Embedded Files
Parts of this website are currently under construction. Come back soon for more content!
In this section you will find information on the use of CT scans to create 3D models of fossils.
What are CT scans?
What are CT scans?
CT means Computed Tomography.
CT scanning is a form of digitalization, as is taking a picture.
Instead of a camera, the machine used to take a CT scan is a tomograph or a CT scanner.
A CT scanner uses x-rays to see inside an object.
For example in medicine, doctors use CT scans to see broken bones in patients.
Another example are paleontologists that use CT scans to see through fossils.
The result of a CT scan is a sequence of CT images.
One scan can compile more than 3000 CT images.
The picture above shows CT images of a fossil.
The bone is white, the sediments are various shades of grey, and the air is black.
A CT scan is a form of digitalization that uses x-rays and computation to see inside an object, for example a fossil.
Why using CT scans?
Why using CT scans?
CT scans allow paleontologists to study the inner anatomy of fossil.
The method has various advantages that are described below.
1. CT scanning does not damage the fossils.
Before the use of CT scans, paleontologists made silicone or metal casts of the cavities inside the fossils.
When casting was not possible, paleontologists would cut sections through the fossils.
These previous methods could damage and even destroy the fossils.
On the contrary, CT scans do not damage the fossils as there is little manual handling of it.
The paleontologist or the CT operator will only handle the fossil from the collection to the CT scanner and back.
2. CT scanning reduces the risk of breaking fossils.
Paleontologists visit museums to learn about the fossils that are deposited in the collections.
In the collection, paleontologists take fossils out of their box to study them.
While manually handling the fossils, there are risks of breaking them, for example by dropping them on the table or even the floor.
This is why paleontologists try to handle fossils as little as they can, in order to reduce the risk of damaging them.
CT images therefore considerably reduce the manual handling of the fossils.
Once the fossil is CT scanned, paleontologists can study the images virtually on a computer while the fossil is safely kept into the collection of the museum.
3. CT scanning increases the value of museum collections.
Within the collections of the museum, some fossils have been deposited more than 100 years ago.
CT scans allow to restudy fossils in light of new methods.
This is for example the case of the sabretooth marsupial.
Various specimens of sabretooth marsupial were collected in 1926.
Elmer S. Riggs studied those fossils and deposited them at the Field Museum of Natural History in Chicago (United States).
Almost a decade later, two of these specimens were CT scanned.
Paleontologists today are still using these scans to study novel aspects of their inner cranium.
(⏳coming soon!)🔗 Click here to see an recent example of use of these CT scans.
4. CT images are easily shareable worldwide.
Once a fossil is scanned, the resulting CT images can be stored in virtual collection on the internet.
Morphosource and Digimorph are examples of virtual repositories for biological and paleontological specimens.
On these virtual repositories anyone can access the CT images of a fossil.
One fossil can therefore be studied by various researchers at the same time from anywhere around the world.
5. CT images allows virtual modeling and reconstruction of the fossils.
With the CT images of a fossil, paleontologists can create 3D virtual models of the fossils using specific software.
In addition, because fossils are often incomplete, broken or deformed, those models can be virtually transformed to reduce deformation or repair breakages.
As an example, the fossil illustrated below had a broken lower jaw (illustrated at the upper right) that did not allow us to correctly fit it to its cranium.
Using another fragment of broken jaw recently found (illustrated at the upper left), we combined the two fragments to reconstruct the jaw.
As a result, we are able to fit the reconstructed jaw to the cranium.
In addition to the model of the fossil itself, paleontologists can create 3D virtual models of the inner parts of the fossil, for example the cavity of the brain.
These models are called virtual casts.
They are nowadays very valued for the amount of novel information they bring.
📋 In summary, CT scanning:
does not damage the fossils.
reduces the risk of breaking fossils.
increases the value of museum collections.
produces images easily shareable worldwide.
allows virtual modeling and reconstruction of the fossils.
How to create 3D virtual models?
How to create 3D virtual models?
The first step in creating 3D virtual models is to check the raw CT images that are called projections.
This can be done in various software, for example Image J.
📽️Let's see how to check projections in the video below:
The original CT images usually weight a lot and might not be appealing.
This is why the images are edited before being used for modeling.
The edition of the images includes for example:
Improving grey contrast or brightness
Cropping the areas of interest
Rotating the images to a more intuitive orientation.
The editing process contributes to reducing the size of the sequence of images.
Downsizing is important to reduce the computer power it takes to process the images for creating 3D models.
Once edited, the CT images can be saved as a new sequence of images that can be uses for creating 3D virtual models.
📽️Let's see how to edit and downsize CT images in the video below:
The edited sequence of CT images are then uploaded in another software, for example 3D Slicer or Amira-Avizo.
These software are made to visualize CT images in 3 dimensions.
They are also built for creating and editing 3D virtual models.
Once the images are uploaded in the software, 3D models can be made.
To do so, the parts that we want as a model must be virtually painted on the CT images, a process called segmenting.
Segmenting CT images is the process of virtually painting parts of the CT images that will create a 3D virtual model.
For example, to create the model of a bone, we virtually paint the bone in all the images that show the bone.
Once all the bone is virtually painted, the software compiles the segmented sections in three dimensions to create a volume.
The volume created in this way can then be saved as a 3D model.
📽️Let's see how to segment CT images and create a model in the video below:
In the video above, the segmentation of the bone is made automatically using threshold.
Using threshold means that the software will paint only a selected range of the grey shades.
The rest of the shades on the images will not be painted.
Oftentimes the automatic segmenting using threshold does not work.
This is almost always the case of fossils because of the presence of sediments and minerals.
Sediments and mineral can be shown on the CT images in the same shades of grey as the bone of interest.
This is due to the density of the sediments being similar to that of the bone.
In those cases it is necessary to make manual corrections to the automatic segmentation.
📽️Let's see how to create a model using both automatic and manual segmenting in the video below:
In other cases, the entire segmentation must be done manually.
This is a time-consuming process, but worth it to study fossils.
📽️Let's see how to create a model using manual segmenting in the video below:
What about printing the 3D models?
What about printing the 3D models?
Once the 3D models are created, why not print them?!
There are many 3D printing companies nowadays.
Each have their own software to prepare the 3D models for printing.
One example of company is Zortrax that created the software Z-suite.
The software Z-suite virtually cuts a 3D model into many thin slices.
📽️Let's see how to prepare a model for 3D printing in the video below:
Those slices are then printed one by one with melted filament by the 3D printer.
Once all the slices are printed and cooled down, the printed 3D model is ready to be used.
📽️Let's see parts of the printing process of 3D models in the videos below:
Why is it useful to 3D print models?
Printing virtual models in 3D is useful both for research and science communication.
When paleontologists study fossils, it is advantageous to have a 3D prints to handle instead of the fossils.
Less handling means less risk of damaging fossils, while a print can be broken and printed again.
In addition, the print can also be scaled larger than the actual fossil, which help visualize small anatomical parts.
An example is the 3D print of the stapes that is often no more than one millimeters in real life.
However, a model of the stapes can be printed at the desired scale.
In science communication, 3D prints have a lot of potential because they can be transported and handled while the fossil is safely stored in the collection of the museum.
One example where such models were used for paleontological outreach is the museum exhibition "Tocar para aprender".
(⏳coming soon!) 🔗 Click here to learn more on the museum exhibition "Tocar para aprender".
Some references and acknowledgments
Some references and acknowledgments
Riggs ES (1933)
Preliminary description of a new marsupial sabertooth from the Pliocene of Argentina
Geological Series of Field Museum of Natural History 325(VI):61-66
Page updated
Google Sites
Report abuse