Workflow Part 1: CT scan to 3D model

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.


A fossil sits on the rotating table in front of the X-ray tube.

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.

Click here for Part 2: preparing a model for 3D printing 

One thought on “Workflow Part 1: CT scan to 3D model

  1. Pingback: Workflow Part 2: preparing a model for 3D printing | A Biologist's Canvas

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