Phillip Vargas

Monotonic penalized-likelihood image reconstruction for X-ray fluorescence computed tomography

In this work, we derive a monotonic penalized-likelihood algorithm for image reconstruction in X-ray fluorescence CT (XFCT) when the attenuation maps at the energies of the fluorescence X-rays are unknown. XFCT is not a transmission tomography modality but rather a stimulated emission tomography modality, and it is thus necessary to correct for attenuation of the incident and fluorescence photons if accurate images are to be obtained. This is challenging because the attenuation map is, in general, known only at the stimulating beam energy and not at the various fluorescence energies. We have developed a penalized-likelihood image reconstruction strategy for this problem. The approach alternates between updating the distribution of a given element and updating the attenuation map for that elements fluorescence X-rays. As derived, the approach is guaranteed to increase the penalized likelihood at each iteration.

Penalized-likelihood image reconstruction for x-ray fluorescence computed tomography

In this paper, we derive a monotonic penalized-likelihood algorithm for image reconstruction in X-ray fluorescence computed tomography (XFCT) when the attenuation maps at the energies of the fluorescence X-rays are unknown. In XFCT, a sample is irradiated with pencil beams of monochromatic synchrotron radiation that stimulate the emission of fluorescence X-rays from atoms of elements whose K- or L-edges lie below the energy of the stimulating beam. Scanning and rotating the object through the beam allows for acquisition of a tomographic dataset that can be used to reconstruct images of the distribution of the elements in question. XFCT is a stimulated emission tomography modality, and it is thus necessary to correct for attenuation of the incident and fluorescence photons. The attenuation map is, however, generally known only at the stimulating beam energy and not at the energies of the various fluorescence X-rays of interest. We have developed a penalized-likelihood image reconstruction strategy for this problem. The approach alternates between updating the distribution of a given element and updating the attenuation map for that elements fluorescence X-rays. The approach is guaranteed to increase the penalized likelihood at each iteration. Because the joint objective function is not necessarily concave, the approach may drive the solution to a local maximum. To encourage the algorithm to seek out a reasonable local maximum, we include in the objective function a prior that encourages a relationship, based on physical considerations, between the fluorescence attenuation map and the distribution of the element being reconstructed

Correction for Resolution Nonuniformities Caused by Anode Angulation in Computed Tomography

Most X-ray tubes comprise a rotating anode that is bombarded with electrons to produce X-rays. A substantial amount of heat is generated, and to increase the area of the anode exposed to the electrons, without increasing the apparent size of the focal spot, the focal track of the anode is generally beveled with a very shallow angle (typically 5deg-7deg in a computed tomography (CT) tube). Due to the line focus principle, this allows a fairly large area of the focal track to be exposed to electrons while retaining a fairly small effective projected focal spot. One side effect of anode angulation is that the focal spot appears different from different positions in the detector array; the effective focal spot size at a constant distance from the tube will be larger for a peripheral detector channel than for a central one. These differences in the effective size of the focal spot across the fleld-of-view lead to worse resolution in the periphery than in the center of reconstructed images. In this work we describe a method for achieving more uniform resolution in fanbeam CT images by correcting for these focal spot angulation effects. We do so by modeling the effects as a series of local blurrings in the space of transmitted CT intensities and determining the effective coefficients of the corresponding discrete convolutions. The effect of these blurrings can then be compensated for in the sinogram domain through the use of a penalized-likelihood sinogram restoration model we have recently developed.

Experimental demonstration of novel imaging geometries for x‐ray fluorescence computed tomography

PURPOSE X-ray fluorescence computed tomography (XFCT) is an emerging imaging modality that maps the three-dimensional distribution of elements, generally metals, in ex vivo specimens and potentially in living animals and humans. At present, it is generally performed at synchrotrons, taking advantage of the high flux of monochromatic x rays, but recent work has demonstrated the feasibility of using laboratory-based x-ray tube sources. In this paper, the authors report the development and experimental implementation of two novel imaging geometries for mapping of trace metals in biological samples with ∼50-500 μm spatial resolution. METHODS One of the new imaging approaches involves illuminating and scanning a single slice of the object and imaging each slices x-ray fluorescent emissions using a position-sensitive detector and a pinhole collimator. The other involves illuminating a single line through the object and imaging the emissions using a position-sensitive detector and a slit collimator. They have implemented both of these using synchrotron radiation at the Advanced Photon Source. RESULTS The authors show that it is possible to achieve 250 eV energy resolution using an electron multiplying CCD operating in a quasiphoton-counting mode. Doing so allowed them to generate elemental images using both of the novel geometries for imaging of phantoms and, for the second geometry, an osmium-stained zebrafish. CONCLUSIONS The authors have demonstrated the feasibility of these two novel approaches to XFCT imaging. While they use synchrotron radiation in this demonstration, the geometries could readily be translated to laboratory systems based on tube sources.PURPOSE X-ray fluorescence computed tomography (XFCT) is an emerging imaging modality that maps the three-dimensional distribution of elements, generally metals, inex vivo specimens and potentially in living animals and humans. At present, it is generally performed at synchrotrons, taking advantage of the high flux of monochromatic x rays, but recent work has demonstrated the feasibility of using laboratory-based x-ray tube sources. In this paper, the authors report the development and experimental implementation of two novel imaging geometries for mapping of trace metals in biological samples with ∼50-500 μm spatial resolution. METHODS One of the new imaging approaches involves illuminating and scanning a single slice of the object and imaging each slices x-ray fluorescent emissions using a position-sensitive detector and a pinhole collimator. The other involves illuminating a single line through the object and imaging the emissions using a position-sensitive detector and a slit collimator. They have implemented both of these using synchrotron radiation at the Advanced Photon Source. RESULTS The authors show that it is possible to achieve 250 eV energy resolution using an electron multiplying CCD operating in a quasiphoton-counting mode. Doing so allowed them to generate elemental images using both of the novel geometries for imaging of phantoms and, for the second geometry, an osmium-stained zebrafish. CONCLUSIONS The authors have demonstrated the feasibility of these two novel approaches to XFCT imaging. While they use synchrotron radiation in this demonstration, the geometries could readily be translated to laboratory systems based on tube sources.

Reduced-Scan Schemes for X-Ray Fluorescence Computed Tomography

X-ray fluorescence computed tomography (XFCT) is a synchrotron-based imaging modality employed for mapping the distribution of elements within slices or volumes of intact specimens. A pencil beam of external radiation is used to stimulate emission of characteristic X-rays from within a sample, which is scanned and rotated through the pencil beam in a first-generation tomographic geometry. The measurements so obtained can be represented as generalizations of the attenuated Radon transform. The range of angular scanning employed is the subject of some variability in the XFCT imaging community, as some groups rotate the object through a full 360deg, while others employ only a 180deg rotation. In both cases, the entire object is scanned through the beam at each projection view. The use of a 180deg rotation is sometimes justified by implicit reference to a well-known symmetry property of the Radon transform, but that symmetry does not hold for the attenuated Radon transform. In this work, we demonstrate that a full scan of the object at each view coupled with a 360deg rotation does contain a two-fold data redundancy. While the redundancy does not give rise to a simple symmetry condition as in the case of the Radon transform, we will show that it does indeed license the use of the 180deg scheme. However, we will also demonstrate that when there is a single external fluorescence detector, the redundancy also licenses a potentially more attractive reduced-scan scheme, in which the object is rotated through a full 360deg, but in which only the half of the object closest to the fluorescence detector is scanned at each projection view. This new scheme may permit both reduced imaging times and improved image quality.

Material identification in x-ray microscopy and micro CT using multi-layer, multi-color scintillation detectors.

We demonstrate that a dual-layer, dual-color scintillator construct for microscopic CT, originally proposed to increase sensitivity in synchrotron imaging, can also be used to perform material quantification and classification when coupled with polychromatic illumination. We consider two different approaches to data handling: (1) a data-domain material decomposition whose estimation performance can be characterized by the Cramer-Rao lower bound formalism but which requires careful calibration and (2) an image-domain material classification approach that is more robust to calibration errors. The data-domain analysis indicates that useful levels of SNR (>5) could be achieved in one second or less at typical bending magnet fluxes for relatively large amounts of contrast (several mm path length, such as in a fluid flow experiment) and at typical undulator fluxes for small amount of contrast (tens of microns path length, such as an angiography experiment). The tools introduced could of course be used to study and optimize parameters for a wider range of potential applications. The image domain approach was analyzed in terms of its ability to distinguish different elemental stains by characterizing the angle between the lines traced out in a two-dimensional space of effective attenuation coefficient in the front and back layer images. This approach was implemented at a synchrotron and the results were consistent with simulation predictions.

Optimizing synchrotron microCT for high-throughput phenotyping of zebrafish

We are creating a state-of-the-art 2D and 3D imaging atlas of zebrafish development. The atlas employs both 2D histology slides and 3D benchtop and synchrotron micro CT results. Through this atlas, we expect to document normal and abnormal organogenesis, to reveal new levels of structural detail, and to advance image informatics as a form of systems biology. The zebrafish has become a widely used model organism in biological and biomedical research for studies of vertebrate development and gene function. In this work, we will report on efforts to optimize synchrotron microCT imaging parameters for zebrafish at crucial developmental stages. The aim of these studies is to establish protocols for high-throughput phenotyping of normal, mutant and diseased zebrafish. We have developed staining and embedding protocols using different heavy metal stains (osmium tetroxide and uranyl acetate) and different embedding media (Embed 812 and glycol methacrylate). We have explored the use of edge subtraction and multi-energy techniques for contrast enhancement and we have examined the use of different sample-detector distances with unstained samples to explore and optimize phase-contrast enhancement effects. We will report principally on our efforts to optimize energy choice for single- and multi-energy studies as well as our efforts to optimize the degree of phase contrast enhancement.

Region of Interest Reconstruction in X-Ray Fluorescence Computed Tomography for Negligible Attenuation

X-ray fluorescence computed tomography (XFCT) is a synchrotron-based imaging modality employed for mapping the distribution of elements within slices or volumes of intact specimens. A pencil beam of external radiation is used to stimulate emission of characteristic X-rays from within a sample, which is scanned and rotated through the pencil beam in a first-generation tomographic geometry. One limitation of XFCT is the long image acquisition time required to acquire a complete set of line integrals one-by-one. Typically, even if only a portion of a slice through the object is of interest, measurement lines are acquired spanning the entire object at every projection view over 180 degrees to avoid reconstructing images with so-called truncation artifacts. In this paper, we show that when attenuation is negligible, recent developments in tomographic reconstruction theory can be used to reduce the scanning effort required to reconstruct regions of interest within the slice. The new theory provides explicit guidance as to which line integrals must be measured for a given ROI and also provides a backprojection-filtration reconstruction algorithm that averts the truncation artifacts that typically plague filtered backprojection reconstructions from truncated data. This is demonstrated through simulation studies and with real synchrotron-based XFCT data.

Comparison of Quadratic- and Median-Based Roughness Penalties for Penalized-Likelihood Sinogram Restoration in Computed Tomography

We have compared the performance of two different penalty choices for a penalized-likelihood sinogram-restoration strategy we have been developing. One is a quadratic penalty we have employed previously and the other is a new median-based penalty. We compared the approaches to a noniterative adaptive filter that loosely but not explicitly models data statistics. We found that the two approaches produced similar resolution-variance tradeoffs to each other and that they outperformed the adaptive filter in the low-dose regime, which suggests that the particular choice of penalty in our approach may be less important than the fact that we are explicitly modeling data statistics at all. Since the quadratic penalty allows for derivation of an algorithm that is guaranteed to monotonically increase the penalized-likelihood objective function, we find it to be preferable to the median-based penalty.

Element Mapping in Organic Samples Utilizing a Benchtop X-Ray Fluorescence Emission Tomography (XFET) System

X-ray fluorescence computed tomography (XFCT) is an emerging imaging modality that maps the three-dimensional distribution of elements, generally metals, in ex vivo specimens and potentially in living animals and humans. Building on our previous synchrotron-based work, we experimentally explored the use of a benchtop X-ray fluorescence computed tomography system for mapping trace-metal ions in biological samples. This system utilizes a scanning pencil beam to stimulate the object and then relies on a detection system, with single or multiple slit apertures placed in front of position-sensitive X-ray detectors, to collect the fluorescence X-rays and to form 3-D elemental map without the need for tomographic imaging reconstruction. The technique was used to generate images of the elemental distributions of a triple-tube phantom and an osmium-stained zebrafish.