Automated high accuracy, rapid beam hardening correction in X-Ray Computed Tomography of multi-mineral, heterogeneous core samples

X-ray Computed Tomography scanning is an innovative procedure that allows representing the internal structure of samples. Among its several purposes, X-ray CT is widely used for investigation of petrophysical properties of porous media. To provide accurate results, it is necessary to have high quality scan images, free of artefacts. One of the most problematic artefacts is beam hardening, which, in cylindrical shapes, increases the attenuation values with increasing distance from the centre. Until now, no automatic solution has been proposed for cylindrically-shaped cores that is both computationally feasible and applicable to all geological media. A new technique is here introduced for correcting beam hardening, using a linearization procedure of the beam hardening curve applied after the reconstruction process. We have developed an automated open source plug-in, running on ImageJ software, which does not require any a priori knowledge of the material, distance from the source or the scan conditions (current, energy), nor any segmentation of phases or calibration scan on phantom data. It is suitable for expert and non-expert use, alike. We have tested the technique on μCT scan images of a plastic rod, a sample of loose sand, several heterogeneous sandstone core samples (with near-cylindrical shapes), and finally, on an internal scan of a Berea sandstone core. The Berea core was also scanned using a medical X-ray CT scanner with a fan-beam geometry, as opposed to a cone beam geometry, showing that our algorithm is equally effective in both cases. Our correction technique successfully removes the beam hardening artefact in all cases, as well as removing the cupping effect common to internal scans. For a Berea Sandstone, with a porosity of 20%, porosity calculated using the corrected scan is 20.54%, which compares to a value of 14.24% using the software provided by the manufacturer

Enabling three-dimensional densitometric measurements using laboratory source X-ray micro-computed tomography

We present new software allowing significantly improved quantitative mapping of the three-dimensional density distribution of objects using laboratory source polychromatic X-rays via a beam characterisation approach (c.f. filtering or comparison to phantoms). One key advantage is that a precise representation of the specimen material is not required. The method exploits well-established, widely available, non-destructive and increasingly accessible laboratory-source X-ray tomography. Beam characterisation is performed in two stages: (1) projection data are collected through a range of known materials utilising a novel hardware design integrated into the rotation stage; and (2) a Python code optimises a spectral response model of the system. We provide hardware designs for use with a rotation stage able to be tilted, yet the concept is easily adaptable to virtually any laboratory system and sample, and implicitly corrects the image artefact known as beam hardening

Correction of beam hardening artefacts in microtomography for samples imaged in containers

We explore the use of referenceless multi-material beam hardening correction methods, with an emphasis on maintaining data quality for real-world imaging of geologic materials with a view towards automation. In particular, we consider cases where the sample of interest is surrounded by a container of uniform material and propose a novel container-only pre-correction technique to allow automation of the segmentation process required for such correction methods. The effectiveness of the new technique is demonstrated using both simulated and experimental data

Micro-Computed Tomography Semi-Empirical Beam Hardening Correction: Method And Application To Meteorites

X-ray micro-computed tomography (μCT) is able to non-destructively provide high- resolution 3D images of the internal structures of dense materials such as meteorites. The widespread availability of instruments capable of biomedical micro-computed tomography means there is ample access to scanners for the investigation of geomaterials, but the scan data can be susceptible to artifacts such as beam hardening, a consequence of high X-ray attenuation in these dense materials. A semi-empirical correction method for beam hardening and scatter that can be straightforwardly applied to available biomedical scanners is proposed and evaluated. This method uses aluminum as a single calibration material to significantly reduce or remove signal intensity errors (i.e. cupping) that occur as a result of beam hardening artifacts. X-ray transmission data are linearized using custom software. Results show that it is possible through careful analysis to determine an effective method of artifact correction for specified protocols using this implementation. Following correction and validation, this technique is applied to imaging of meteorite samples. Four meteorites are examined using μCT in combination with this processing technique: Three ordinary chondrites (Grimsby, Gao-Guenie, and Ozona) and an olivine diogenite (NWA 5480). Information from μCT is compared to that of traditional methods of analysis of meteoritic samples, and the advantages and disadvantages are discussed

Maximum-Likelihood Dual-Energy TomographicImage Reconstruction

Dual-energy (DE) X-ray computed tomography (CT) has shown promise for material characterization and for providing quantitatively accurate CT values in a variety of applications. However, DE-CT has not been used routinely in medicine to date, primarily due to dose considerations. Most methods for DE-CT have used the filtered backprojection method for image reconstruction, leading to suboptimal noise/dose properties. This paper describes a statistical (maximum-likelihood) method for dual-energy X-ray CT that accommodates a wide variety of potential system configurations and measurement noise models. Regularized methods (such as penalized-likelihood or Bayesian estimation) are straightforward extensions. One version of the algorithm monotonically decreases the negative log-likelihood cost function each iteration. An ordered-subsets variation of the algorithm provides a fast and practical version.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/85934/1/Fessler172.pd

3-D fracture tracing for X-ray computed tomography data

X-ray computed tomography (CT) is a nondestructive imaging method that shows differences in X-ray attenuation, which is a proxy for density. Sensitivity to density differences makes CT a good choice for imaging open natural fractures because of the significant density contrast between air and rock. The image data, however, are prone to artifacts and blurring, which makes taking accurate measurements challenging. As a first step to addressing this problem, a tool was created to quantify the spatial resolution of CT data with a point-spread function (PSF). The PSF tool permits accurate measurement of fine-scale features in CT data – critical for measuring fractures, which are often thinner in one dimension than the PSF size, in turn influencing measurement of aperture. The difference between the measurements given by the PSF method and a simple threshold value pick is shown to demonstrate a non-trivial improvement in accuracy. In addition, a 3-D fracture network tracing algorithm was developed, for which the PSF is a necessary input, to characterize accurately the network’s attributes, such as fracture orientations, apertures, and roughnesses. To date, only single, isolated, relatively flat fractures have been characterized thoroughly in 3-D for CT data, and most numerical modeling has been conducted on 2D subsets. Additionally, research involving fracture networks is currently limited to simplified numerical models and simulations. This new work extends CT fracture characterization to the majority of fractured materials with 3-D networks, thus providing a source of real data for studying the difference between fracture networks and single fractures. A sample of Packsaddle schist, with a large number of thin fractures and complex, anastomosing bifurcations, was selected as a testing ground for the network tracing algorithms being developed. Preliminary analysis verifies the method’s efficacy.Geological Science

Development of energy selective techniques in x-ray computed tomography

X-ray micro computed tomography (Micro-CT) has emerged as a powerful tool in petroleum industry for non-destructive 3D imaging of rock samples, that offers micron-scale spatial resolution images of the distribution of porosity, permeability, and fluid phases of the specimens. Micro-CT obtain the radiographic projections of a sample at different angles and use a mathematical procedure to reconstruct a 3D tomogram of the sample's X-ray attenuation coefficients. Through my thesis, the aim was to investigate and improve two main issue which micro-CT suffers from: 1) beam hardening (BH) artefacts and, 2) the requirement of material characterisation. This thesis contributes in addressing these fundamental issues by providing the "energy selective techniques" as follows. Chapter 1 provides an overview of the basics of tomography including physics of X-rays and energy dependent form of attenuation coefficient. Chapter 2 reviews the BH effects and the existing correction methods, followed by a brief review of the material characterisation methods. Chapter 3 assess the accuracy of five different linearisation BH correction models including polynomial, bimodal, power law, cubic spline and zero-order using the sample that have been imaged at ANU CT facility by measuring the BH curves directly and remapping the inverse of the models to data. Chapter 4 is based on a published conference proceeding paper [1] that applies the power law BH correction method of chapter 3 to correct the artefacts of specimens composed of concentric cylinders, e.g., a rock core within a container. Chapter 5 is based on a published paper in the Journal of Applied Physics [2] that uses dual-energy CT and the Alvarez and Macovski [3] transmitted intensity (AMTI) model to estimate the maps of density (rho) and atomic number (Z) of mineralogical samples. In this method, the attenuation coefficients are represented in the form of the two most important interactions of X-rays with atoms that is, PE and CS. This enables material discrimination as PE and CS are respectively dependent on Z and rho of materials [3]. Chapter 6 implements two simplified form of the full model of chapter 5: 1) Alvarez and Macovski polynomial (AMP) model [3], Alvarez and Macovski presented the full model but used a polynomial simplified form of it to estimate rho and Z of materials, 2) Siddiqui and Khamees (SK) model [4] that simplified the attenuation model, by assuming two monochromatic radiations. Chapter 7 presents a method to estimate the properties of sample materials from measurements of transmitted intensity and its statistical variance (TIV model). The method only requires single energy imaging, i.e., eliminates the need for requirements of dual-energy imaging for AMTI method and its simplified forms. The registered intensity on the detector is proportional to a form of "average" energy of detected quanta of X-ray spectra. The variance images can serve the same purpose as the higher energy information required in dual-energy imaging. Chapter 8 modified the TIV model of chapter 7 to apply it directly for BH correction without necessarily estimation of the properties of sample materials. The chapter also presents a simplified form of TIV model (STIV) that normalises the average intensity image

High-quality nodule analysis in spheroidal graphite cast iron using X-ray micro-computed tomography

This work is a continuation of the studies presented in a recent paper by the authors, where a methodology to obtain different nodule quality categories in spheroidal graphite cast iron, was proposed. In this study, an exhaustive analysis of the highest-quality graphite nodules was performed. The experimental methodology involves X-ray micro-computed tomography analysis and digital image post-processing of the high-quality graphite nodule population. Furthermore, different subpopulations were selected, following a nodular size criterion. The procedure involves the evaluation and comparison of the sphericity and compactness distributions and the distances between neighbouring nodules by using ad-hoc image processing software. The results reveal the complementary nature of the sphericity and compactness parameters, which allow classifying, with great accuracy, different nodular quality categories of spheroidal graphite cast iron. Additionally, new viewpoints about the nodular morphology study and the distribution of quality nodules in the metallic matrix was provided, which could be extended to other heterogeneous materials

Three-dimensional distribution of primary melt inclusions in garnets by X-ray microtomography

open6X-ray computed microtomography (X-mu CT) is applied here to investigate in a non-invasive way the three-dimensional (3D) spatial distribution of primary melt and fluid inclusions in gamets from the metapeitic enclaves of El Hoyazo and from the migmatitcs of Sierra Alpujata, Spain. Attention is focused on a particular case of inhomogeneous distribution of inclusions, characterized by inclusion-rich cores and almost inclusion-free rims (i.e., zonal arrangement), that has been previously investigated in detail only by means of 2D conventional methods. Different experimental X-mu CT configurations, both synchrotron radiation- and X-ray tube-based, are employed to explore the limits of the technique. The internal features of the samples are successfully imaged, with spatial resolution down to a few micrometers. By means of dedicated image processing protocols, the lighter melt and fluid inclusions can be separated from the heavier host garnet and from other non-relevant features (e.g., other mineral phases or large voids). This allows evaluating the volumetric density of inclusions within spherical shells as a function of the radial distance from the center of the host garnets. The 3D spatial distribution of heavy mineral inclusions is investigated as well and compared with that of melt inclusions. Data analysis reveals the occurrence of a clear peak of melt and fluid inclusions density, ranging approximately from 1/3 to 1/2 of the radial distance from the center of the distribution and a gradual decrease from the peak outward. heavy mineral inclusions appear to be almost absent in the central portion of the garnets and more randomly arranged, showing no correlation with the distribution of melt and fluid inclusions. To reduce the effect of geometric artifacts arising from the non-spherical shape of the distribution, the inclusion density was calculated also along narrow prisms with different orientations, obtaining plots of pseudo-linear distributions. The results show that the core-rim transition is characterized by a rapid (but not step-like) decrease in inclusion density, occurring in a continuous mode. X-ray tomographic data, combined with electron microprobe chemical profiles of selected elements, suggest that despite the inhomogeneous distribution of inclusions, the investigated garnets have grown in one single progressive episode in the presence of anatectic melt. The continuous drop of inclusion density suggests a similar decline in (radial) garnet growth, which is a natural consequence in the case of a constant reaction rate. Our results confirm the advantages of high-resolution X-mu CT compared to conventional destructive 2D observations for the analysis of the spatial distribution of micrometer-scale inclusions in minerals, owing to its non-invasive 3D capabilities. The same approach can be extended to the study of different microstructural features in samples from a wide variety of geological settings.openParisatto, Matteo; Turina, Alice; Cruciani, Giuseppe; Mancini, Lucia; Peruzzo, Luca; Cesare, BernardoParisatto, Matteo; Turina, Alice; Cruciani, Giuseppe; Mancini, Lucia; Peruzzo, Luca; Cesare, Bernard

New reconstruction strategies for polyenergetic X-ray computer tomography

Mención Internacional en el título de doctorX-ray computed tomography (CT) provides a 3D representation of the attenuation coefficients of patient tissues, which are roughly decreasing functions of energy in the usual range of energies used in clinical and preclinical scenarios (from 30 KeV to 150 KeV). Commercial scanners use polychromatic sources, producing a beam having a range of photon energies, because no X-ray lasers exist as a usable alternative. Due to the energy dependence of the attenuation coefficients, low-energy photons are preferably absorbed, causing a shift of the mean energy of the X-ray beam to higher values; this effect is known as beam hardening. Classical reconstruction methods assume a monochromatic source and do not take into account the polychromatic nature of the spectrum, producing two artifacts in the reconstructed image: 1) cupping in large homogeneous areas and 2) dark bands between dense objects such as bone. These artifacts hinder a correct visualization of the image and the recovery of the true attenuation coefficient values. A fast correction of the beam-hardening artifacts can be performed with the so-called post-processing methods, which use the information of a segmentation obtained in a preliminary reconstruction. Nevertheless, this segmentation may fail in low-dose scenarios, leading to an increase of the artifacts. An alternative for these scenarios is the use of iterative methods that incorporate a beam-hardening model, at a cost of higher of computational time compared to post-processing methods. All previously proposed methods require either knowledge of the X-ray spectrum, which is not always available, or the heuristic selection of some parameters, which have been shown not to be optimal for the correction of different slices in heterogeneous studies. This thesis is framed in a research line focused on improving radiology systems of the Biomedical Imaging and Instrumentation Group (BiiG) from the Bioengineering and Aerospace Department of Universidad Carlos III de Madrid. This research line is carried out in collaboration with the Unidad de Medicina y Cirugía experimental of Hospital Gregorio Marañón through Instituto de Investigación Sanitaria Gregorio Marañón, the Electrical Engineering and Computer Science (EECS) department of the University of Michigan and SEDECAL, a Spanish company among the ten best world companies in medical imaging that exports medical devices to 130 countries. As part of this research line, a high-resolution micro-CT was developed for small-animal samples, which operates at low voltages, leading to strong beam-hardening artifacts. This scanner allows preclinical studies to be carried out, which can be divided into cross-sectional and longitudinal studies. Since cross-sectional studies consist of one acquisition at a specific point in time, radiation dose is not an issue, allowing for the use of standard-dose protocols with good image quality. In contrast, longitudinal studies consist of several acquisitions over time, so it is advisable to use low-dose protocols, despite the reduction of signal to noise ratio and the risk of artifacts in the image. This thesis presents a bundle of reconstruction strategies to cope with the beam-hardening effect in different dose scenarios, overcoming the problems of methods previously proposed in the literature. Since image quality is not an issue in the standard-dose scenarios, the speed of the strategies becomes a priority, advising for post-processing strategies. The main advantage of the proposed post-processing strategy is the inclusion of empirical models of the beam-hardening effect, either through a simple calibration phantom or through the information provided by the sample, which eliminates the need of the knowledge of the spectrum or tunning parameters. The evaluation against previously proposed correction methods with real and simulated data showed a good artifact compensation for a standarddose scenario (cross-sectional studies), while not optimum in a low-dose scenario, as expected. For longitudinal studies, where the reduction of dose delivered to the sample is advisable, this thesis presents an iterative method that incorporates the mentioned experimental beam-hardening models. The evaluation with real and simulated data and different dose scenarios showed excellent results but with the known drawback of high computational time. Finally, a deep-learning approach was explored with the idea of looking for a joint solution that would require low-computational time and, at the same time, compensate the beam-hardening artifacts regardless the dose scenario. The chosen architecture is U-net++, based on an encoder-decoder, with the mean-squared error as the cost function. Results in real data showed a good compensation of the beam-hardening and low-dose artifacts with a considerable reduction of time, rising the interest of further exploring this path in the future. The incorporation of these reconstruction strategies in real scanners is straightforward, only requiring a small modification of the calibration step already implemented in commercial scanners. The methods are being transferred to the company SEDECAL for their implementation in the new generation of micro-CT scanners for preclinical research and a multipurpose C-arm for veterinary applications.Programa de Doctorado en Multimedia y Comunicaciones por la Universidad Carlos III de Madrid y la Universidad Rey Juan CarlosPresidente: Jorge Ripoll Lorenzo.- Secretario: José Vicente Manjón Herrera.- Vocal: Adam M. Alessi