X-ray microtomography

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.

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. The ASTRA Toolbox is a MATLAB and python toolbox of high-performance GPU primitives for 2D and 3D tomography, from 2009 to 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.

For 3D visualization, tomviz is a popular open-source tool for tomography.

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

• Reconstructing fire-damaged artifacts, such as the En-Gedi Scroll and Herculaneum papyri
• Unpacking cuneiform tablets wrapped in clay envelopes and clay tokens

Biomedical

• Both in vitro and in vivo small animal imaging
• Neurons
• Human skin samples
• Bone samples, including teeth, 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
• Insects – Insect development
• Parasitology – migration of parasites, parasite morphology
• Tablet consistency checks

Developmental biology

• Tracing the development of the extinct Tasmanian tiger during growth in the pouch
• Model and non-model organisms (elephants, zebrafish, and whales)

Electronics

• Small electronic components. E.g. DRAM IC in plastic case.

Microdevices

• Spray nozzle

[[Composite materials]] and metallic foams

• Ceramics and Ceramic–Metal composites. Microstructural analysis and failure investigation
• Composite material with glass fibers 10 to 12 micrometres in diameter

[[Polymers]], plastics

• Plastic foam

Diamonds

• Detecting defects in a diamond and finding the best way to cut it.

[[Food]] and seeds

• 3-D imaging of foods
• Analysing heat and drought stress on food crops
• Bubble detection in squeaky cheese

[[Wood]] and paper

• Piece of wood to visualize year periodicity and cell structure

Building materials

• Concrete after loading

Geology

In geology it is used to analyze micro pores in the reservoir rocks, it can be used in microfacies analysis for sequence stratigraphy. In petroleum exploration it is used to model the petroleum flow under micro pores and nano particles.

It can give a resolution up to 1 nm.

• Sandstone
• Porosity and flow studies

Fossils

• Vertebrates
• Invertebrates

Microfossils

• Benthonic foraminifers

Palaeography

• Digitally unfolding letters of correspondence which employed letterlocking.

Space

• Locating stardust-like particles in aerogel using X-ray techniques
• Samples returned from asteroid 25143 Itokawa by the Hayabusa mission

Stereo images

• Visualizing with blue and green or blue filters to see depth

Others

• Cigarettes
• Social insect nests

References

References

1. {{MeshName. X-Ray+Microtomography
2. (2006-07-26). "Airway dimensions measured from micro-computed tomography and high-resolution computed tomography". Eur Respir J.
3. (2013-01-07). "High-resolution micro-CT for morphologic and quantitative assessment of the sinusoid in human cavernous hemangioma of the liver". [[PLOS One]].
4. (1982). "X-ray microtomography". Journal of Microscopy.
5. (January 2016). "Investigation of spatial resolution characteristics of an in vivo micro computed tomography system". Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment.
6. (2017). "Industrial X-Ray Computed Tomography". Springer.
7. (October 2015). "The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography". Ultramicroscopy.
8. (October 2016). "Fast and flexible X-ray tomography using the ASTRA toolbox". Optics Express.
9. (1999). "A Quasi-realtime X-ray Microtomography System at the Advanced Photon Source". United States. Department of Energy.
10. (2013-01-01). "Digital rock physics benchmarks—Part I: Imaging and segmentation". Computers & Geosciences.
11. (January 2021). "Tortuosity of porous media: Image analysis and physical simulation". Earth-Science Reviews.
12. (2019-08-21). "Gold Nanoparticles for X-ray Microtomography of Neurons". ACS Chemical Neuroscience.
13. (May 2013). "Quantitative high contrast X-ray microtomography for dental research". J. Dent..
14. (2017-01-27). "Advanced Non-Destructive Ocular Visualization Methods by Improved X-Ray Imaging Techniques". PLOS ONE.
15. (February 2012). "X-ray microtomography in biology". Micron.
16. (July 2011). "A biological screw in a beetle's leg". Science.
17. (July 2013). "Metamorphosis revealed: time-lapse three-dimensional imaging inside a living chrysalis". Journal of the Royal Society, Interface.
18. (May 2017). "Development of structural colour in leaf beetles". Scientific Reports.
19. (April 2016). "Trichobilharzia regenti (Schistosomatidae): 3D imaging techniques in characterization of larval migration through the CNS of vertebrates". Micron.
20. (2016-07-01). "First 3D reconstruction of the rhizocephalan root system using MicroCT". Journal of Sea Research.
21. (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.
22. (2022). "Micro-computed tomography and brightness-mode ultrasound show air entrapments inside tablets". Current Directions in Biomedical Engineering.
23. (February 2018). "Letting the 'cat' out of the bag: pouch young development of the extinct Tasmanian tiger revealed by X-ray computed tomography". Royal Society Open Science.
24. (June 2012). "Skeletal development in the African elephant and ossification timing in placental mammals". Proceedings. Biological Sciences.
25. (May 2019). "Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography". eLife.
26. (May 2015). "Prenatal cranial ossification of the humpback whale (Megaptera novaeangliae)". Journal of Morphology.
27. (2019). "Compressive performance and crack propagation in Al alloy/Ti₂AlC composites". Materials Science and Engineering A.
28. Gerard van Dalen, Han Blonk, Henrie van Aalst, Cris Luengo Hendriks [http://www.cb.uu.se/~cris/Documents/GIT2003.pdf 3-D Imaging of Foods Using X-Ray Microtomography] {{webarchive. link. (July 19, 2011 . G.I.T. Imaging & Microscopy (March 2003), pp. 18–21)
29. (2017-11-01). "Non-destructive, high-content analysis of wheat grain traits using X-ray micro computed tomography". Plant Methods.
30. (2023). "Micro-computed tomography shows silent bubbles in squeaky mozzarella". Current Directions in Biomedical Engineering.
31. (2021-01-01). "Upscaling Reservoir Rock Porosity by Fractal Dimension Using Three-Dimensional Micro-Computed Tomography and Two-Dimensional Scanning Electron Microscope Images". Journal of Energy Resources Technology.
32. (2019-04-01). "Rock properties evaluation for carbonate reservoir characterization with multi-scale digital rock images". Journal of Petroleum Science and Engineering.
33. (2013-01-01). "Digital rock physics benchmarks—part II: Computing effective properties". Computers & Geosciences.
34. (2021-02-01). "The role of microporosity on the permeability of volcanic-hosted geothermal reservoirs: A case study from Los Humeros, Mexico". Geothermics.
35. (December 2009). "High-fidelity X-ray micro-tomography reconstruction of siderite-hosted Carboniferous arachnids". Biology Letters.
36. Kachovich, S., Sheng, J. and Aitchison, J.C., 2019. Adding a new dimension to investigations of early radiolarian evolution. Scientific reports, 9(1), pp.1-10. {{doi. 10.1038/s41598-019-42771-0.
37. Castellanos, Sara. (2 March 2021). "A Letter Sealed for Centuries Has Been Read—Without Even Opening It". The Wall Street Journal.
38. (2 March 2021). "Unlocking history through automated virtual unfolding of sealed documents imaged by X-ray microtomography". Nature Communications.
39. (2003). "Locating Stardust-like Particles in Aerogel Using X-Ray Techniques". Lunar and Planetary Science.
40. (August 2011). "Three-dimensional structure of Hayabusa samples: origin and evolution of Itokawa regolith". Science.
41. (January 2017). "When social behaviour is moulded in clay: on growth and form of social insect nests". The Journal of Experimental Biology.