Beautiful Bordeaux and Hardcore Software

I’ve been back home from my paleoanthropology journey for over a week now, okay two weeks when this goes up. Boy oh BOY did I miss my family. I spent 30 days in France without my partner and our six-year-old daughter, and let me tell you, I had not been that homesick since I was 15 at boarding school in Denmark, 5,000 miles (8,000 km) away from my family in the States. But it makes sense. I’ve been a single adult for a long time. I’ve had very close friends and even serious boyfriends I guess, but until I had a kid and settled down with my partner for real, there wasn’t really anything to miss. I mean sure I missed people and things, but not like this. Not this deep down heartache longing. I might have thought I did with a boyfriend who had moved away, but no, it was never ever like this. Anyway.

Tower and feet wetThe first three weeks of my stay was excavating in Saint-Cesaire. This last week in Bordeaux, though, is what paid for my plane tickets (thanks to two small grants to help with expenses associated with grad students’ theses). My master’s thesis is studying the three-dimensional scans of Neandertal teeth from Goyet, Belgium – one isolated incisor, one isolated premolar, and a portion of a maxilla with three additional teeth. So that means I won’t be studying the actual, physical teeth. I may never actually see them in real life. I will be studying these 3D scans using the very powerful Avizo software. So my fourth week in France was learning how to do this at Bordeaux University under Priscilla. Priscilla was also kind enough to put me up in her house in Bordeaux. And more than that, she fed me dinner and breakfast and took me all over Bordeaux on my one weekend off. Lucky me!

Bordeaux. A beautiful, charming city that I would just LOVE to return to for a longer visit. ActuaMe and seafood lower quality croppedlly, I immediately began fantasizing about ways my studies or new career could put me in Bordeaux for even longer. Hmmm, I need to work on that. That and learning more French. Some highlights for me were: walking the picturesque streets and hopping on and off the tram, sitting at an outdoor café with Priscilla eating quiche Lorraine and chatting, eating oysters and drinking chilled white wine at the market, and shopping for French lingerie. This last experience Priscilla talked me into, and I am now convinced that regularly wearing fancy underwear is an actual thing that French women do, not just a cliché. Ooo la la! Which, by the way, is an expression French people actually say, especially Priscilla to her five-month-old mischievous kitten, Bichou. Bichou kitchen floorKittens, with their tiny needle claws, are programmed to KILL anything that moves. So Priscilla’s house was equal parts charmingly comfortable and nerve-wracking.

So about those Neandertal teeth. Priscilla, as well as other students who had worked with the software before and happened to be working in the computer lab, helped me learn how to use Avizo 3D imaging software. The teeth have been 3D-scanned at another facility and I was given the file – really hundreds of stacks of files of virtual slices of the tooth in different angles – that I will be studying for the next two years or so. The process is a bit like Photoshop. Okay, actually I don’t know if that’s true, since I’ve never really used Photoshop. But I imagine that it is, since I’ve seen people use it and I’ve used more basic software like Paint.net.
The idea with 3D scanning, well of ancient teeth anyway, is to look at the internal structure. To measure and compare the different materials contained in the object. So in this case that is: enamel, dentine, and the pulp chamber (since the actual pulp – nerves and blood vessels – is soft tissue and does not survive). The software recognizes the various densities of the tooth, and assigns them to different materials. There is another step, sometimes two other steps, using other software before Avizo can start making these assignments, but let’s skip that part. Hey, this is a blog. So now you can look at a 3D image of your tooth. You can use the mouse to drag it around and look at it from every angle. Cool! Then you can look at individual virtual “slices” of your tooth. But then you’ll notice something. There are lots and lots of mistakes. This is a fossil tooth, so some dentine has fossilized, causing it to appear denser and be incorrectly labeled as enamel. Also the pulp chamber is full of sediment (dirt and tiny rocks), which may be assigned to dentine or enamel depending on their density. But the kicker: cracks. Tens of thousands of years’ worth of cracks. Do I just fill them in, in other words assign them to the surrounding material, I ask? No, I must delineate each crack and create two new materials: enamel cracks and dentine cracks. If you just blend them in it will distort the volume of the tooth, since cracks add space. And since ultimately I will be measuring dentine versus enamel volume (to compare with teeth studied by other people) it is important to note which material is cracked and how much. Usually one crack goes through both materials, complicating things further. Also the software misses some cracks that you can otherwise see on the scan, so you add those manually too.

Cropped Doing science lower qualityThis process of assigning materials to their proper label is called tooth segmentation and it is as time consuming as it sounds. Some of the students there had segmented hundreds of teeth and were pros at it. I spent a couple of days segmenting an incisor, and then somehow screwed it up so bad I had to start over. I chalk it up to learning how to use the program, but it still sucks to see all that work disappear. Note to self: learn how to save different versions of a tooth, so I can go back a day or half a day instead of a whole week. That’s as far as I’ve gotten with this project. Priscilla says the next steps are easier. Rendering I think she said was next. Not sure what that entails. And then I have to look at the numbers – the point of the whole thing – and compare them to other teeth. I don’t know yet whether it will be to other Neandertal teeth or modern humans or more ancient species, or all three.

Lots of cool things can be learned from teeth. 3D scans cannot, however, show me fun things like pollen trapped in calculus (tartar) that give clues about what people ate. That is done with real teeth and microscopes in a lab. What I can learn are things about evolutionary changes in teeth over time, and about how teeth mature in an individual’s lifetime. I don’t really know what my focus will be or what my scientific question is yet, but I’m excited to find out. This semester I’m taking my first class that helps me get started on my thesis, so I’m well underway already.

If you’ve read this far, you must already think this is interesting stuff (you nerd!). But in case you don’t, or if you just have to have more, here is a video that shows the Wow Factor of 3D scans of teeth way better than I ever could. Check it out.

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2 Responses to Beautiful Bordeaux and Hardcore Software

  1. Nanci says:

    Thanks for this-so very fun. And so very useful for folks like me who get to use those results later. Xo

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