mattbk.com

As previously mentioned, we have a Leica Scanstation here at UND that is used for scanning large areas for geomorphology projects. I borrowed it yesterday to try out how it did at close range. Although I probably don’t need to say this, things did not go as well as well as planned.

First, the setup:

Since we’re neither scanning a large area nor worrying about repeatability, there was no need for a leveled tripod or targets. The metal base of the scanner is designed for these sorts of applications, so no harm is being done by setting it down on the table like this. The bricks are used to keep the specimen up in front of the scanner, and the computer runs the whole setup. You can see the Triceratops “model” and the gastropod (snail) specimen as well, to judge their size:

I’ll skip over the mechanics of scanning, except to mention that the Leica licensing system is still giving us problems; under one Windows 7 account I couldn’t access the license but under another I could. Such is life with computers!

The problems came from trying to scan at very fine detail. The scanner was set up just under 0.5 m from the objects being scanned, and the resolution (density of scanning points at that distance) was varied as I tried to make things work.

At 0.1 mm point spacing, I ran into this problem (gastropod):

Hitting the limit of the resolution causes this weird striping pattern. This might be okay if the surface were accurately represented, but at this point you lose depth perception as well: the scatter on those stripes averages around 9 mm between the front “surface” and the back, meaning that the surface itself (if I modeled this scan) would vary that much. Not so good.

At 1 mm point spacing, things were better but not so great (gastropod):

The stripes are toned down, but the error is just too large for a decent 3D model to be produced :-(. With 1 mm spacing between points, even if the points were a surface rather than a cloud, this is about the smallest object I would try to scan with it.

Finally, fellow graduate student Ted wanted to try out the Triceratops model. With 1 mm spacing, this is what we got:

Although I’m sure the morphology is incorrect in the details, such a scan fits in nicely with the current horned dinosaur publishing extravaganza going on.

Final verdict: while the Leica Scanstation is good for some things, scanning small fossils is not one of them.

I’ve had these taking up shelf space for a while, and since I need to pay off some bills, they’re going up for sale on Amazon.com. Prices were chosen based on that site and Alibris, so if anyone has a better idea of what I can charge, let me know. I’m trying to be competitive so I can get these off my hands.

If you wish to buy from me, make sure you’re buying from seller ‘meburt01.’

Geological Survey Professional Paper 213: Gold deposits of the southern Piedmont

Geological Survey Professional Paper 255: Pegmatite investigations, 1942-45, New England

Geological Survey Professional Paper 256: Geology of the San Manuel copper deposit, Arizona

Geological Survey Professional Paper 292: Geology of the southern Elkhorn Mountains, Jefferson and Broadwater Counties, Montana

Geological Survey Professional Paper 419: Miocene Marine Mollusks from the Astoria Formation in Oregon

Geological Survey Professional Paper 420-A: Geology of the Los Angeles Basin California – an Introduction

Geological Survey Professional Paper 420-B: Geology and oil resources of the eastern Puente Hills area, southern California

Geological Survey Professional Paper 421-B: Bedrock geology of the Kassler quadrangle, Colorado

Geological Survey Professional Paper 422-A: Morphology and hydrology of a glacial stream–White River, Mount Rainier, Washington

This post is a summary of my research over the past few days; I’ll continue to update it or make new posts as necessary.

Introduction
One of the growing subfields of paleontology is the digitization of fossil material via 3D laser scanning. There are several reasons to do this: protecting valuable specimens from potentially destructive handling, making virtual models available for morphometric analysis, and producing physical replicas of specimens, either for sharing with other institutions or for performing physical tests relating to size and shape. Two disparate technologies must come together for all of the above to come to pass: first, a scanning system to accurately digitize specimens (via laser or, in some cases, photography) so that they can be visualized and manipulated on-screen; second, a rapid prototyping system that can accurately reproduce objects with fine detail and accuracy to the original model. I am concurrently researching both of these technologies to determine the options we have at my institution.

Specimens and Detail
The collection at UND comprises mostly invertebrate fossils, and of those a great many are freshwater mussels and gastropods. Generally these objects are a good size to scan and do not have “important” morphological features that are very small; however we currently have two graduate students studying mammals via teeth and one student studying microsnails. These items range to several millimeters, so when it comes to detail we need to be pushing the edges of the technology as much as we can afford, in order to get good data. (I don’t have to worry as much since I’m studying normal-sized mussels, but in paleo as in everything else, the more decimal places, the better.) It would be excellent if we could capture surface features less than 0.1 mm in height.

Laser Scanning
Several systems are available for digitizing physical objects; I am focusing on laser scanning because it can produce virtual models of highly detailed objects that are very accurate to the original. Other methods of creating 3D models are photogrammetry and to a lesser extent morphometric probes that record the position of landmarks in three dimensions but not the intervening surfaces.

Build-your-own scanning systems:

• DAVID
• MakerScanner
• Cyclops

These systems generally utilize a line laser and a webcam to digitize objects, although the Cyclops uses a “shadow line” and the DAVID can use both. The object is digitized by the interpretation of the bright laser line (or dark shadow line) on the image pulled from the webcam: the position of the surface is calculated based on the known relationship between the laser and the camera or the laser and the background. From my rough experience (earlier this summer with DAVID and just today with a hacked version of MakerScanner), it is quite difficult to get a really good scan, although some of the planeless scans done by people on the DAVID forum are amazingly good. If you want a good scan, you can do it, but you’re going to use up a lot of time and effort getting to that point. I will be playing with replicating a MakerScanner some more over the next few days and hope to report on the results.

“Cheap” scanning systems:

• NextEngine

Currently, only the NextEngine scanner is priced “cheaply” when it comes to laser scanning. For $2,995 you can get the basic package, and for $995 more you can get even better precision. I’ve seen a lot of commentary on this scanner, and all of it good, but I’m not sure it will capture enough detail for our needs. The “dimensional accuracy” is +-0.0005″, or about 0.0127 mm. That’s pretty darn good, but will it work for us? We’ll have to go visit someone and see. [Polo and Felicísimo found less desirable accuracy: “±0.81 mm and ±1.66 mm”. 2014-04-07]
– http://palaeo-electronica.org/2008_2/134/index.html
– http://reporting.journalism.ku.edu/fall08/adler-noland/2008/11/ku-geologist-preserves-dinosau.html

Expensive scanning systems:

• ???

I had a larger list of these systems a couple months back, but since that information is probably out of date by now, I’ll refrain from posting it. Most of the issues I remember running into are: cost (of course), intended use (if they’re designed for reverse engineering, will they work for fossils?), and, well, cost. Now, I’m all for getting the top-of-the-line scanner so you can do the most awesome digital models possible, but paleo is one of those disciplines in which you do what you can with what you have, because the cashflow isn’t always the steadiest. On this note, we do have a Leica Scanstation in the department that I have experience with scanning landscape features; I will be testing it out soon to see how well it can do with closeups on small items.

All in all, more research needs to be done on the available laser scanners to see which is best suited for our purposes. I will be posting as I can talk to people about their experiences.

I’ll leave things there for today and pick up in a little while with the next section: rapid prototyping.

Matt Might (who knows when) came up with a license for academics to release code used for research. You all know the code: it barely works, comes with little documentation, and you’re really embarrassed every time someone asks to see it in relation to a publication. The solution? The CRAPL–the Community Research and Academic Programming License.

He says “Academics rarely release code, but I hope a license can encourage them,” and I am strongly encouraged. Although I’ve “published” the code used in my MS thesis in an appendix, it’s not available for download anywhere. When I have a few hours sometime I plan on getting things moving with this. For the good of science!

[EDIT: Obviously, my domain name has changed and I’m on shared hosting now, but this still outlines the process. 2014-02-04]

Dynamic DNS is a system where you update the nameserver every time the IP address changes, so you don’t lose links.

I’m using freedns.afraid.org right now because it lets me use my own domain name (protichnoctem.com) for, well, free.

I set the nameservers in GoDaddy, then set cron to run wget every hour (of the “Direct URL” on this page)to update the nameservers with the current IP address. I know this is much more often than my IP address changes, but if it should change I’d like the domain name not to be broken for more than an hour (a cron wget is a fairly light task anyway).

If it works, I will be happy.

Traditional dispersal: A pair of goats wanders over a mountain.
Geodispersal: A mountain wanders under a pair of goats.