X-ray microtomography

3D rendering of a µCT scan of a leaf piece, resolution circa 40 µm/voxel.

X-ray microtomography, like tomography and x-ray computed tomography, uses x-rays to create cross-sections of a physical object that can be used to recreate a virtual model (3D model) without destroying the original object. The prefix micro- (symbol: µ) is used to indicate that the pixel sizes of the cross-sections are in the micrometre range.[1] These pixel sizes have also resulted in the terms high-resolution x-ray tomography, micro–computed tomography (micro-CT or µCT), and similar terms. Sometimes the terms high-resolution CT (HRCT) and micro-CT are differentiated,[2] but in other cases the term high-resolution micro-CT is used.[3] Virtually all tomography today is computed tomography.

Micro-CT has applications both in medical imaging and in industrial computed tomography. In general, there are two types of scanner setups. In one setup, the X-ray source and detector are typically stationary during the scan while the sample/animal rotates. The second setup, much more like a clinical CT scanner, is gantry based where the animal/specimen is stationary in space while the X-ray tube and detector rotate around. These scanners are typically used for small animals (in vivo scanners), biomedical samples, foods, microfossils, and other studies for which minute detail is desired.

The first X-ray microtomography system was conceived and built by Jim Elliott in the early 1980s. The first published X-ray microtomographic images were reconstructed slices of a small tropical snail, with pixel size about 50 micrometers.[4]

Working principle

Imaging system

Fan beam reconstruction

The fan-beam system is based on a one-dimensional (1D) X-ray detector and an electronic X-ray source, creating 2D cross-sections of the object. Typically used in human computed tomography systems.

Cone beam reconstruction

The cone-beam system is based on a 2D X-ray detector (camera) and an electronic X-ray source, creating projection images that later will be used to reconstruct the image cross-sections.

Open/Closed systems

Open X-ray system

In an open system, X-rays may escape or leak out, thus the operator must stay behind a shield, have special protective clothing, or operate the scanner from a distance or a different room. Typical examples of these scanners are the human versions, or designed for big objects.

Closed X-ray system

In a closed system, X-ray shielding is put around the scanner so the operator can put the scanner on a desk or special table. Although the scanner is shielded, care must be taken and the operator usually carries a dosimeter, since X-rays have a tendency to be absorbed by metal and then re-emitted like an antenna. Although a typical scanner will produce a relatively harmless volume of X-rays, repeated scannings in a short timeframe could pose a danger. Digital detectors with small pixel pitches and micro-focus x-ray tubes are usually employed to yield in high resolution images.[5]

Closed systems tend to become very heavy because lead is used to shield the X-rays. Therefore, the smaller scanners only have a small space for samples.

3D image reconstruction

The principle

Because microtomography scanners offer isotropic, or near isotropic, resolution, display of images does not need to be restricted to the conventional axial images. Instead, it is possible for a software program to build a volume by 'stacking' the individual slices one on top of the other. The program may then display the volume in an alternative manner.

Image reconstruction software

For X-ray microtomography, powerful open source software is available, such as the ASTRA toolbox. [6] [7] The ASTRA Toolbox is a MATLAB toolbox of high-performance GPU primitives for 2D and 3D tomography, from 2009–2014 developed by iMinds-Vision Lab, University of Antwerp and since 2014 jointly developed by iMinds-VisionLab, UAntwerpen and CWI, Amsterdam. The toolbox supports parallel, fan, and cone beam, with highly flexible source/detector positioning. A large number of reconstruction algorithms are available, including FBP, ART, SIRT, SART, CGLS.

Volume rendering

Volume rendering is a technique used to display a 2D projection of a 3D discretely sampled data set, as produced by a microtomography scanner. Usually these are acquired in a regular pattern (e.g., one slice every millimeter) and usually have a regular number of image pixels in a regular pattern. This is an example of a regular volumetric grid, with each volume element, or voxel represented by a single value that is obtained by sampling the immediate area surrounding the voxel.

Image segmentation

Where different structures have similar threshold density, it can become impossible to separate them simply by adjusting volume rendering parameters. The solution is called segmentation, a manual or automatic procedure that can remove the unwanted structures from the image.

Typical use

Archaeology

Biomedical

Electronics

Microdevices

Composite materials and metallic foams

Polymers, plastics

Diamonds

Food and seeds

Wood and paper

Building materials

Geology

Fossils

Microfossils

Space

Stereo images

Others

References

  1. ↑ X-Ray Microtomography at the US National Library of Medicine Medical Subject Headings (MeSH)
  2. ↑ Dame Carroll JR, Chandra A, Jones AS, Berend N, Magnussen JS, King GG (2006-07-26), "Airway dimensions measured from micro-computed tomography and high-resolution computed tomography", Eur Respir J, 28 (4): 712–720, doi:10.1183/09031936.06.00012405, PMID 16870669.
  3. ↑ Duan J, Hu C, Chen H (2013-01-07), "High-resolution micro-CT for morphologic and quantitative assessment of the sinusoid in human cavernous hemangioma of the liver", Plos One, 8 (1): e53507, doi:10.1371/journal.pone.0053507, PMC 3538536Freely accessible, PMID 23308240.
  4. ↑ Elliott, J. C.; Dover, S. D. (1982). "X-ray microtomography". Journal of Microscopy. 126 (2): 211–213. doi:10.1111/j.1365-2818.1982.tb00376.x.
  5. ↑ Ghani, Muhammad U.; Zhou, Zhongxing; Ren, Liqiang; Wong, Molly; Li, Yuhua; Zheng, Bin; Yang, Kai; Liu, Hong (2016-01-21). "Investigation of spatial resolution characteristics of an in vivo microcomputed tomography system". Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 807: 129–136. doi:10.1016/j.nima.2015.11.007. PMC 4668590Freely accessible. PMID 26640309.
  6. ↑ Van Aarle, W., Palenstijn, W.J., De Beenhouwer, J., Altantzis T., Bals S., Batenburg K. J., and J. Sijbers (October 2015). "The ASTRA Toolbox: a platform for advanced algorithm development in electron tomography". Ultramicroscopy. 157: 35–47. doi:10.1016/j.ultramic.2015.05.002. PMID 26057688.
  7. ↑ W. Van Aarle, W J. Palenstijn, J. Cant, E. Janssens, F. Bleichrodt, A. Dabravolski, J. De Beenhouwer, K. J. Batenburg, and J. Sijbers (2016). "Fast and flexible X-ray tomography using the ASTRA toolbox". Optics Express. 24 (22): 25129. doi:10.1364/OE.24.025129.
  8. ↑ Mizutani, R; Suzuki, Y (2012). "X-ray microtomography in biology". Micron (Oxford, England : 1993). 43 (2–3): 104–15. doi:10.1016/j.micron.2011.10.002. PMID 22036251.
  9. ↑ Van De Kamp, T.; Vagovic, P.; Baumbach, T.; Riedel, A. (2011). "A Biological Screw in a Beetle's Leg". Science. 333 (6038): 52. doi:10.1126/science.1204245. PMID 21719669.
  10. ↑ Bulantová, Jana; Macháček, Tomáš; Panská, Lucie; Krejčí, František; Karch, Jakub; Jährling, Nina; Saghafi, Saiedeh; Dodt, Hans-Ulrich; Horák, Petr (2016-04-01). "Trichobilharzia regenti (Schistosomatidae): 3D imaging techniques in characterization of larval migration through the CNS of vertebrates". Micron (Oxford, England: 1993). 83: 62–71. doi:10.1016/j.micron.2016.01.009. PMID 26897588.
  11. ↑ Noever, Christoph; Keiler, Jonas; Glenner, Henrik (2016-07-01). "First 3D reconstruction of the rhizocephalan root system using MicroCT". Journal of Sea Research. Ecology and Evolution of Marine Parasites and Diseases. 113: 58–64. doi:10.1016/j.seares.2015.08.002.
  12. ↑ Nagler, Christina; Haug, Joachim T. (2016-01-01). "Functional morphology of parasitic isopods: understanding morphological adaptations of attachment and feeding structures in Nerocila as a pre-requisite for reconstructing the evolution of Cymothoidae". PeerJ. 4: e2188. doi:10.7717/peerj.2188. PMC 4941765Freely accessible. PMID 27441121.
  13. ↑ Gerard van Dalen, Han Blonk, Henrie van Aalst, Cris Luengo Hendriks 3-D Imaging of Foods Using X-Ray Microtomography Archived July 19, 2011, at the Wayback Machine.. G.I.T. Imaging & Microscopy (March 2003), pp. 18–21
  14. ↑ Russell Garwood, Jason A. Dunlop & Mark D. Sutton (2009). "High-fidelity X-ray micro-tomography reconstruction of siderite-hosted Carboniferous arachnids". Biology Letters. 5 (6): 841–844. doi:10.1098/rsbl.2009.0464. PMC 2828000Freely accessible. PMID 19656861.
  15. ↑ Jurewicz, A. J. G.; Jones, S. M.; Tsapin, A.; Mih, D. T.; Connolly, H. C., Jr.; Graham, G. A. (2003). "Locating Stardust-like Particles in Aerogel Using X-Ray Techniques" (PDF). Lunar and Planetary Science. XXXIV.
  16. ↑ Tsuchiyama, A.; Uesugi, M.; Matsushima, T.; Michikami, T.; Kadono, T.; Nakamura, T.; Uesugi, K.; Nakano, T.; Sandford, S. A. (2011). "Three-Dimensional Structure of Hayabusa Samples: Origin and Evolution of Itokawa Regolith". Science. 333 (6046): 1125–8. doi:10.1126/science.1207807. PMID 21868671.
  17. ↑ Lowe, Tristan; Garwood, Russell P.; Simonsen, Thomas; Bradley, Robert S.; Withers, Philip J. (2013). "Metamorphosis revealed: three dimensional imaging inside a living chrysalis". Metamorphosis revealed: three dimensional imaging inside a living chrysalis. 10 (84): 20130304. doi:10.1098/rsif.2013.0304.
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