X-ray Microscopic Examination of Murine Bones Using the SkyScan Sample Changer

Figure 1: Volumetric rendering of mouse skull imaged on the SkyScan 1275

X-Ray Microscopic Imaging of Mouse Bones Using the SkyScan Carousel Tube Set

Using our new mouse and rat bone imaging tube set for the SkyScan Carousel, we imaged both femora and skulls from mouse samples. While a formal announcement of the new tube set accessory is forthcoming, we’re happy to be able to present some information on the benefits of the new accessory within this article.

The set consists of specially adapted polypropylene tubes designed to easily fit on top of your existing SkyScan carousel mounts for both the SkyScan 1272 and SkyScan 1275 instruments. The smaller of the two tubes, designed with mouse bone imaging in mind, has an inner diameter of about 7 mm and a length of about 30 mm, which should hold one or more mouse long bones nicely centered within your field of view in a sealed environment. The larger of the tubes in the set has an inner diameter of about 16 mm and a length of about 45 mm to accommodate either rat long bones or mouse heads for imaging. In re-launching this product, it was important to move to a more solvent-resilient container. The switch to polypropylene as the material to hold the bones achieves this aim while also remaining low density, minimizing any influence on the imaging data.

For this study, we are presenting the results of imaging a mouse head at an isotropic voxel size of 12 micrometers and a mouse femur at an isotropic voxel size of 8um using the SkyScan 1275 high speed desktop micro-CT.


Figure 2: Planar 2D views of a mouse skull (top) and femur (bottom) imaged within the new carousel tube set

As shown in Figure 2, the SkyScan 1275 micro-CT quickly imaged both samples with the total scan time for the full skull around an hour while only about a half hour of imaging time was required for the femur. Especially when coupled with the high speed acquisitions possible on the SkyScan 1275, the new mouse and rat bone imaging tube set allows researchers to mount and set up sixteen or more individual samples at a time to be run consecutively using the SkyScan Carousel accessory. Having each bone in a sealed, water-tight and solvent resilient container preserves their integrity for the full duration of the imaging process for all samples and can greatly improve throughput on large phenotyping studies.

Figure 3: Mouse (left) and rat (right) tube accessories mounted on SkyScan carousel bases

While your SkyScan Carousel comes with several different diameter bases of mounts to use for imaging, finding an appropriate container and securely fastening it while keeping it centered can be a challenge. The soon to be released revised mouse and rat bone imaging tube set provides solutions to these challenges in a compact and efficient way (Figure 3). Each piece of the set, either the smaller tubes designed for mouse imaging or the larger tubes designed for rat imaging, arrive with a specialized adapter which perfectly fits upon your SkyScan Carousel base to keep your sample tube centered within your imaging field of view. The tubes have been designed to maximize the available imaging space and while they mount securely to the metal bases, they do not interfere with automatic pixel size selection based on the diameter of the metal stem used.

Figure 4: Mouse femur mounted within the mouse imaging tube on the SkyScan 1275 carousel

Once the adapters containing the bones are added to the standard SkyScan Carousel metal bases, sample insertion and instrument programming proceed as normal (Figure 4).

Figure 5: Clipped volumetric CTVox 3D rendering of the mouse skull highlighting the jaw structure

Further examining the skull data, we see the SkyScan 1275 captured a high detailed dataset for the sample in only about an hour of imaging time. (Figure 5). Using CTVox we explored a live rendering of the dataset to further examine the jaw structure and the location of the teeth. While this produces remarkably useful data, the images can be further enhanced by exporting the dataset as a defined set of parameterized models before rendering with a more specialized third-party 3D software program, as shown in Figure 1.

Figure 6: Clipped volumetric CTVox 3D rendering of the mouse femur highlighting the trabecular bone near the growth plate

In about half the time required for the full skull, the mouse femur was also imaged on the SkyScan 1275 at sufficient resolution for morphometric analysis (Figure 6). Using standard morphometric analysis procedures, a region of interest 2.5 mm in length was isolated offset above the growth plate by 0.25mm.

Figure 7: Clipped volumetric 3D rendering of the trabecular bone (purple) isolated from the cortical bone (white) within a 2.5mm long region of interest

Using advanced rendering software, the trabecular bone analyzed for the morphometric study can be presented alongside the cortical bone, which surrounds it as shown in Figure 7. For this image, the top half of the cortical bone was cut away from the rendering to allow for a clearer view of the color-enhanced trabecular structures.


The SkyScan 1275 is a versatile desktop instrument geared towards high-speed imaging of medium and low-density samples like the mouse bones explored in this project. To improve throughput, Bruker offers automated sample changing capabilities with the SkyScan Carousel for both the SkyScan 1272 and SkyScan 1275 desktop instruments. To better assist our customers in imaging many similar samples, Micro Photonics developed and launched an accessory tube set designed with high throughput imaging of mouse and rat bones. After several years in the field, the design has been updated based on customer feedback to increase solvent resiliency to common storage solutions like ethanol.

We hope you found this Image of the Month informative and encourage you to subscribe to our newsletter and social media channels in preparation for the continuation of our Image of the Month series next month.

Scan Specifications

Sample Skull Femur
Voltage (kV) 80 80
Current (µA) 125 125
Filter 0.5 mm Aluminum 0.5 mm Aluminum
Pixel Size (µm) 12 8
Rotation Step 0.4 0.4
Exposure Time (ms) 125 125
Rotation Extent (deg.) 360 180
Scan Time (HH:MM:SS) 01:05:54 00:35:50


These scans were completed on our SkyScan 1275 micro-CT system at the Micro Photonics Imaging Laboratory in Allentown, PA. Reconstructions were completed using NRecon 2.0 while visualization and volumetric inspection of the 2D and 3D results were completed using DataViewer and CTVox. Isolation of the femoral trabecular bone within a region of interest utilized CTAnalyzer. Individual components were meshed using Synopsis Simpleware ScanIP* with the CAD Module (Synopsys, Inc., Mountain View, USA) before 3D rendering using Maverick Render Indie (Random Control, Madrid, Spain).

Would you like your work to be featured in our monthly newsletter? If so, please contact us by calling Seth Hogg at 610-366-7103 or e-mailing seth.hogg@microphotonics.com.


*Simpleware software enables you to comprehensively process 3D image data (MRI, CT, micro-CT, FIB-SEM…) and export models suitable for CAD, CAE and 3D printing. Use Simpleware’s capabilities to visualize, analyze, and quantify your data, and to export models for design and simulation workflows.

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