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. 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, but in other cases the term high-resolution micro-CT is used. 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.
- 1 Working principle
- 2 3D image reconstruction
- 3 Typical use
- 4 References
- 5 External links
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.
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
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.   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 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.
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.
- Reconstructing fire-damaged artifacts, such as the En-Gedi Scroll
- Both in vitro and in vivo small animal imaging
- Human skin samples
- Bone samples, ranging in size from rodents to human biopsies
- Lung imaging using respiratory gating
- Cardiovascular imaging using cardiac gating
- Imaging of the human eye, ocular microstructures and tumors 
- Tumor imaging (may require contrast agents)
- Soft tissue imaging
- Parasitology – migration of parasites, parasite morphology
- Ceramics and Ceramic - Metal composites. Microstructural analysis and failure investigation
- Composite material with glass fibers 10 to 12 micrometres in diameter
- Detecting defects in a diamond and finding the best way to cut it.
- 3-D imaging of foods using X-ray microtomography
- Piece of wood to visualize year periodicity and cell structure
- Concrete after loading
- Benthonic foraminifers
- Locating stardust-like particles in aerogel using X-ray techniques
- samples returned from asteroid 25143 Itokawa by the Hayabusa mission
- Visualizing with blue and green or blue filters to see depth
- "Compressive performance and crack propagation in Al alloy/Ti2AlC composites". Materials Science and Engineering A. 672: 247–256. 2016. doi:10.1016/j.msea.2016.06.073.
- X-Ray Microtomography at the US National Library of Medicine Medical Subject Headings (MeSH)
- 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.
- 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 , PMID 23308240.
- 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.
- 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 . PMID 26640309.
- 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.
- 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.
- Enders, Christian; Braig, Eva-Maria; Scherer, Kai; Werner, Jens U.; Lang, Gerhard K.; Lang, Gabriele E.; Pfeiffer, Franz; Noël, Peter; Rummeny, Ernst (2017-01-27). "Advanced Non-Destructive Ocular Visualization Methods by Improved X-Ray Imaging Techniques". PLoS ONE. 12 (1). doi:10.1371/journal.pone.0170633. ISSN 1932-6203. PMC . PMID 28129364.
- 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.
- 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.
- 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.
- 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.
- 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 . PMID 27441121.
- 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
- 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 . PMID 19656861.
- 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.
- 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.
- 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.
- "Development of structural colour in leaf beetles". Scientific Reports. 2017. doi:10.1038/s41598-017-01496-8.
- MicroComputed Tomography: Methodology and Applications
- Synchrotron and non synchrotron X-ray microtomography threedimensional representation of bone ingrowth in calcium phosphate biomaterials
- Microfocus X-ray Computer Tomography in Materials Research
- Locating Stardust-like particles in aerogel using x-ray techniques
- Use of micro CT to study kidney stones
- Use of micro CT in ophthalmology
- Application of the Gatan X-ray Ultramicroscope (XuM) to the Investigation of Material and Biological Samples
- 3D Synchrotron X-ray microtomography of paint samples[permanent dead link]