photo comes from the silver screen: http://bit.ly/ihcdfF).

First ever example of "maisanofication" whereby Jessie Maisano used the CT scan data of the extinct amphisbaenian Rhineura (at left) to digitally isolate the bones, such as the premaxilla at right. From Journal of Morphology 264:1-33 (2005).

Paying homage to UTCT
Any CT-scan-based work on alligators must acknowledge the pioneering work of Tim Rowe at the University of Texas at Austin’s UTCT facility, as well as his then doctoral student Chris Brochu (who is now a leader of our profession). In 1999, they published Alligator: Digital Atlas of the Skull, with a CD-ROM. It presented mostly CT slices, many of which were labeled by Chris. It may feel a little dated now, but it’s a monumental and still useful landmark. Another clear inspiration for our 3D Alligator work is hereby named “maisanofication” in honor of Jessie Maisano, another UTCT person, who rocked the anatomical world in 2005 by digitally disarticulating an intact skull by painstakingly going through the CT scan data and separating bones at their sutural boundaries. The Holliday Lab and WitmerLab teams maisanofied our gators. Thanks, Jessie!

The future of the 3D Alligator
It’s Casey’s and my intention to keep building up these 3D models, adding anatomical components along the way. In a sense, the 3D Alligator provides us with an outlet for aspects of our work that don’t quite fit into our question-based, hypothesis-driven projects. Still, these “incidental outcomes” are potentially useful to a variety of people of all ages and in a variety of contexts. Please check both our sites for updates down the road, and please share your comments, suggestions, and criticisms here.

–Larry Witmer