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Micro-CT of a Mouse Mandible

Figure 1 Mouse Mandible

Figure 1. Mouse jawbone showing tooth segmentation


Click here see a 3-D video of the mouse tooth and jawbone

Why Segment Samples?

If your region of interest in a sample is composed of a material of different density than what surrounds it, Micro-CT segmentation offers a way to virtually segment it, without breaking the sample. Using our CTAnalyzer (CTAn) software, you can select a region of interest, resave the images, and even perform complex functions and analyses on the segmented sections. As a demonstration, we have virtually segmented a tooth from a mouse mandible.

The Mouse Jawbone and Tooth Segmentation

The mouse jawbone and tooth were kept intact through the scan. After the usual scanning procedures and image generation, the full dataset shows that the jawbone and the tooth fit snuggly together. To segment these, we utilized the region of interest (ROI) tools in our CTAn software. The ROI tools allow you to highlight sections in the slices through the use of preset shapes, draw a freeform ROI, or use thresholding (selection of a certain grayscale range).

In our example, we used a threshold for our ROI, which first required performing advanced segmentation algorithms that are built in to CTAn. The details on how to do this type of segmentation can be found in the February 2017 Tip of the Month. A brief example of this is shown in Figure 2, where a threshold was used to select only the tooth, which was then converted to an ROI.


Figure 2 Mouse Mandible

Figure 2. Segmentation of the mouse tooth using advanced image selection techniques. Original grayscale image (left), thresholded tooth (middle), and threshold converted to a region of interest (right).

The ROI now allows you to save just the grayscale images of the tooth or to create a 3-D virtual model. The same process was also performed on the jawbone. Combining the saved grayscale images in CTVox creates an easy method for showing and coloring the models (Figure 3, left). If 3-D virtual models were made, then these too can be combined and represented in CTVol (Figure 3, right). Both methods give similar results, so feel free to choose whichever one works best for you.

Figure 3 Mouse Mandible

Figure 3. Combined grayscale images in CTVox (left) and combined 3-D models in CTVol (right).



We hope this image of the month demonstrated a new way to look at your samples and to segment them through virtual renditions. If you have an image of the month sample, or know of someone that is interested in getting micro-CT imaging done on their sample, we are always looking for new and exciting projects. Please feel free to call Brandon Walters at 610-366-7103 or e-mail to learn more about what micro-CT can offer you.




SkyScan 1272 Micro-CT





Pixel Size


Rotation Step:


Scan Time

2:14:53 (HH:MM:SS)


NRecon, DataViewer, CTVox, CTAn


Micro Photonics Imaging Laboratory, Allentown, PA

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