Yesterday I feel like I really got to grips with the software that my 2 coursemates and I are going to be using in our Virtual Anatomies module for the next 6 weeks.
It took a good 4 hours but I finally reconstructed the skull of a macaque monkey (Wikipedia). It may sound like a long time just to do what you’re about to see, but the software (Avizo) is a bit touchy about whether it wants to do what you tell it when you tell it to. I was lucky to finish, my coursemates weren’t quite so lucky.
I am by no means an Avizo prodigy.
Our task was to reconstruct the missing cheek bone (zygoma) on a macaque skull which had been 3D-scanned into the computer.
Check out all the screen shots. Pretty cool, I hope you’ll agree.
This is what the skull looked like without any work done to it:
As you can see, the macaque’s right zygoma is intact, but is missing on its left side.
And this is a cross-section of the skull shown from the front, where you can also see that the zygoma is missing.
The first thing to do was select the matching region of the right zygoma and treat it as a separate object from the rest of the skull (segment it).
After this, you need to copy and reflect the selected segment, at which point the new left zygoma is recognised as a separate file:
Making the skull visible again, you can see that the reflected zygoma isn’t in the correct place on the opposite side of the skull. This is because the skull wasn’t perfectly aligned with the scanner during the scanning process.
To get in the right place takes quite a bit of time, patience, spatial awareness and motor skills. But mostly patience.
The reflected zygoma needs to be slid (or translated, if you remember pre-GCSE maths) to the correct place:
The zygoma segment can then be rotated in any direction,
resized in all directions at once (what I now have to call isometric scaling in lectures),
Or in just one direction at a time (what I now have to call allometric scaling).
After I’d actually done all of these, it ends up looking a bit like this.
(The screen shots come from afterwards so I’m just demonstrating each step – doing it again would take ages, and I didn’t think to capture them as I went along)
But as you can see, the Avizo software is still treating the macaque’s left zygoma as a separate segment.
The next part is the one that took the most of the time and the greatest amount of luck – merging the reflected zygoma with the rest of the skull so that it’s all stored as just one file again.
After a couple of hours of trial, error and workarounds in the indecisive Avizo software I ended up with this:
The macaque now has 2 zygomas! And just to prove it in cross section:
Success! It’s difficult to put into words exactly how happy I felt for a good hour after finishing. Ecstatic is probably a good start. Whatever, it means that I have pretty much all of the practical skills necessary to pass this module, Avizo’s touchiness ignored.
The upside of having a complete 3D virtual model like this is that you can then subject it to virtual forces and try to figure out a bone’s function in real life by measuring how it deals with different types of motion or weight applied to it. This whole reconstruction-plus-testing process can work for anything from zygomas to teeth to the long bones that are in your arms and legs.
This process is also really useful for recontructing the fossils of ancestors, particularly their skulls, faces and hips so we can see their distinguishing features and work out how they would have walked.
Also, you can do another really cool thing which is 3D-PRINT THE MODEL YOU’VE MADE. Yes. It ends up looking something like this:
I know, this isn’t a print of the reconstructed macaque skull, but somone higher up in the department did the same thing to this baby chimpanzee skull and printed it out at 1/3 size. Cute, no?
I hope you enjoyed that latest insight into my life. Anthropology certainly isn’t as boring as I thought it was 2 years ago.
p.s. Avizo isn’t as bad as I make it out, it’s actually an incredibly powerful and useful tool. In light of its applications it’s a lot easier to overlook the occasional flaws, which are generally caused by the computer not being powerful enough.
Avizo: Konrad-Zuse-Zentrum. 20/03/2012. Avizo Standard Edition (7.0.1) [computer programme]. Berlin: Konrad-Zuse Zentrum.