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X-ray computed tomography

Nature Reviews Methods Primers volume 1, Article number: 18 (2021) Cite this article

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Abstract

X-ray computed tomography (CT) can reveal the internal details of objects in three dimensions non-destructively. In this Primer, we outline the basic principles of CT and describe the ways in which a CT scan can be acquired using X-ray tubes and synchrotron sources, including the different possible contrast modes that can be exploited. We explain the process of computationally reconstructing three-dimensional (3D) images from 2D radiographs and how to segment the 3D images for subsequent visualization and quantification. Whereas CT is widely used in medical and heavy industrial contexts at relatively low resolutions, here we focus on the application of higher resolution X-ray CT across science and engineering. We consider the application of X-ray CT to study subjects across the materials, metrology and manufacturing, engineering, food, biological, geological and palaeontological sciences. We examine how CT can be used to follow the structural evolution of materials in three dimensions in real time or in a time-lapse manner, for example to follow materials manufacturing or the in-service behaviour and degradation of manufactured components. Finally, we consider the potential for radiation damage and common sources of imaging artefacts, discuss reproducibility issues and consider future advances and opportunities.

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Fig. 1: Common X-ray computed tomography configurations.
Fig. 2: Phase contrast computed tomography.
Fig. 3: Backprojection reconstruction method for a single slice obtained by parallel beam computed tomography.
Fig. 4: Segmentation processes for an idealized sample and a gravel filter pack.
Fig. 5: Examples of X-ray computed tomography in different fields.
Fig. 6: Real-time imaging of the solidification of an aluminium–24 wt% copper alloy melt showing dendritic growth.
Fig. 7: Computed tomography slices illustrating common reconstruction artefacts.

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Acknowledgements

P.J.W. acknowledges funding from the European Research Council (ERC) under grant CORREL-CT No. 695638.

Author information

Authors and Affiliations

  1. Henry Royce Institute, Department of Materials, University of Manchester, Manchester, UK

    Philip J. Withers

  2. School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA

    Charles Bouman

  3. Department of Management and Engineering, University of Padova, Vicenza, Italy

    Simone Carmignato

  4. Pore-Scale Processes in Geomaterials Research (PProGRess) — UGCT, Department of Geology, Ghent University, Ghent, Belgium

    Veerle Cnudde

  5. Environmental Hydrogeology, Department of Earth Sciences, Utrecht University, Utrecht, Netherlands

    Veerle Cnudde

  6. Division of Invertebrate Zoology, Gilder Graduate School, American Museum of Natural History, New York, NY, USA

    David Grimaldi

  7. Department of Medical Physics and Biomedical Engineering, University College London, London, UK

    Charlotte K. Hagen

  8. Universite de Lyon, INSA-Lyon, MATEIS, CNRS UMR5510, Villeurbanne, France

    Eric Maire

  9. Department of Food Science, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa

    Marena Manley

  10. Research Group 3D Innovation, Stellenbosch University, Stellenbosch, South Africa

    Anton Du Plessis

  11. Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA

    Stuart R. Stock

Authors
  1. Philip J. Withers
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  2. Charles Bouman
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  3. Simone Carmignato
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  4. Veerle Cnudde
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  5. David Grimaldi
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  6. Charlotte K. Hagen
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  7. Eric Maire
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  8. Marena Manley
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  9. Anton Du Plessis
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  10. Stuart R. Stock
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Contributions

Introduction (P.J.W.); Experimentation (S.R.S. and C.K.H.); Results (C.B., S.R.S. and P.J.W.); Applications (E.M., S.C., C.K.H., V.C., D.G., M.M. and P.J.W.); Reproducibility and data deposition (A.D.P. and S.C.); Limitations and optimizations (P.J.W., C.B., S.C., A.D.P. and S.R.S.); Outlook (P.J.W., C.B., S.C., V.C., D.G., C.K.H., E.M., M.M., A.D.P. and S.R.S.); Overview of the Primer (P.J.W.).

Corresponding author

Correspondence to Philip J. Withers.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information

Nature Reviews Methods Primers thanks C. Acevedo, K. Dobson, D. Parkinson, T. Sun and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Related links

Digital Fish Library: http://digitalfishlibrary.org/

Digital Morphology at the University of Texas: http://www.digimorph.org/

Digital Rocks: https://www.digitalrocksportal.org

ESRF heritage database for palaeontology, evolutionary biology and archaeology: http://paleo.esrf.eu/

GigaByte: https://gigabytejournal.com/

Mendeley Data: https://data.mendeley.com/

MorphoMuseuM: https://morphomuseum.com/

Morphosource: https://morphosource.org/

Phenome10K: https://www.phenome10k.org/

The Materials Data Facility: https://materialsdatafacility.org/

Supplementary information

43586_2021_15_MOESM1_ESM.wmv

Supplementary video 1: 3D rendering of the head of a 49 million year old Huntsman spider (Eusparassus crassipes) in dark (largely opaque) fossilised amber (phase contrast enhanced tube source microCT). Courtesy of J. A. Dunlop, D. Penney, N. Daluge, P. Jager, A. McNeil, R. S. Bradley, P. J. Withers, and R. F. Preziosi.

43586_2021_15_MOESM2_ESM.avi

Supplementary video 2: 3D rendering of the pupation of a Painted Lady butterfly chrysalis (tube source microCT). Courtesy of T. Lowe, R. J. Garwood, T. J. Simonsen, R. S. Bradley and P. J. Withers.

43586_2021_15_MOESM3_ESM.mp4

Supplementary video 3: Dimensional metrology of the lattice structure within an additively manufactured Ti alloy biomedical implant (tube source microCT). Courtesy of A. Du Plessis.

43586_2021_15_MOESM4_ESM.wmv

Supplementary video 4: 3D rendering of impact damage in a [(0°/90°)2]s carbon fibre reinforced polymer (CFRP) panel subjected to impact damage (energy 20J) (recorded on tube source microCT). Courtesy of F. Leonard and P. J. Withers.

43586_2021_15_MOESM5_ESM.avi

Supplementary video 5: time lapse 3D rendering showing the infiltration of Savonnières limestone with caesium chloride (Tube source microCT). Courtesy of T. Bultreys, M. A. Boone, M. N. Boone, T. De Schryver, B. Masschaele, L. Van Hoorebeke and V. Cnudde.

43586_2021_15_MOESM6_ESM.avi

Supplementary video 6: In situ propagation of a fatigue crack initiated from a focused ion beam notch in a titanium alloy (Ti-beta 21 S) sample. The color scale represents the height of the crack surface Loading frequency 25 Hz, σmax = 320MPa, R = 0.03. grain size 55 µm. Courtesy of H. Proudhon.

43586_2021_15_MOESM7_ESM.mp4

Supplementary video 7: Real-time imaging of the solidification of an aluminium-24wt% copper alloy melt showing dendritic growth (synchrotron microCT reconstructed using iterative reconstruction). Courtesy of C. Bouman.

Glossary

Radiographs

Images formed by X-rays transmitted through an object, originally collected on a photographic plate but now acquired digitally.

Projections

Radiographs of the object acquired at a given angle of illumination that, when combined with many others, provide the data for numerically reconstructing the object. Normally, between 100 and 3,600 projections are used to reconstruct a tomogram.

Greyscale

A synonym for the range of voxel values within a slice, volume or tomographic data set.

Tomogram

Originally a two-dimensional (2D) slice through an object reconstructed computationally from a sinogram. Now often used to refer to the 3D reconstructed image.

Attenuation contrast

Contrast in a radiograph or tomogram resulting from differences between the intrinsic attenuation of components in an object.

Phase contrast

Contrast in a radiograph or tomogram resulting from the difference in phase developed by beams as they pass through an object.

Linear attenuation coefficient

(µ). A measure of how easily X-rays can penetrate a material, given by the fraction of incident photons in a monoenergetic beam that are attenuated per unit thickness of that material.

Temporal resolution

The time required to acquire enough projections, of sufficient signal to noise ratio, to reconstruct an image of the desired quality. The time per scan can often be shortened by using fewer projections combined with iterative reconstruction techniques.

Pixels

(Abbreviation for picture elements). The basic digital unit of a two-dimensional image or radiograph.

Voxels

(An abbreviation for volume elements). The basic unit of a three-dimensional digital representation of an image or object. The voxel size should not be confused with the spatial resolution.

Spatial resolution

The smallest linear distance between two points that can be distinguished in the reconstructed image. Usually larger than the voxel size, depending on the scanned materials and the scanning conditions.

Contrast agents

Highly attenuating particles, gases or stains used to increase the X-ray attenuation contrast of specific structures or defects.

Monochromatic beam

A beam (of X-rays) containing photons with a single energy (wavelength) or a narrow range of energies.

Polychromatic beam

A beam (of X-rays) containing photons having a wide range of wavelengths. Typical of X-ray tube sources, but also available at some synchrotron beamlines. For tube sources, the accelerating voltage determines the maximum X-ray energy but the majority of the X-ray photons have a much lower energy.

X-ray tube

A relatively low-cost and compact source of polychromatic X-rays, typically used in cone beam tomography, producing X-rays by accelerating energetic electrons into a metal target with the subsequent deceleration producing a divergent beam of a broad spectrum of X-ray energies along with characteristic peaks.

Synchrotron

A large-scale facility in which electrons circulate continuously around an essentially circular path defined by bending magnets. Bending magnets and insertion devices deflect the electrons, thereby creating X-ray beams tangential to the ring.

X-ray flux

The number of X-ray photons in the incident beam per second per unit area.

Accelerating voltage

The electrical potential difference that accelerates the electrons that produce X-rays; this voltage determines the maximum X-ray energy.

Bending magnets

Magnets used to maintain the trajectory of the electrons in a synchrotron storage ring. They produce X-rays over a continuous spectrum and are typically much less intense and less focused than the beam of X-rays from an insertion device.

Insertion devices

Magnetic devices used in a synchrotron to produce X-rays from the circulating electrons.

Flat field correction

An image collected without the specimen in place, used to correct for the different sensitivity of each pixel in the detector or non-uniformities across the X-ray beam.

Laminography

A variant of X-ray computed tomography suited to the imaging of flat objects.

Absorption edges

Characteristic sharp discontinuities in the absorption spectrum of a substance that are related to the sharply defined energy levels that electrons occupy in the atoms of a given element.

Coherent radiation

An X-ray beam in which all of the photons in a plane have the same (wave) phase.

Segmentation

An image-processing procedure of assigning a label to every voxel in a volume such that voxels with the same label share certain characteristics.

Volume rendering

Three-dimensional representation of data, often with certain segmented regions colourized or rendered transparent.

Radon transform

An integral transform that projects a cross-sectional slice along a given direction to give the one-dimensional profile. In X-ray computed tomography, the plot of the Radon transform for a slice is represented by a sinogram.

Sinogram

A graph created by plotting the signal recorded by a line of voxels as the sample (or source and detector) is rotated through 180°.

Greyscale thresholds

Greyscale levels used in an image-processing procedure to segment a reconstructed volume based on the greyscale value of the voxel being above or below the given thresholds.

Histogram

A graph that shows how many times an event occurs across various groups of data or classes. Often used to display the frequency of greyscale levels recorded in a tomogram.

Partial volume effect

The appearance of greyscale levels in reconstructed data intermediate between those corresponding to two constituent materials when the voxel is partially filled by both. Simple greyscale threshold methods can mis-segment such voxels.

Pore throats

Characterizations of the smallest cross-sectional area of a pore channel, equal to the radius of a circle drawn perpendicular to fluid flow at the narrowest point.

Tortuosity

A measure of how winding a path or shape is, defined as the ratio of actual path length to the straight distance between the ends of the path. It is sensitive to the spatial resolution of the tomogram.

Ortho-sections

(Also known as ortho-slices). Three orthogonal virtual slices through the volume.

Region of interest scanning

Normally, computed tomography scans include the whole of the sample width in the field of view, but, in cases where higher resolution is required than this allows, it is possible to reconstruct data sets for which a smaller field of view is present in all of the projections, albeit with the introduction of some imaging artefacts such as uneven contrast.

Percolation

The measure of the connectivity of a constituent domain in an object.

Histology

The branch of biology studying tissues by optical or other microscopies.

Scaffold

A structure that ‘supports’ tissue and is at the core of many tissue engineering applications.

Petrography

The branch of petrology dealing with the description and classification of rocks, especially by microscopic examination.

Grey

The unit or radiation dose absorbed, equal to the absorption of 1 J of radiation energy per kilogram of matter being irradiated.

Effective dose

Expressed in millisieverts, the dose calculated for the whole body taking into account not only the nature of the incoming radiation but also the sensitivities of all of the organs to radiation.

Digital volume correlation

A method of correlating the location of features between successive observations (here, computed tomography scans) in order to map material movement, deformation or strain in three dimensions.

Spectral CT

The acquisition of several computed tomography reconstructions with the collected photons apportioned to a small number of energy channels, on the basis of which some level of element differentiation can be undertaken.

Hyperspectral CT

Assignment of the detected photons to many energy channels, enabling computed tomography reconstructions as a function of energy, on the basis of which different elements can be differentiated, often on the basis of their characteristic absorption edges.

Ptychography

A computational imaging technique in which the image is computationally reconstructed from many coherent interference patterns.

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Withers, P.J., Bouman, C., Carmignato, S. et al. X-ray computed tomography. Nat Rev Methods Primers 1, 18 (2021). https://doi.org/10.1038/s43586-021-00015-4

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