Current trends in publishing 3D Anatomy

From Rybczinski et al., 3D modeling of Hadrosaur Chewing, PE, 2008.: a beautiful 3D model pasted onto a 2D page and defaced with 2D muscles

One might say that the past decade has been the decade of 3D visualization in paleontology. Although techniques such as CT, MRI, laser scanning, serially-reconstructed histology, and confocal microscopy (and of course molding/casting)  have been around for a long time, and championed by a few, only recently have they become common enough to be available to so many different researchers, students, and enthusiasts alike. With these 3D data-driven techniques have come new ways of disseminating 3D data via the internet. Publications such as Paleontologica Electronica and PLoS have made it easier to include movies  (check out Alex Tirabasso’s movie of Hadrosaur Chewing in PE 2008) and 3D models directly into the publication, rather than as supplementary files which were long the only means to append video files–a common occurrence in journals like Journal of Experimental Biology, Journal of Zoology, Journal of Morphology, and the like. But the ability to post 3D material directly onto the web has really changed the game.

During the past 15years, we’ve seen numerous new virtual museums enter the Web, offering new views, visualizations, and interactive features that allow viewers to study a variety of specimens, bones, and raw data. The real heroes of this movement, ones that first grabbed my attention, were sites like Digimorph at U Texas and  3D Museum at UC Davis. Numerous others have cropped up like Paleoview at Marshall, Larry Witmer’s 3D visualization page, and most recently Aves3D at Holy Cross. These were  spearheaded by Tim Rowe, Ryosuke Motani, Suzanne Strait, Larry Witmer, and Leon Claessens respectively. I’m sure there are others, and our lab too has a growing assortment of 3D content on its page.

From Holliday Lab 3D database: a 2D picture of a 3D model

What they all have in common is that they share 3D specimen data freely, which is awesome. How they differ is in the way they process and present it. Digimorph offers views of the raw CT data (in stacked .tiffs) via their Inspector Java applet as well as movie files of 3D reconstructions of the specimen. 3D museum and Aves3D make use of a software package called WireFusion, which converts the 3D model, in these cases taken from laser scan data, and embeds it as a .vrml object in a 3D interactive environment where you can manipulate the object directly on the webpage. We gave this method a shot 2 years ago where Nick Gardner made a number of WireFusion models of our Lizard microCT data used in our ongoing histology studies. Thanks to Leon for turning me on to that. Paleoview 3D and the WitmerLab page take it one step further, by sharing the 3D data in downloadable formats such as .obj (works well with Maya, 3DSmax), .wrp (Geomagic), .stl (most CAD programs), and finally 3D pdf formats.

The 3D pdf is particularly slick because everyone has access to Adobe Acrobat, which is all you need to view the models; but also you can generate models that have parts you can highlight, select, or hide thus enabling the viewer to see inside of structures. This method is particularly useful if you study endocasts, or models of brains or pneumatic cavities, or jaw muscles that happen to be inside that pesky skull. Check it out its awesome. We’ve generated some of these ourselves and use them teaching medical students, high school students, or include them in long format talks where there’s time to switch out of your powerpoint presentation. We’ll have online 3D and raw CT content for a new crocodilian species we’re writing up too, these, along with the raw CT data, will also go to the accessioning museum upon the return of the specimen. They’ll be posted soon enough on our lab page.

To generate a 3D pdf, first you need a 3D dataset that you can then turn into one of many file types that Adobe 3D (v8, or 9 extended) can read. We use Amira, since we primarily use CT and MRI data, but if you’re using laser scan data, there are several different file formats you can export from SolidWorks, RapidForm, Geomagic, etc.  into Adobe. Also there’s VGStudio, Mimics, and the handy freeware Slicer, all of which export models into readable formats such as .stl or .obj. Those of you that don’t have access to the pricier software packages, Slicer is nice and, geez, now years ago, Andy Farke over at the Open Source Paleontologist posted an inspiring tutorial on how to use this software package. Finally, I learned many of these tricks during my dissertation at Ohio University w/ Larry. His lab has remained a useful go-to place for help on occasion.

Besides the general ease, the slick look, and the accessibility of these 3D models, what I like these days, since I don’t necessarily have as much time to “color” as I used to, is that undergrads, and even high school students (and of course, hopefully, grad students) can easily master the skills necessary to dive into a data set and make a 3D model and see it published/shared on the web. During this process, they learn a particular animal, and its parts pretty well, while also learning how to use some still “cutting-edge” software. This is particularly useful to students that have interests in radiology, surgery, and various health care professions let alone those that choose to go to graduate school


Axial section of alligator embryo, with muscles and nerves, soon to be a model (and pubbed).

Currently both Rebecca and Cortaiga (our Undergrads), Henry the PhD student, and Ian, a rotation PhD student, all have models in preparation that complement research projects and will be ready for our Annual Health Sciences Day Nov 11. Each of these projects will find their way into the publication pipeline in the next few months as well and some form of a 3D model in 3Dpdf format (and more) will be made available. So stay tuned.

Putting these data up for free is cool, and indeed they will be used initially in particular papers (where we can ‘spin’ their utility), and likely others in the future. But how does one “get credit” for sharing data? Funding agencies like NSF apparently like this behavior of making data and models available, so I’ll stick with it just for that; though I have to say, when I included our 3D lizard page  as an example of public dissemination as well as UG training  in my Broader Impacts a grant or so ago, it was called “fleeting” (Since apparently the webpage might disappear one day, a reviewer opined) as well as “lipservice”. I’m still not sure wtf that means since I have an ok record of getting things out, and then getting them up on the page, and have had the pleasure of having several most excellent undergrads working in the lab. But it takes time, people, and funding to expand before one can share significantly, and easily.

But for readers, here’s a question: Are there outlets where one can actually “publish” online atlases, or small modeling projects? Are there good, or bad things you see happening regarding 3D data dissemination? Do you find it easy to get 3D data and scanning facilities, easy access to software, or help with software? Or if you’re without these things, do people share their model data if you bug them enough?

-Casey

Making Connections: SVP 2010 Symposium and More

Mark your Calendars!!! One week from today Matt Vickaryous (University of Guelph) and I will be co-convening a Symposium on Joint Biology entitled:

Making Connections: the Evolution and Function of Joints in Vertebrates

This series of talks will complement numerous other exciting new findings shared at the Annual Meeting of the Society of Vertebrate Paleontology (SVP) in Pittsburgh this year.  Everyone knows vertebrate paleontologists study bones, but it’s not always common knowledge that they also rely on linkages between bones to tell their stories. Joints are obviously central to the ability for an organism to grow and move parts of its skeleton, whether it be the limbs, vertebral column or jaws; and vertebrates do a lot of different things with them. We took this opportunity to highlight the spaces in between the bones so characteristic to our field by bringing a variety of expert faculty and students to one room to discuss some of the most current, integrative research on the topic. The full symposium schedule is at the bottom of the post.

For those of you up for the 8am time slot (who sleeps at SVP anyway?), I’ll be kicking things off with our findings from our recent Anatomical Record paper but will intro with rapid review of reptilian cranial joints to highlight some new projects we have going, and why they’re relevant to understanding the evolution and function of cranial joints in lizards, crocs, and dinosaurs. My coauthor, Nick Gardner was an undergraduate in my lab during the  project and an important member of our research team. He helped design our 3D anatomy database at the bottom of the linked page above. The 3D anatomy database will be growing significantly since we’ve got tons more histology and 3D models (of more than just lizards) to put up when I get a chance. It will have 3D reconstructions of serial histology, interactive models made from CT and MRI data, muscle reconstructions, and some other goodies.

I expect the symposium to go well. It’s a full schedule (16 talks; 2 posters); each talk is only 15min tops (which is kinda short for symposium talks) and we will have to rule with iron fists to keep on time (I reserve the right to start things off late ;) ). Moreover, we don’t get 5 or so minutes at the start to introduce the symposium itself, which is typical at many other meetings. Regardless, it will be awesome. It’s opposite a session on birds and flying reptiles (so I will have to remain ignorant of pterosaurs)  and then the 3rd, concurrent session on mammalzzzzzzzz.

I wanted to hype two other posters. 1st is again Marshall Undergraduate student Nick Gardner’s poster on the braincase of the primitive reptile Youngina using microCT (with Robin O’Keefe , Helen Zhu, and myself). This is Nick’s first presentation at SVP, come check it out, it’s wicked. Also, Henry Tsai, who just started his PhD with me this semester at Missouri’s Integrative Anatomy Program will be presenting his Undergraduate research project from his very interesting work with Tomasz Owerkowicz and Jim Hicks at UC Irvine on locomotion and adaptive plasticity of the bone of  Alligator. It’s Henry’s first SVP presentation as well, come check it out.

Finally, our still fledgling, 3yr old Integrative Anatomy program will have a good showing at SVP this year: 3 talks (Ward, Ravosa, Holliday) and 3 posters (McAfee, Hammond, Tsai). We also have 2 Lecturer positions open, so if interested, find one of us at the meeting.

Sunday Poster Session

Gardner, N., Holliday, C., Zhu, H., O’Keefe, F. BRAINCASE ANATOMY OF THE BASAL DIAPSID YOUNGINA CAPENSIS FROM HIGH-RESOLUTION X-RAY CT SCANNING

Tuesday Poster Session

Tsai, H., Owerkowicz, T., Felbinger, K., Andrade, F., Hicks, J. CHRONIC EXERCISE DOES NOT ALTER LIMB BONE MORPHOLOGY OR MICROSTRUCTURE IN THE AMERICAN ALLIGATOR (ALLIGATOR MISSISSIPPIENSIS)

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Straight from the program, the full list of Symposium participants is below:

TUESDAY MORNING, OCTOBER 12, 2010

SYMPOSIUM: MAKING CONNECTIONS: THE EVOLUTION AND FUNCTION OF JOINTS IN VERTEBRATES

MODERATORS: Casey Holliday, Matthew Vickaryous

8:00 Holliday, C., Gardner, N. STRUCTURE AND FUNCTION OF THE REPTILIAN MANDIBULAR SYMPHYSIS: INSIGHTS FROM SQUAMATES

8:15 Osi, A. JAW MECHANISM, DENTAL OCCLUSION AND EFFECTIVE ORAL FOOD PROCESSING INHETERODONT CROCODYLIFORMS: AN UNEXPECTED VARIABILITY

8:30 Gill, P., Rayfield, E., Robson-Brown, K., Gostling, N. A FUNCTIONAL INVESTIGATION INTO THE JAW JOINTS OF TWO OF THE EARLIEST STEM MAMMALS; MORGANUCODON WATSONI AND KUEHNEOTHERIUM PRAECURSORIS

8:45 Ravosa, M., Ning, J., Stock, S., Stack, M. JAW-JOINT FUNCTION AND PLASTICITY IN MAMMALS

9:00 Luo, Z. MORPHOLOGICAL EVOLUTION OF THE DOUBLE CRANIOMANDIBULAR JOINT IN THE CYNODONT-MAMMALIAFORM TRANSITION

9:15 Curtis, N., Jones, M., Evans, S., O’Higgins, P., Fagan, M. THE ROLE AND FUNCTION FOR CRANIAL SUTURES IN REPTILES: A FINITE ELEMENT ANALYSIS OF THE SKULL OF SPHENODON (DIAPSIDA: LEPIDOSAURIA: RHYNCHOCEPHALIA)

9:30 Bright, J., Gröning, F., Rayfield, E. MAMMALIAN SKULL CONSTRUCTION AND THE IMPORTANCE OF CRANIAL SUTURES IN BIOMECHANICAL FINITE ELEMENT ANALYSIS

9:45 Maddin, H., Wake, M. EXPLORING THE INFLUENCE OF FOSSORIALITY ON TETRAPOD CRANIAL ARCHITECTURE, A FOCUS ON CRANIAL JOINTS

10:00 BREAK

10:15 Vickaryous, M., Reisz, R., Modesto, S., Head, J. TAIL AUTOTOMY IN THE FOSSIL RECORD: NEW INFORMATION ABOUT VOLUNTARY TAIL LOSS IN CAPTORHINID REPTILES

10:30 Pierce, S., Molnar, J., Hutchinson, J., Clack, J. REGIONAL VARIATION OF INTERVERTEBRAL JOINT STIFFNESS IN EXTANT AND EXTINCT TETRAPODS AND ITS IMPORTANCE FOR THE WATER-LAND TRANSITION

10:45 Claessens, L., Hirasawa, T. RIBCAGE ANATOMY, SKELETAL CONSTRAINT AND KINEMATICS IN EXTANT AND EXTINCT ARCHOSAURS

11:00 Ward, C., Hammond, A., Plavcan, J., Begun, D., Kordos, L. HIP JOINT MORPHOLOGY AND HOMINOID EVOLUTION: FROM QUADRUPEDAL TO SUSPENSORY TO BIPEDAL LOCOMOTION

11:15 Gatesy, S., Kambic, R., Roberts, T. BEYOND HINGES: 3-D JOINT FUNCTION IN ERECT BIPEDS

11:30 Su, A., Patel, B., Carlson, K. SUBCHONDRAL AND TRABECULAR BONE MORPHOLOGICAL CORRELATES OF LOCOMOTOR BEHAVIOR

11:45 Sullivan, C., Xu, X., Zhang, F., Drake, A., Cooper, M. FUNCTION AND EVOLUTION OF THE ANKLE JOINT IN THEROPOD DINOSAURS

12:00 Bonnan, M., Sandrik, J., Nishiwaki, T., Wilhite, R., Elsey, R. NON-AVIAN DINOSAUR AND EXTANT ARCHOSAUR LIMB JOINTS: WHAT’S MISSING, WHAT’S NOT, AND WHERE DO WE GO FROM HERE?

And Two Symposium Poster Participants:

Hammond, A., Koscielniak, N., Plavcan, J., Ward, C. 3D ANALYSIS OF PRIMATE HINDLIMB JOINTS: RECONSTRUCTING POSITIONAL ABILITIES IN EXTINCT PRIMATES

Shychoski, L., Snively, E., Burns, M. MANEUVERED OUT OF A CORNER: LIGAMENT ENTHESES OF THE ARCTOMETATARSUS ENHANCED TYRANNOSAURID AGILITY