Diplodocus goes digital

August 21, 2018

No time for a proper post, so here’s a screenshot from Amira of Diplodocus caudal MWC 8239 (the one you saw being CT scanned last post) about to be digitally hemisected. Trust me, you’ll want to click through for the big version. Many thanks to Thierra Nalley for the Amira help.

Further bulletins as time and opportunity allow.

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John Yasmer, DO (right) and me getting ready to scan MWC 8239, a caudal vertebra of Diplodocus on loan from Dinosaur Journey, at Hemet Valley Imaging yesterday.

Alignment lasers – it’s always fun watching them flow over the bone as a specimen slides through the tube (for alignment purposes, obviously, not scanning – nobody’s in the room for that).

Lateral scout. I wonder, who will be the first to correctly identify the genus and species of the two stinkin’ mammals trailing the Diplo caudal?

A model we generated at the imaging center. This is just a cell phone photo of a single window on a big monitor. The actual model is much better, but I am in a brief temporal lacuna where I can’t screenshot it.

What am I doing with this thing? All will be revealed soon.

Preserved bits of the Snowmass Haplocanthosaurus, MWC 8028, with me for scale. Modified from Wedel (2009: fig. 10), but not much – MWC 8028 was about the same size as CM 879.

Let’s say you had a critter with weird neural canals and super-deeply-dished-in centrum-ends, and you wanted to digitally rearticulate the vertebrae and reconstruct the spinal cord and intervertebral cartilages, in a project that would bring together a bunch of arcane stuff that you’d been noodling about for years. Your process might include an imposing number of steps, and help from a LOT of people along the way:

1. Drive to Dinosaur Journey in Fruita, Colorado, to pick up the fossils and bring them back to SoCal. (Thank you Paige Wiren, John Foster, and Rebecca Hunt-Foster for an excuse to come to the Moab area, thank you Brian Engh for the awesome road trip, and thank you Julia McHugh for access to specimens and help packing them up!).

2. Take the fossils to the Hemet Valley Medical Center for CT scanning. (Thank you John Yasmer and team.)

3. Find a colleague who would help you generate 3D models from the CT scans. (Thank you Thierra Nalley.)

4. Talk it over with your university’s 3D vizualization team, who suggest a cunning plan: (Thank you Gary Wisser, Jeff Macalino, and Sunami Chun at WesternU.)

5. They print the best-preserved vertebra at 75% scale. (50% scale resin print shown here.)

6. You and a collaborator physically sculpt in the missing bits with some Super Sculpey. (Thank you Jessie Atterholt for sculpting, and thank you Jeremiah Scott for documenting the process.)

(7.) The 3D-viz team use their fancy optical scanner (basically a photogrammetry machine) to make:

  • a second-generation digital model (digital)
  • from the sculpted-over 3D print (physical)
  • of the first-generation digital model (digital)
  • made from the CT scans (digital)
  • of the original fossil material (physical).

(8.) With some copying, pasting, and retro-deforming, use that model of the restored vert as a template for restoring the rest of the vertebrae, stretching, mirroring, and otherwise hole-filling as needed. (Prelim 2D hand-drawn version of caudal 1 shown here.)

(9.) Test-articulate the restored vertebrae to see if and how they fit, and revise the models as necessary. (Low-fi speculative 2D version from January shown here.)

(10.) Once the model vertebrae are digitally rearticulated, model the negative spaces between the centra and inside the neural canals to reconstruct the intervertebral cartilages and spinal cord.

(11.) Push the university’s 3D printers to the limit attempting to fabricate an articulated vertebral series complete with cartilages and cord in different colors and possibly different materials, thereby making a third-generation physical object that embodies the original idea you had back in January.

(12.) Report your findings, publish the CT scans and 3D models (original and restored), let the world replicate or repudiate your results. And maaaybe: be mildly astonished if people care about the weird butt of the most-roadkilled specimen of the small obscure sauropod that has somehow become your regular dance partner.

We did number 6 yesterday, so just counting the arbitrarily-numbered steps (and ignoring the fact that 7-12 get progressively more complicated and time-consuming), we’re halfway done. Yay! I’ll keep you posted on how it goes from here.

The most complete caudal vertebra of the Snowmass Haplocanthosaurus (Foster and Wedel 2014) in right lateral view: specimen photo, CT scout, 3D model, 3D print at 50% scale. The photos of the specimen and the 3D print probably match the worst with the others, because they are subject to perspective distortions that the digital reconstructions are free from.

Here’s one nice thing about having a 3D print of a specimen that you’re working on: you can hand it to other anatomists and paleontologists and get their take on its weird features, and it’s small enough and light enough that you can bring it halfway across the country to show in person to an entirely different set of colleagues. For all that we hear about humans being a visual species, we are also a tactile one, and in my admittedly limited experience, grokking morphology by handling 3D printed fossils is almost as good as – and for big, heavy, fragile sauropod vertebrae, sometimes better than – handling the real thing.

Many thanks to Julia McHugh at Dinosaur Journey for access to the specimen, John Yasmer at the Hemet Valley Medical Center for CT scanning, Thierra Nalley at Western University of Health Sciences for help with segmenting and visualization in Amira, and Gary Wisser, WesternU’s 3D visualization specialist, for the sweet print. Further bulletins as events warrant.

Reference

Foster, J.R., and Wedel, M.J. 2014. Haplocanthosaurus (Saurischia: Sauropoda) from the lower Morrison Formation (Upper Jurassic) near Snowmass, Colorado. Volumina Jurassica 12(2): 197–210. DOI: 10.5604/17313708 .1130144

Peter Falkingham and Nick Gardner independently put me onto Sketchfab: a website that provides a way to view and navigate 3D models without needing to download any software beyond the browser that you’re already running.

So get yourself over to the live Xenoposeidon model! Verify for yourself that the laminae are as I described them, that the posterior margin of the neural arch really does grade into the posterior articular surface of the centum, etc. Really, this is worth ten times whatever set of illustrations I might have provided.

Truly, we are living in the future!

UPDATE, 23 November 2017: see also this beautiful 3d model of the skull of Triceratops horridus, photogrammetrised from images taken at the Museum National d’Histoire Naturelle, Paris, France, by Benoît Rogez; and the same creator’s Nanotyrannus lancensis model, also from MNHN photos. And, most astonishingly, his model of the whole MNHN palaeontology gallery!

In writing the recent preprint “Xenoposeidon is the earliest known rebbachisaurid sauropod dinosaur” (Taylor 2017), it was invaluable to have a 3D model of the Xenoposeidon vertebra available. Here’s a short clip of viewing the model in the free MeshLab program. (It’s well worth full-screening to get the full impact.)

As I pan around, I look first at the upper margin of the posterior articular facet of the centrum, showing how the posterior margin of the neural arch shades into it — something that is not really apparent from photos, but needs the shifting perspectives that 3D offers to eliminate the interpretation that this contiguous border is due to damage.

Then I zoom in on the complex of laminae at the top of the left side of the neural arch, and explore the shapes of the intersections (ACPL with lateral CPRL, and PCDL with CPOL).

Finally I look at the distinctive sets of laminae on the anterior face of the vertebra which enclose the big, teardrop shaped centroparapophyseal fossa: lateral CPOL coming in from the lateral face of the arch, medial CPOL emerging from the pedicels, and the additional arched laminae that bound the space.

It’s just great to be able to do this. Time and again as I was preparing that manuscript, I went back to the model to check some detail — much as, twenty years earlier, Matt kept driving into the OMNH late at night to look at the Sauroposeidon holotype, to check out some idea he’d had as he worked on the description. The difference is, I didn’t need to drive into Norman, Oklahoma — or even London, England. The idea now of going back to trying to understand fossils from photos seems ridiculous.

A few years back, Matt wrote:

The idea of superseding photographs with 3D photogrammetric models is not original. I got religion last week while I was having beers with Martin Sander and he was showing me some of the models he’s made. He said that going forward, he was going to forbid his students to illustrate their specimens only with photographs; as far as he was concerned, now that 3D models could be cheaply and easily produced by just about everyone, they should be the new standard.

I’m totally on board with that, and said as much in the concluding paragraph of the new preprint.

The last thing I want to say here is to acknowledge the enormous amount of help I’ve had from Heinrich Mallison, digitizer extraordinaire at the Museum für Naturkunde Berlin. He’s invested many, many hours building models for me from my photos, pointing me to programs that I can use to view them, and helping me get started on making my own models. The greatest regret of my palaeontological life is that, when I happened to be in Berlin on 19th November 2008 and Heinrich invited me to come and watch the Germany-England friendly at his place, I couldn’t do it, and missed out on a pretty unique chance to see England beat Germany, in Germany, with a German. I doubt that chance will come up again any time soon.

I leave you with EmperorDinobot‘s life restoration of Xenoposeidon, which I stumbled across a few days ago. Obviously it’s wildly speculative, but I’m cool with that.

References

  • Taylor, Michael P. 2017. Xenoposeidon is the earliest known rebbachisaurid sauropod dinosaur. PeerJ PrePrints 5:e3415. doi: 10.7287/peerj.preprints.3415 [PDF] [PeerJ page]