X-ray Microscopic Examination of a Cocklebur (Xanthium)

Figure 1: Photograph of cocklebur (covered in white dog fur) imaged using the SkyScan 1275

A bur (or burr) is a seed or fruit that has hooks that help to spread the seeds of its plant, often by catching on the fur of passing animals and being transported. In addition, the spines and hooks help protect the seeds from herbivores. With the popularity of our previous article on biomimicry and the creation of Velcro® (Velcro Article), we are excited to revisit imaging a similar bur sample using the high speed SkyScan 1275 micro-CT instrument within our laboratory.

Nature has developed many unique structures that scientists use for inspiration in developing innovative technologies through biomimicry. Velcro was invented by George de Mestral in 1941 and was inspired by the burrs he found on himself and on his dog. Being an engineer and entrepreneur, he realized the small hooks of the burr and loops of the fur/fabric allowed the burr to adhere exceedingly well. This sparked his idea to mimic the structure as a potential fastener.

X-Ray Microscopic Imaging of Botanical Samples

We examined a cocklebur sample removed from a dog’s fur and found an unexpected surprise using our high-speed SkyScan 1275 micro-CT at an isotropic voxel size of 10µm.


Figure 2: Planar 2D views of the cocklebur sample

As shown in Figure 2, the SkyScan 1275 micro-CT resolved the large structures of the cocklebur sample and provided us a high-resolution view of the interior contents of the bur. While burs are used in nature to spread seeds and propagate a plant’s survival in the ecosystem, in this case it appears a parasitic insect species was also present in our sample. In looking at the chambers within the cocklebur, we see the large seed present in one of the two central chambers. However, within the other chamber the seed is missing and is instead replaced by a small pupa, which likely consumed the seed during its growth. The bright white spots within the image are dense inclusions present within the pupa itself and could represent locally high concentrations of either inorganic components or even metals.


Figure 3: Clipped 3D CTVox volumetric rendering of the cocklebur sample showing both the seed and pupa

When moving out to a volumetric view of each dataset, the surface detail present on the pupa is even more evident than within the 2D views (Figure 3). The ability to non-destructively dissect samples is a particular advantage of micro-CT imaging.

Figure 4: Comparison of global threshold (yellow, left) and background flood fill tool (blue right) within Synopsys’ Simpleware™ ScanIP software

The volumetric datasets provided by micro-CT imaging are ideal for conversion to surface models, which can be used for computational simulations or additive manufacturing. One key step in the process is the segmentation of a grayscale dataset arising from micro-CT imaging into a distinct model. The most typical way segmentation occurs in Bruker CTAnalyzer is through thresholding, with global thresholding being the most popular. In many cases, different portions of the sample may be represented in the grayscale images with overlapping intensity values, requiring either careful definition of a region of interest or several cleanup steps to isolate only the feature of interest for modeling.


Within our laboratory, we also often utilize Simpleware ScanIP ScanIP software (Version V-2023.09; Synopsys, Inc., Mountain View, USA) to import our Bruker SkyScan data and then produce optimized 3D models. While Simpleware ScanIP software does allow us to utilize a traditional global threshold to select portions of our sample, in this case a background flood fill tool is a better option to allow us to digitally isolate only the seed from the surrounding sample volume (Figure 4). With the background flood fill tool, you can define a seed starting point in your background images and select an upper and lower threshold value to be included or excluded from your selection. From this point, the software will grow the seed point in 3D space within the bounds of your threshold selection to capture the component of interest.

Figure 5: Comparison of the seed model’s mesh surface as originally produced (blue, top) and after cleanup and decimation within Synopsys’ Simpleware™ ScanIP software(yellow, bottom)

After segmenting the portion of the sample we wish to model, we often will find the meshes resulting directly from micro-CT imaging to be overly dense in regards to the total number of triangles due to the high resolution of the images directly from the instrument. While you might be able to directly utilize the meshes from datasets occasionally, often the file size of the mesh is needlessly large due to the total number of points in the mesh, and this can either slow down or entirely preclude additional downstream work with the file. The most common ways to reduce the file size while maintaining the utility of the meshed model are through decimation2 or remeshing of the model. Within the surfaces tool menu, Simpleware ScanIP software has both decimation and remeshing available as tools, amongst several other options which can be deployed with warranted by the situation (Figure 5). For our case, our model of the seed started off with about one million individual triangles when directly converted from the SkyScan 1275 dataset and the decimation process quickly reduced the total by about seventy five percent with no significant loss of detail.


Figure 6: Maverick 3D rendering of the individually meshed model components from the cocklebur sample

Once we’ve isolated our relevant features and created unique modeled meshes for each, we’re free to move into any downstream 3D software suite to complete further work. In our case, we imported our meshed into Maverick Render Indie to create high resolution photo realistic renderings and videos of our scan data as shown in Figure 6.


While the SkyScan portfolio has several instruments optimized for specific applications, the SkyScan 1275 is a good general-purpose tool to quickly image samples with good resolution and is a workhorse in our laboratory testing services program. For this project, the SkyScan 1275 imaged the full cocklebur sample at high resolution within two hours.

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 Cocklebur
Voltage (kV) 30
Current (µA) 150
Filter None
Voxel Size (µm) 10
Rotation Step 0.4
Exposure Time (ms) 400
Rotation Extent (deg.) 360
Scan Time (HH:MM:SS) 01:55:48


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. Individual components were meshed using Synopsys’ Simpleware ScanIP software software with the CAD add-on 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.


  1. https://www.paenflowered.org/apgii/asterales/asteraceae/xanthium


  1. https://gomeasure3d.com/article/everything-you-need-to-know-decimating-3d-scan-data/

*Simpleware software (Synopsys, Inc., Mountain View, USA) 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 software’s capabilities to visualize, analyze, and quantify your data, and to export models for design and simulation workflows. Simpleware™ is a trademark of Synopsys, Inc. in the U.S. and/or other countries.


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