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Review
. 2017 Jun 1;6(6):1-11.
doi: 10.1093/gigascience/gix027.

Laboratory x-ray micro-computed tomography: a user guideline for biological samples

Anton du Plessis  1   2 , Chris Broeckhoven  3 , Anina Guelpa  1 , Stephan Gerhard le Roux  1
Affiliations
Review

Laboratory x-ray micro-computed tomography: a user guideline for biological samples

Anton du Plessis et al. Gigascience. .

Abstract

Laboratory x-ray micro-computed tomography (micro-CT) is a fast-growing method in scientific research applications that allows for non-destructive imaging of morphological structures. This paper provides an easily operated "how to" guide for new potential users and describes the various steps required for successful planning of research projects that involve micro-CT. Background information on micro-CT is provided, followed by relevant setup, scanning, reconstructing, and visualization methods and considerations. Throughout the guide, a Jackson's chameleon specimen, which was scanned at different settings, is used as an interactive example. The ultimate aim of this paper is make new users familiar with the concepts and applications of micro-CT in an attempt to promote its use in future scientific studies.

Keywords: 3D imaging; micro-computed tomography; nano-computed tomography; non-destructive analysis; x-ray tomography.

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Figures

Figure 1:
Figure 1:
Photograph of the micro-CT scanner used during the study showing the fundamental components of the setup. A typical micro-CT scanner consists of an x-ray tube (A) that emits x-rays, which pass through a sample (B) before being recorded by an x-ray detector (C).
Figure 2:
Figure 2:
Mounting of a Jackson's chameleon. Florist foam mounting material forms the basis onto which the sample is placed (A). A 2D x-ray projection image shows the very low density of the mounting material (B).
Figure 3:
Figure 3:
Summary of Guidelines I–III showing how the optimal scanning settings for our Jackson's chameleon example were determined. Note that these guidelines are based on a 2000 pixel detector. See text for further information.
Figure 4:
Figure 4:
Micro-CT slice images of a Jackson's chameleon illustrating the common artifacts. In (A), a metal tag is included in the scan volume, resulting in streaky artifacts (bottom right in image). In (B), an insufficient voltage was used, thereby creating image artifacts around the dense parts of sample. In (C), the voltage setting was too high, resulting in poor contrast. In (D), poor image quality is caused by reconstruction clamping, which was set too high. In (E), double edges are present due to incorrect offset calculations during reconstruction. In (F), slight blur is present due improper mounting.
Figure 5:
Figure 5:
Three-dimensional reconstructions of a Jackson's chameleon illustrating a surface view (A) and a semi-transparent view showing the skeleton in yellow (B).
Figure 6:
Figure 6:
A high-resolution (30 μm) scan of a Jackson's chameleon showing the skeletal elements present in the head.
Figure 7:
Figure 7:
Slice images of the horn of a Jackson's chameleon obtained by using nano-CT showing the bony core at 10 μm (A) and 4 μm (B). At a very high resolution of 0.95 μm (C), the bone micro-architecture becomes clearly visible. A 3D rendering of the structure of the bony core inside the chameleon horn is visualized in (D).
See this image and copyright information in PMC

References

    1. Kalender WA. X-ray computed tomography. Phys Med Biol 2006;51(13):29–43. - PubMed
    1. Brunke O. High-resolution CT-based defect analysis and dimensional measurement. Insight-Non-Destruct Testing Condition Monitor 2010;52(2):91–3.
    1. Singhal A, Grande JC, Zhou Z. Micro/nano CT for visualization of internal structures. Microscopy Today 2013;21(02):16–22.
    1. Schoeman L, Williams P, du Plessis A, et al. . X-ray micro-computed tomography (μCT) for non-destructive characterisation of food microstructure. Trends Food Sci Technol 2016;47:10–24.
    1. Cnudde V, Boone MN. High-resolution x-ray computed tomography in geosciences: a review of the current technology and applications. Earth-Sci Rev 2013;123:1–17.

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