It is well known that beam-hardening gives rise to errors in the reconstructed linear attenuation coefficient that vary with position, thus invalidating post-reconstruction calibration methods. Prior to reconstruction, projections can be linearized, but this works only for samples composed of a single phase. Two-dimensional beam-hardening correction has been proposed for the two-phase case. A method for forward projection from polyhedral phantoms has also been proposed in the past. Here, this method has been extended to simulate polychromatic radiation and a hierarchical representation of phantom materials is proposed. This is used to create a liquid-immersed tooth phantom. The phantom projection data was then used to validate and improve the two-dimensional beam-hardening correction algorithm.
When using X-ray microtomography (XMT) to look for small mineral changes between successive scans in, for example, extracted human teeth, it is necessary to use a carefully designed protocol to ensure maximum accuracy. Our protocol is divided into four main elements: Mounting: The sample, in this case a tooth, must be mounted in such a way that it can be precisely relocated in the same place in the scanner (height and tilt must be precise; rotation can be changed post-scanning). Calibration: Over time (possibly weeks or months), the X-ray spectrum may change (with anode potential and current constant). This is due primarily to gradual anode pitting, which causes varying amounts of self-absorption. A calibration carousel is used to characterize the X-ray spectrum after every scan. Alignment: To ensure that the same regions are measured for every scan, it is necessary that all reconstructed images are perfectly aligned. We use a 7 degree-of-freedom alignment algorithm for this. To avoid loss of resolution when realigning data sets, second and subsequent scans are reconstructed with a 2× scale factor and “shrunk” during the realignment. Equalization: In spite of best efforts for calibration, repeatability for linear attenuation coefficient (LAC) measurement is of the order of 1%. To improve on this, regions are defined in which no change in mineral concentration should occur. In every scan, the mean LAC for these regions is measured and an appropriate LAC scaling factor is applied to the reconstructed volumes for the second and subsequent scans.
X-ray microtomography (XMT) is a well-established technique in dental research. The technique has been used extensively to explore the complex morphology of the root canal system, and to qualitatively and quantitatively evaluate root canal instrumentation and filling efficacy in extracted teeth; enabling different techniques to be compared. Densitometric information can be used to identify and map demineralized tissue resulting from tooth decay (caries) and, in extracted teeth, the method can be used to evaluate different methods of excavation. More recently, high contrast XMT is being used to investigate the relationship between external insults to teeth and the pulpal reaction. When such insults occur, fluid may flow through dentinal tubules as a result of cracking or porosity in enamel. Over time, there is an increase in mineralization along the paths of the tubules from the pulp to the damaged region in enamel and this can be visualized using high contrast XMT. The scanner used for this employs time-delay integration to minimize the effects of detector inhomogeneity in order to greatly increase the upper limit on signal-to-noise ratio that can be achieved with long exposure times. When enamel cracks are present in extracted teeth, the presence of these pathways indicates that the cracking occurred prior to extraction. At high contrast, growth lines are occasionally seen in deciduous teeth which may have resulted from periods of maternal illness. Various other anomalies in mineralization resulting from trauma or genetic abnormalities can also be investigated using this technique.
Fracture of nickel-titanium (NiTi) endodontic files is an uncommon but potentially damaging occurrence during root canal preparation. If the broken portion of the file remains inside the tooth canal it can prevent complete preparation of the root canal with consequent negative impact on treatment outcomes. Removal of file fragment from the tooth canal is currently a mechanical process, which due to the limited working space and restricted view can lead to further problems including perforation of the tooth. Electrochemical dissolution is a relatively new method proposed to dissolve a fractured instrument, fully or partially within the canal, to enable its removal. In this article we explore the effects of electrochemical dissolution on the root canal environment using high contrast time delay integration (TDI) X-ray micro-tomography (XMT) designed specifically for dental research.
Beam hardening artefacts arise in tomography and microtomography with polychromatic sources. Typically, specimens
appear to be less dense in the center of reconstructions because as the path length through the specimen increases, so the
X-ray spectrum is shifted towards higher energies due to the preferential absorption of low energy photons. Various
approaches have been taken to reduce or correct for these artefacts. Pre-filtering the X-ray beam with a thin metal sheet
will reduce soft energy X-rays and thus narrow the spectrum. Correction curves can be applied to the projections prior to
reconstruction which transform measured attenuation with polychromatic radiation to predicted attenuation with
monochromatic radiation. These correction curves can be manually selected, iteratively derived from reconstructions
(this generally works where density is assumed to be constant) or derived from a priori information about the X-ray
spectrum and specimen composition. For hard tissue specimens, the latter approach works well if the composition is
reasonably homogeneous. In the case of an immersed or embedded specimen (e.g., tooth or bone) the relative
proportions of mineral and “organic” (including medium and plastic container) species varies considerably for different
ray paths and simple beam hardening correction does not give accurate results. By performing an initial reconstruction,
the total path length through the container can be determined. By modelling the X-ray properties of the specimen, a 2D
correction transform can then be created such that the predicted monochromatic attenuation can be derived as a function
of both the measured polychromatic attenuation and the container path length.
In laboratory X-ray microtomography (XMT) systems, the signal-to-noise ratio (SNR) is typically determined by the
X-ray exposure due to the low flux associated with microfocus X-ray tubes. As the exposure time is increased, the SNR
improves up to a point where other sources of variability dominate, such as differences in the sensitivities of adjacent
X-ray detector elements. Linear time-delay integration (TDI) readout averages out detector sensitivities on the critical
horizontal direction and equiangular TDI also averages out the X-ray field. This allows the SNR to be increased further
with increasing exposure. This has been used in dentistry to great effect, allowing subtle variations in dentine
mineralisation to be visualised in 3 dimensions. It has also been used to detect ink in ancient parchments that are too
damaged to physically unroll. If sufficient contrast between the ink and parchment exists, it is possible to virtually unroll
the tomographic image of the scroll in order that the text can be read. Following on from this work, a feasibility test was
carried out to determine if it might be possible to recover images from decaying film reels. A successful attempt was
made to re-create a short film sequence from a rolled length of 16mm film using XMT. However, the “brute force”
method of scaling this up to allow an entire film reel to be imaged presents a significant challenge.
“Can brute-force high-contrast tomography techniques and image processing techniques retrieve textual content
from damaged heritage materials?”
The Dental Institute at Queen Mary University of London (QMUL) is the leading centre for very high contrast
X-Ray Microtomography imaging. The Apocalypto Project is our collaboration with the heritage community
and experts in Computer Vision systems in the Computer Science Department at Cardiff University. This
collaboration has developed techniques and a workflow that allows us to reveal textual content from moisture-damaged
parchment rolls. This article will also present some initial results from burned and heat shrunken
parchment rolls, an insect damaged Mamluk cap and a birch bark roll.
The goal of the MuCAT scanner development at Queen Mary University of London is to provide highly accurate maps of a specimen’s X-ray linear attenuation coefficient; speed of data acquisition and spatial resolution having a lower priority. The reason for this approach is that the primary application is to accurately map the mineral concentration in teeth. Synchrotron tomography would generally be considered more appropriate for such a task, but many of the dental applications involve repeated scans with long intervening periods (from hours to weeks) and the management of synchrotron facilities does not readily allow such research. Development work is concentrated in two areas: beam hardening correction algorithms and novel scanning methodology. Beam hardening correction is combined with calibration, such that the raw X-ray projection data is corrected for beam hardening prior to reconstruction. Recent developments include the design of a multi-element calibration carousel. This has nine calibration pieces, five aluminium, three titanium and one copper. Development of the modelling algorithm is also yielding improved accuracy. A time-delay integration CCD camera is used to avoid ring artefacts. The original prototype averaged out inhomogeneities in both the detector array and the X-ray field; later designs used only software correction for the latter. However, at lower X-ray energies, the effect of deposits on the X-ray window (for example) becomes more conspicuous and so a new scanning methodology has been designed whereby the specimen moves in an arc about the source and equiangular data is acquired, thus overcoming this problem.
Stored in various public archives and private collections around the world, there are untold numbers of documents whose content is lost to memory and history. They cannot be read by normal means, because the parchment and paper they are written on has degraded; any attempt to handle or process the document for reading will at the very least cause it permanent damage. One of the prime catalysts of document degradation is the iron gall ink used in their writing; this provides a contrast for X-Ray imaging. The low attenuation produced by the tiny quantities of iron and other metals in the inks requires a system with a very high contrast ratio and excellent immunity from artifacts to enable ink imaging. The new generation XMT TDI scanner being developed at Queen Mary fulfills these criteria. A 3D volumetric dataset produced by XMT scanning the document is modeled and digitally re-created, producing a readable image of the text. The post-processing is performed in six stages, noise removal, data segmentation, surface construction, flattening, data projection and image generation. The scanning process takes upwards of a day, so it is important that the documents are not damaged by long exposure to the X-Ray flux. Investigations ongoing and due to be be published have shown no detectable extra damage to either old or modern scanned parchment.
Impact-source X-ray microtomography (XMT) is a widely-used benchtop alternative to synchrotron radiation microtomography. Since X-rays from a tube are polychromatic, however, greyscale ‘beam hardening' artefacts are produced by the preferential absorption of low-energy photons in the beam path.
A multi-material ‘carousel' test piece was developed to offer a wider range of X-ray attenuations from well-characterised filters than single-material step wedges can produce practically, and optimization software was developed to produce a beam hardening correction by use of the Nelder-Mead optimization method, tuned for specimens composed of other materials (such as hydroxyapatite [HA] or barium for dental applications.) The carousel test piece produced calibration polynomials reliably and with a significantly smaller discrepancy between the calculated and measured attenuations than the calibration step wedge previously in use.
An immersion tank was constructed and used to simplify multi-material samples in order to negate the beam hardening effect of low atomic number materials within the specimen when measuring mineral concentration of higher-Z regions. When scanned in water at an acceleration voltage of 90 kV a Scanco AG hydroxyapatite / poly(methyl methacrylate) calibration phantom closely approximates a single-material system, producing accurate hydroxyapatite concentration measurements. This system can then be corrected for beam hardening for the material of interest.
In 1981, Elliott and Dover designed an X-ray microtomography scanner as a means of measuring the local mineral
concentration in teeth. Although slow, this first generation system gave accurate measurements of the X-ray linear
attenuation coefficient (LAC) due to its use of energy dispersive photon counting apparatus. Attaining such accuracy
with integrating detectors in third generation scanners is difficult, but has been the goal of our ongoing development.
The current "MuCat 2" system uses a 6cm square CCD chip with a parallel fibre-optic faceplate coupled to a CsI
scintillator. Time delay integration readout (with sliding camera) is used to eliminate ring artefacts and enable high
dynamic range X-ray projections to be acquired. The beam is collimated with a moving aperture (tracking the camera) to
reduce X-ray scatter. Beam hardening is reduced by the use of filtering and corrected using data from an aluminium step
wedge to optimise a model of polychromatic X-ray generation, attenuation and detection. Adjustments can be made to
the model to allow for known specimen composition. Projections are corrected for distortion and repeatable wobble in
the rotation stage. Where high absolute accuracy of the LAC is required, a pure aluminium wire is included in the scan
and used to "fine-tune" the grey level after reconstruction.
Beam hardening in X-ray tomography is often corrected using an arbitrary polynomial whose coefficients are subjectively selected. A better approach is to model X-ray generation, transmission and detection and to use step wedge transmission measurements to fit the model parameters. This allows for extrapolation of linearization curves beyond the range of the step wedge and it allows this curve to be adjusted according to the specimen composition without changing
the composition of the step wedge. This paper presents the principles behind beam-hardening and the model used for correction. Initial tests of this method have shown very good results where a priori knowledge of the specimen composition is available.
The way in which microtomography developed in the authors' laboratory in the early 1980s is described, together with some background material. Later developments in scanning geometries and detectors, mainly in other laboratories, are described. Some present problems and possible future directions will be considered.
Optical coupling between the X-ray scintillator and digital camera (typically CCD) is a major design consideration in X-ray microtomography. Previously, we used a pair of 50mm f1.2 lenses, which we determined to be approximately 60 % efficient, that is, the signal to noise ratio is that which would occur if 60 % of the X-ray photons absorbed by the scintillator were directly detected. For larger CCDs, lenses become excessively large, heavy and expensive. For our 60 x 60 mm time-delay integration CCD camera, we used parallel fibre-optic coupling, giving greater efficiency. A problem with this is the scattering of light through the fibre cladding, which reduces image contrast, adding a very blurred image to the sharp image transmitted through the fibres. This problem is ideally suited to solution by deconvolution. Since the high frequency image components are present (direct fibre image) deconvolution can be used to eliminate the low frequency scatter image, without the problems normally associated with de-blurring. The point spread function was assumed to be rotationally symmetrical and was determined from an edge image of a lead plate positioned close to the scintillator. In frequency space, the mid frequency portion was extrapolated into the low frequency portion using a parabolic fit. The difference between the extrapolated and measured low frequency portions was deemed to be the scatter response. This was then added to the frequency response for a perfect delta function to obtain the frequency response used for deconvolution. The results showed excellent correction of the X-ray microtomographic images.
We have developed a high definition X-ray microtomography scanner using time-delay integration CCD readout mode, whereby the camera is moved through the X-ray “shadow” during simultaneous readout. This method eliminates ring artefacts in the reconstructed image and allows the recorded image to be larger than the CCD itself. To maximise dynamic range, the reflective coated scintillator was lens coupled (two back-to-back 50mm f1.2 camera lenses). Equivalent X-ray photons per pixel were derived from noise measurements in specimen-absent projections. This was typically 600,000 for a 10 second exposure (90kV, 200μA, 25 cm source to camera). To quantify relay lens efficiency, this was re-measured at aperture settings from f1.2 to f11. The results closely fitted a model based on two noise sources (one from finite X-ray photons and one from finite light photons per X-ray photon), yielding an efficiency of 60% at f1.2. Although higher efficiency is desirable, this is a good compromise that avoids CCD saturation. This suggests that when using the more efficient direct fibre-optic coupling, a reflective scintillator coating may be undesirable, as the marginal increase in efficiency would not justify any loss of resolution or dynamic range. Correction for beam hardening is currently carried out using a 7 step Al wedge to measure experimental attenuation vs theoretical attenuation for monochromatic radiation. We intend to modify this method to improve accuracy in a more diverse range of materials. Dishing artefacts were decreased further by using a moving X-ray aperture to reduce scattered radiation.
KEYWORDS: X-rays, Sensors, Image quality, Signal attenuation, Signal to noise ratio, X-ray imaging, Reconstruction algorithms, Scanners, Photons, 3D image reconstruction
It is known that the reconstruction produced by the standard cone beam back-projection algorithm, with circular orbit, gives only an approximation to the true three dimensional x- ray attenuation map. It is generally thought that the errors are acceptable if the cone angle is not too large. Such assumptions are based, at least in part, on reconstructions of ellipsoids or spheres. However, this is not representative of most of the specimens used for microtomography which may give rise to larger errors. We have therefore designed a mathematical cone beam phantom generator, capable of calculating a projection data set from analytical specimens described by surface polygons. Using this phantom generator, we have tested a variety of different types of 'specimen' and have shown that when they have certain characteristics, serious errors can occur with very small cone angles, while others will tolerate much larger angles. For a more authentic simulation, a polygon surface was generated from a microtomography scan of a real piece of walrus tusk. This has been used to determine the susceptibility of this type of specimen to cone-beam related errors for various cone angles.
The term microtomography generally refers to x-ray computed tomography with a resolution of better than 100 microns. Because of the range of different specimens that can be studied, it is important that resolution, x-ray energy and exposure are matched to the composition and size of the specimen. Where control over specimen size is possible, it should be made as small as possible since there is a third order relationship between size and required exposure for a given resolution and contrast. In first generation microtomography systems the specimen is stepped though a single collimated x-ray beam and the attenuation recorded by a single detector. The ability of such systems to record both number and energy of transmitted photons facilitates quantitative evaluation of noise and errors in the detection system and their propagation through to the reconstructed image. Most microtomography scanners are similar in principle to third generation medical scanners, except that the specimen, rather than the source/detector system, rotates. Images from such scanners are subject to ring artifacts because of slight differences in response of the detector elements. Fourth generation medical scanners overcome this problem by using fixed ring of detectors with only the source rotating, but it is impractical to build a microtomography scanner using the same principle. We have designed a fourth generation microtomography scanner which uses a CCD camera operated in time delay integration mode. This overcome the problem of ring artifacts and allows specimens larger than the CCD imaging area to be scanned.
Most applications of x-ray microtomography in medicine have been to the study of bones and teeth. Of these, the majority have been devoted to investigations aimed at characterization of trabecular structure in normal and osteoporotic bone. Such studies are hindered by partial volume effects, both at the level of the trabecular boundaries, and also on a finer scale, from cells and cell processes embedded within the bone tissue. The effect of the latter on the determination of mineral concentration has been modelled by computer simulation. Primarily as a result of these partial volume effects, most studies of trabecular bone have been based on binary images produced by thresholding. If the resolution of laboratory systems were improved, changes in mineral concentration within trabeculae could also be assessed. Although most microtomography uses detector arrays, useful results can be obtained with first generation systems. These are illustrated by quantitative mineral concentration studies of bones and teeth; determination of concentrations of elements with accessible absorption edges derived from absorption spectra recorded at all points in the projections; and demonstration of diffusion of KI into cortical bone. A very exciting use of 3D microtomography is to observe changes in bone structure after specific treatments. Others have used this for in vivo studies, but here is illustrated by preliminary observation of in situ cracking of cortical bone under mechanical load.
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