Dieser Beitrag auf Deutsch.

The post below is in part a bit cryptic. Specifically, I leave you in the dark with regards to the exact specimen and what is so interesting about it. There’s good reasons for that, so bear with me!

The last night ranks high in the Top Ten list of MUNL (Most Uncomfortable Nights in my Life). I spent it on a train – a nice, normally very fast speed train, admittedly, – slowly making my way from Berlin to Bonn. Not slow compared to the timetable, but that’s a slow timetable caused by the aftermath of the great flood many parts of Germany experienced this summer, and the Deutsche Bahn’s inability to have sufficient personnel for their rail control centers. Overall, it’s a very uncomfortable way of getting from A to B, because for a person of my size it is utterly impossible to find a comfortable position for sleeping in a German high-speed ICE train. The seats are very straight-backed, and there is nothing to put the feet up against if you sit on a table. Sitting behind another row of seats doesn’t help either, because the seatbacks are smooth and your feet or knees will slide down without anything to stop them. Also, the seat rows are comfortably spaced for sitting, so you can’t wedge yourself in the way some airlines force you to by spacing seats closely. Sitting upright is not an option either, as lateral support by the head rest is inexistent, so that your head will slide down and down and down until you wake up with a jolt and an aching neck. Bah! Worse, you can’t even sit awake in the seats for long, because they do not support any position except upright without any back support unless you slouch! Blergh!

Ending up in Cologne at 3 AM is an ugly end to such a journey, but at least better than ending up in Bonn at 4:14 AM. I chose the former simply because there is a fast food place in the Cologne main station that’s open 24/7 – much better than the shuttered fronts I expected in Bonn. Trains to Bonn run regularly once the morning commute starts. Still, not my favourite place to spend a sleepless night, especially when for some reason the free 1 h of internet isn’t working.

Now, on the way home, I am patronizing that same place again – still no internet. I’ll have to upload this post later tonight, when I get back to Berlin. Yes, that’s right: Berlin to Cologne Sunday night, Cologne to Bonn Monday in the early morning, Bonn to Cologne just now (thanks for the ride, Armin!), and back to Berlin in about an hour. Arrival at midnight, if Deutsche Bahn is punctual (a big if), and then nearly an hour‘s drive home.

Why, then, did I set out on this ordeal? Because I wanted to get professionally frustrated. No, not really, obviously I hoped for an exciting result, not a frustrating one. But it did not turn out this way. Still, it was worth the try.

I went to Bonn to get a dinosaur bone microCT scanned. The MfN has a microCT scanner, a really neat one. But the high resolution it delivers comes at the price of a small specimen range it can scan. The Steinmann Institute in Bonn has one that gives a less good resolution, but can scan specimens up ~50 cm. That’s impressive, and for the bone I wanted scanned it was the only easy option.

I arrived at the Institute in Bonn on autopilot, but the CT technician Peter Göddertz immediately went to work on the bone, letting me run off to grab some breakfast. I felt much better when I got back 20 minutes later and saw the bone almost ready to go into the scanner. In medical CT scanners, the scan subject rests, and the scanner rotates around it. In some technical scanners, including the one in Bonn, the scan subject is rotated, whereas the scanner doesn‘t move. Therefore, the bone had to be mounted on the holder so that it wouldn’t fall off or jitter, or otherwise shift position in relation to the holder during the scan. Herr Göddertz did a very nice job with some Styrofoam and adhesive tape, and we were ready for the scan.

The scan itself took less than an hour, plus some time to copy the files and calculate slices from the raw data. Yes, I also received the raw data, and it will be stored and, once the project is completed, made available for other researchers. I also received a file that contains all the relevant scan parameters. That’s important, because it is no good to have just a stack of slices or a 3D file. You need the info how that data was derived from the original bone, otherwise it is not useable research data. Only if you have all the info can you show exactly what resolution your files have, and what accuracy – and that is information you need!

So I got a bunch of file, roughly 4.7 GB worth. That includes a stack of JPG images and a stack of TIFs, thus some of it is redundant (you can always create the JPGs from the TIFs). Now for my first look at the results – and the disappointment. Instead of the hoped-for clear distinction between two different tissues in the specimen, everything looked like a perfectly uniform mass of bone. Nothing to see here, move right along!

A colleague of mine at the Steinmann Institute, Armin Schmitt, is a bit of a CT extraction wizard. I ran to him with my data before we tried a second scan. Sadly, Armin was unable to do anything useful with the data, too. But he suggested a second scan with slightly different settings: higher amperes and lower voltage. Because the specimen was still set up in the scanner, we could go right ahead and run the scan. Again, it took about 45 minutes, most of which I spent dozing upright in my chair. Then came lunch with more colleagues, and then finally we checked out the resulting data. And lo and behold, amid quite a mass of artefacts, there seems to be a slight contrast between different parts of the bone!


Very slight, in fact less than the differences across the bone’s width within each of the two parts I want to separate, but it is there! Now, it is a matter of teasing it out of the clutter and seeing if it means what I think it means: does it fit the differences I can see on the outside of the bone? Does it fit the predictions for the inside I made based on the external appearance and my (admittedly limited) knowledge of bone formation? We shall see – and if the answers are „Yes“ and „Yes“, you will read about them in a very nice journal within a year, I hope!

Now, off to Berlin – if I don’t fall asleep before I reach the train! YAWN!


About Heinrich Mallison

I'm a dinosaur biomech guy working at the Museum für Naturkunde Berlin.
This entry was posted in rants. Bookmark the permalink.

One Response to Palaeofrustration

  1. Pingback: Paläofrust | dinosaurpalaeo auf Deutsch

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s