3D printing is steadily becoming more available to amateur users, with units becoming available in schools and public libraries across the country. At the same time, industrial CT scanners are becoming more accessible and cost effective for researchers. With a good CT scan, a paleontologist can observe detailed anatomy, such a bone matrix, or otherwise hidden anatomy, such as developing teeth. Taken together, these two technologies make a powerful team.
Our lab got a Makerbot Replicator 2 in 2013. Its inaugural project was to print a Hadrocodium skull for the documentary, “Your Inner Fish”. Following that, the Replicator was frequently used to print models generated from CT scans. These included models that were magnified replicas of the fossil, anatomical components digitally dissected out from the scan, or reconstructions of bones that were broken or warped in the specimen. These models were useful for observing details on small and delicate bones, demonstrating anatomy to students, and testing possible articulation.
In 2014 our department got an industrial CT scanner, perfect for scanning small to medium sized fossils and bones. Surprisingly, there are very few resources available addressing the problem of mounting specimens. The scanner itself is equipped with a lathe chuck, which is not very good for attaching samples directly to. Instead, a range of attachments are needed to accommodate different sized specimens. This is where a 3D printer comes in very handy. Falcon tubes are useful for small samples. More complex clamps could be made in a machine shop. With a 3D printer, custom built platforms/containers/cradles can be produced quickly and cheaply. What follows are some examples of the attachments we have made in all or in part using a 3D printer.
This holder was custom printed to hold multiple small bird skulls.
These U-shaped holders have been printed in a variety of sized to accommodate slab specimens or anything else that will fit in them and are very versatile.
These holders are more generic and use a combination of found materials (a clear plastic cylinder, a falcon tube, and a tupperware container) and 3D printed parts. The hot glue gun is very useful for these.
In February I decided to take a short animal illustration class at Lillstreet Art Center and found the experience rewarding, mostly for the community, inspiration, and motivation that I got from it. The first two illustrations here came from that class. I plan on staying involved in this lively community and have signed up for an embroidery class for May, which I plan on using as another way to express biological visualization and for fun. The second two images here are samplings of sketches I did on trips to the Lincoln Park Zoo. Though it can be difficult to capture animals in motion, I found the experience very relaxing, and enjoyed spending time observing the way the animals move and behave.
Some of you may be familiar with the recent proliferation of the five day art challenge on Facebook. If not, it is, as the name states, a five day challenge to post 3 or more pieces of new or old art. When I was nominated, I found that the combination of looking through my old work and sharing new work energized me to sketch and create more. It was a valuable experience, I think. Whereas I don’t plan on posting work here everyday, I will make it a goal to post some work (sketches, work in progress, even past work) monthly or bi-monthly. Today, I’d like to share some sketches that I’ve played around with since the beginning of the year.
I started this illustration as a from a sketchbook sketch to practice color and light, and fur techniques. I believe that as a result of the initial painting phase being fast, this illustration has a more painterly style than I normally achieve, though I’m pleased with the texture. I plan on doing more small illustrations like this one in the future to explore color, composition, movement, story, etc.
Our lab bought a MakerBot Replicator2 a couple months back. I was super excited about using it, and still am excited about maker technology, but quickly realized that this was not like a regular printer; you could not simply take it out of the box, plug it in and expect it to work. It has been a steep learning curve getting it to cooperate and I think I’m getting closer to having a more consistent success rate with the prints. Since taking charge of the printer, I have walked a couple of people through the process of creating a 3D print from a CT scan, which is what has inspired this series of posts. Hopefully someone finds these helpful for their own endeavors.
Part1: CT scan to 3D model
Fossils are usually scanned using an industrial scanner that can pump a higher than medically allowed dose of radiation into the specimen. Denser materials need a higher amount of radiation to penetrate them and, obviously, fossils are far more dense than flesh and bone. If it is a micro CT scanner (microtomography), the resulting images can also have a great deal more resolution that a typical medical scanner.
After the fossil has been scanned, the outcome is usually a stack of .tiff or .jpg files. A medical scanner would produce a DICOM file. The difference is this: a DICOM file comes with metadata that describes the voxel size and orientation of the scan, whereas for a .tiff stack, the voxel size and orientation needs to be entered manually. A voxel is a three dimensional pixel. To produce an accurate model, you need to know the exact dimensions of the voxels, otherwise the models may be squished or stretched. The X and Y voxel size (which should always be the same) can also be calculated by dividing the field of view (aka the size represented by the width) by the number of pixels in that width.
There are several programs you can use once you have obtained the dataset to extract the information (aka make a 3D model from it). The more common ones I have encountered are Mimics, Amira, Avizo, Osirix, and VG Studio. The bulk of my experience is with Mimics, as this is what we use in the lab. However, Mimics is a professional piece of software and likely out of the budget for a casual user. If you happen to be extracting CT data for your own use and use a Mac, I recommend Osirix, which has a free license. By the way, if you have ever had a CT scan done of yourself, you have the right to ask for that data from your doctor, but make sure you ask for the DICOM dataset. You can also request that your patient information is removed from the file that you receive, for privacy purposes. This is just one situation that the casual user might find the need for Osirix.
Next you need to section out the relevant geometry. This process obviously differs between software, but all are based on selecting a portion of data based on the density of the sample. This can be tough if the fossil and matrix have similar densities. Samples that contain metallic elements can also be problematic. These high density irregularities can cause flaring and makes it difficult to get a wide range of grays (as is desirable) for the fossil and matrix. In effect, this throws an outlying cluster of high density that tips the histogram in that direction.
Once you have your model sectioned out, it gets exported as an .stl file. In the next post, I will discuss how to clean and process the .stl file for 3D printing.