Spine-tingling. I’m there. This is the post you’ve been waiting for for weeks – what can the spine of primates can tell us about the way they get around?
Exciting news: this week is my final week of term! This also means that all deadlines are go, so here’s a poster I’ve had to make about gibbons. It’s got cute pictures!
The ecology and evolution of monogamy in the white-handed gibbon. (Clickable link).
Although it doesn’t sound like it, poster-making is a standard and important academic skill – the idea is to get a lot of information across in a clear and concise manner, without the information being too complicated. Posters are also meant to grab the attention of people just browsing and make them want to ask questions so you can show off all your hard-earned knowledge.
I know that some of the terms I’ve used may be a bit technical for people not working in the field so here are a few definitions, in order the order they appear in the poster:
Mya: million years ago
Sympatric: Living in the same area as
Brachiation: Swinging through the trees using only your arms. Like this: Brachiating gibbon.
Ulnar styloid: the protruding bit of bone at the bottom the left long bone (the ulna) in the diagram.
Semilunar meniscus: A unique structure in the wrists of apes (including humans).
Pronosupination: Twisting your wrist between palm down and palm up.
That’s it for this week!
p.s. this is also a slightly more correct version in spelling and stuff than the one I submitted for real. Count yourselves lucky!
This week I’m going to show you how I carried out my assessment in the Virtual Anatomies module, in a similar way to James Makes a Monkey Skull with a similar over exaggerating title but less complaining about the software.
This time my task was to reconstruct the missing right canine of a chimpanzee skull that had been scanned in an MRI machine and make it look acceptable to be 3D-printed. Sadly, the 3D printing part is very unlikely to happen.
The first thing to do is open the DICOM stack, or series of images which are taken in an MRI scanner or a CT machine. Then open up some orthoslices to get an idea of what the scan looks like.
Once I was orientated I had to choose a brightness threshold by selecting the whole image so that I have to do less work later on separating parts out – if the image is too bright, all of the parts merge into one from the software’s point of view.
My threshold was from -670 to 3250 grey value units. Any lower than -670 and too much thin trabecular bone is lost. The really high value is necessary to make sure all of the tooth enamel (really hard, therefore bright) is included.
Unfortunately, this doesn’t get rid of the mat the skull was resting on, nor the skull cap or chin of the skulls in front of and behind this one in the scanner (top left panel in the image above). I deleted all these by adding them to the ‘material’ Exterior.
Next, I separated the mandible where my threshold value hadn’t separated it fully from the skull (the top and bottom teeth were too close together and the brightness had leaked from one to the other). I could then select the mandible in all slices just by clicking on one slice…
… and give it its own identity.
I could now save the mandible as a separate file and delete it from this file by adding it to Exterior, leaving just the cranium. This makes it easier to segment the upper left canine (you can see this best in the second image below).
Segmenting the canine
This part involves manual selection of the canine in each slice of the image – no short cuts here. I started in the XY plane to get a nice round shape to the external part of the tooth.
The top left panel shows the tip of the canine taking shape in 3D (blue).
I continued in the YZ plane to get the internal architecture right. The gap in the middle is the pulp cavity of the tooth where the nerves and blood vessels lie.
To finish off the segmentation of the tooth root I returned to the XY plane to get the tubular shape right.
Once the canine was fully segmented I deleted the cranium leaving just the canine, and saved it as a separate file.
For it to be useful in filling the gap on the chimp’s right-hand side, I needed to flip or reflect the finished canine in the X axis.
Then I adjusted the bounding box down to a reasonable size to make it easier to manipulate for the next stage.
Merging the canine with the skull.
First, I needed to have the canine and skull open together in the same window.
Then slide, rotate and resize until the canine fits well in the socket at a similar angle to the one on the chimp’s left.
And merge the canine with the cranium.
You might be able to see in the pictures above that more of the canine is exposed on the chimp’s right, so the time has come to attempt to cover this up by creating more bone in the upper jaw, or maxilla.
There are a couple of ways I could have done this. One option is going through layer by layer, selecting a region of Exterior and adding it to cranium, but I chose the harder option of selecting the corresponding area on the left side of the face, segmenting it out and flipping it in the same way as the canine. This is harder because it also involves going through layer by layer afterwards and smoothing bits that don’t look quite right.
So, segment out some maxilla:
Flip in X and adjust the bounding box:
Open the merged canine and cranium along with the mandible and position the maxillary bone appropriately:
And merge the maxilla segment with the cranium. I also changed the colour of the mandible to make it more obviously a separate segment.
And that’s how I made a chimp face, free of all complaints about Avizo software because it worked like a charm.
Until next week,
Also, a happy birthday to Dr Phil Cox, and big thank you to Jason and Miguel for hosting such a wonderful party last night. I hope Miguel enjoys his time at home.
Avizo: Konrad-Zuse-Zentrum. 20/03/2012. Avizo Standard Edition (7.0.1) [computer programme]. Berlin: Konrad-Zuse Zentrum.
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.
Today, I thought I’d give you a taste of what I’ve been introduced to over the last 2 weeks in my Primate Ecology and Evolution module.
Have a look at these evolutionary trees which I’ve drawn showing (to the best of my knowledge) the order in which different groups of primates diverged from one another.
Then realise that we’ve also been taught this for ALL MAMMALS from the egg-laying platypus right up to the blue whale.
Lots of people have asked me what exactly MSc Human Evolution means, and I generally reply that it’s a very anatomical course looking at how human anatomy has evolved to allow us to go from tree-dwelling chimp look-alikes to upright bipedal walkers. That’s not a very detailed answer though, so I’m going to answer it a bit more here by looking at a very important technique which allows us to track changes in our skeleton as they occurred during evolution.
That technique is geometric morphometrics.
No, I hadn’t heard of it either.
That is, until I looked at what I’d be learning during the next 12 months of my life. Maybe now is a good time to find out what it is before I have to start using it.
Why not join in?
So for the first post of this blog, there unfortunately isn’t going to be much new material.
I talk on my homepage (if you haven’t already seen it) about interpreting the research that goes on behind the scenes at the Powell-Cotton Museum (PCM) in Birchington, Kent. It mainly involved whittling down PhD-level and post-Doctoral research carried out on themes ranging from gorilla ecology to the preservation of amphibian specimens currently owned by the museum.
Here, then, is a link to a double page spread that I put together during my time there, to give you an idea what the rest of this blog will sound like when you read it.
A blast from the past.
So go ahead, click on the link for your blast from the past, both mine and the more distant past of Major Percy Powell-Cotton. It also has relevance to the much more distant evolutionary past too, since gorillas count themselves among the organisms most closely related to us – the great apes.
The apes are a group made up of gibbons, orang-utans, gorillas, chimpanzees and humans, and are distinguished from monkeys in that they don’t possess tails. The great apes are useful comparisons for us when we study fossils thought to belong to direct human ancestors, although it’s critical to remember that none of the other great apes alive today (extant) are actually our ancestors, and even though our closest extant relatives may be very important, the last common ancestor of purselves and chimps was probably not very similar to either [reference 1].
The modern great apes can also be used as a yardstick for comparing genetic differences between modern humans, when studying how, when and where modern humans arose and then dispersed across the globe.
But much more of that later – that’s what this blog is all about!
A glimpse of the future.
Also to be found in the link! All Jaimie’s hard work will contribute to understanding the ecology of gorillas and help towards targeting conservation efforts in years to come, as well as making the job of future researchers at the PCM far easier. It should also help her gain her PhD. Lucky girl.
p.s. I’d love some feedback on my writing style so please feel free to leave your (vaguely constructive) opinions in the comments section or on twitter (link is near the top of the page on the right, beneath the giant picture of my face).