A software system has been developed for high-performance Computed Tomography (CT) reconstruction, simulation
and other X-ray image processing tasks utilizing remote computer clusters optionally equipped with multiple Graphics
Processing Units (GPUs). The system has a streamlined Graphical User Interface for interaction with the cluster. Apart
from extensive functionality related to X-ray CT in plane-wave and cone-beam forms, the software includes multiple
functions for X-ray phase retrieval and simulation of phase-contrast imaging (propagation-based, analyzer crystal based
and Talbot interferometry). Other features include several methods for image deconvolution, simulation of various
phase-contrast microscopy modes (Zernike, Schlieren, Nomarski, dark-field, interferometry, etc.) and a large number of
conventional image processing operations (such as FFT, algebraic and geometrical transformations, pixel value
manipulations, simulated image noise, various filters, etc.). The architectural design of the system is described, as well as
the two-level parallelization of the most computationally-intensive modules utilizing both the multiple CPU cores and
multiple GPUs available in a local PC or a remote computer cluster. Finally, some results about the current system
performance are presented. This system can potentially serve as a basis for a flexible toolbox for X-ray image analysis
and simulation, that can efficiently utilize modern multi-processor hardware for advanced scientific computations.
KEYWORDS: X-rays, Data modeling, Electron beams, Strontium, Signal attenuation, Corrosion, Tomography, Scanning electron microscopy, 3D modeling, Titanium dioxide
Conventional X-ray CT is not usually sufficient to determine microscopic compositional distributions. A dataconstrained
microstructure modeling (DCM) methodology has been developed which uses multiple CT data sets
acquired with different X-ray spectra, and incorporates them as model constraints. The DCM approach has been applied
to predict the distributions of corrosion inhibitor and filler in a polymer matrix. The DCM-predicted compositional
microstructures have a reasonable agreement with EDX images taken on the sample surface.
We are developing and exploring the imaging performance of, an in vivo, in-line holography, x-ray phase-contrast, micro-CT system with an ultrafast laser-based x-ray (ULX) source. By testing and refining our system, and by performing computer simulations, we plan to improve system performance in terms of contrast resolution and
multi-energy imaging to a level beyond what can be obtained using a conventional microfocal x-ray tube. Initial CT projection sets at single energy (Mo Kα and Kβ lines) were acquired in the Fresnel regime and reconstructed for phantoms and a euthanized mouse. We also performed computer simulations of phase-contrast micro-CT scans for low-contrast, soft-tissue, tumor imaging. We determined that, in order to perform a phase-contrast, complete micro-CT scan using ULX, the following conditions must be met: (i) the x-ray source needs to be stable during the scan; (ii) the laser focal spot size needs to be less than 10 μm for source-to-object distance greater than 30 cm; (iii) the laser light intensity on the target needs to be in the range of 5 × 1017 to 5 × 1019 W/cm2; (iv) the ablation protection system needs to allow uninterrupted scans; (v) the laser light focusing on the target needs to remain accurate during the entire scan; (vi) a fresh surface of the target must be exposed to consecutive laser shots during the entire scan; (vii) the effective detector element size must be less than 12 μm. Based on the results obtained in this research project, we anticipate that the new 10 Hz, 200 TW laser with 50W average power that is being commissioned at ALLS will allow us practical implementation of in vivo x-ray phase-contrast micro-CT.
We discuss theoretical, experimental and numerical aspects of several new techniques for quantitative phase-contrast tomography using, for example, unfiltered radiation from a polychromatic X-ray microfocus source. The proposed algorithms allow one to reconstruct the three-dimensional distribution of complex refractive index in a sample consisting of one or more constituent materials, given one or more projection images per view angle. If the sample is weakly absorbing or consists predominantly of a single material, these reconstruction algorithms can be simplified and fewer projections may be required for an unambiguous quantitative reconstruction of the spatial distribution of the refractive index. In the case of weakly absorbing samples, the reconstruction algorithm is shown to be achromatic and stable with respect to high-spatial-frequency noise, in contrast to conventional tomography. A variation of the algorithm exploits the natural combination of binary tomography with a phase-retrieval method that makes explicit use of the single-material nature of the sample. Such consistent use of a priori knowledge dramatically reduces the number of required projections, implying significantly reduced dose and scanning time when compared to most alternative phase-contrast tomography methods. Experimental demonstrations are also given, using data from a point-projection X-ray microscope. The refractive index distribution, in test samples of both a polymer fibre scaffold and an adult mouse, is accurately reconstructed from polychromatic phase-contrast data. Applications of the new techniques to rapid non-destructive testing in materials science and biomedical imaging are considered.
X-ray phase-contrast tomographic microimaging is a powerful tool to reveal the internal structure of opaque soft-matter objects that are not easily seen in standard absorption contrast. In such low Z materials, the phase shift of X-rays transmitted can be important as compared to the absorption. An easy experimental set up that exploits refractive contrast formation can deliver images that are providing detailed structural information. Applications are abundant in fields
including polymer science and engineering, biology, biomedical engineering, life sciences, zoology, water treatment and filtration, membrane science, and micro/nanomanufacturing. However, available software for absorptive contrast tomography cannot be simply used for structure retrieval as the contrast forming effect is different. In response, CSIRO has developed a reconstruction code for phase-contrast imaging. Here, we present a quantitative comparison of a micro phantom manufactured at SSLS with the object reconstructed by the code using X-ray images taken at SSLS. The phantom is a 500 μm thick 800 μm diameter cylindrical disk of SU-8 resist having various eccentric cylindrical bores with diameters ranging from 350 μm to 40 μm. Comparison of these parameters that are well known from design and post-manufacturing measurements with reconstructed ones gives encouraging results.
To assess the feasibility of small soft tissue avascular tumor
micro-CT imaging with x-ray phase-contrast in-line
holography, we have studied micro-CT imaging with in-line geometry of small spheroidal avascular tumor models
with quiescent cell core (< 250 μm) and various distributions of the proliferating cell density (PCD) forming the outer
shell. We have simulated imaging with an ultrafast laser-based x-ray source with a Mo target. We observe
phase-contrast enhancement of the tumor boundaries in the reconstructed transaxial images, resulting in improved
detection of small soft tissue tumors, providing that the PCD density gradient is sufficiently large.
We have investigated experimentally and theoretically the imaging performance of our newly constructed in-line
holography x-ray phase-contrast imaging system with an ultrafast laser-based x-ray source. Projection images of nylon
fibers with diameters in the 10-330 μm range were obtained using an ultrafast (100 Hz, 28 fs, 40 mJ) laser-based x-ray
source with Mo and Ta targets and Be filter, and Gaussian spatial-intensity distribution (FWHMS = 5 μm). A cooled
CCD camera (24 μm pitch) with a Gd2OS2 screen coupled via 1:1 optical taper was used (FWHMD = 50 μm). We have investigated nylon-fiber image quality vs. imaging setup geometry and x-ray spectra. The following parameters were
evaluated: contrast, signal-to-noise ratio (SNR), resolution, and sampling. In addition, we performed theoretical
simulation of image formation for the same objects but within a wide range of geometrical parameters. The rigorous
wave-optical formalism was used for modeling of the free-space propagation of x-rays from the object plane to the
detector, and the "projection approximation" was used. We found reasonable agreement between predictions of our
analytical model and the experiments. We conclude that: a) Optimum magnification maximizing contrast and SNR is
almost independent of the source-to-detector (R) distance and depends strongly on the diameter of the fiber. b) The
corresponding maximum values of the contrast and SNR are almost linear with respect to R; the optimum magnification
decreases with fiber diameter. c) The minimum diameter of fiber defines the minimum source-to-object distance R1 if R is fixed and the object is moved.
We have investigated theoretically the mean absorbed dose to the mouse in our newly constructed, in-line
holography, x-ray phase-contrast, in-vivo, micro-CT system with an ultrafast laser-based x-ray (ULX) source. We
assumed that the effective mouse diameter was 30 mm and the x-ray detector required minimum 30 μGy per frame
to produce high quality images. The following laser target-filter combinations were considered: Ag-Ag, Mo-Mo, Sn-
Sn. In addition, we considered narrow-pass multilayer x-ray mirrors. The corresponding ULX spectra were obtained
using a CZT solid-state spectrometer. The approach used for dose computation was similar to human dose
estimation. The mouse was modeled as a tissue-equivalent cylinder located at the isocenter with diameter 30 mm
and density 1g/cm3. A layer of dermis (skin and fur) with 1 mm thickness was also modeled. Imparted energy per
volume was estimated for 1 keV wide x-ray energy intervals in the 6-100 keV range. Monte Carlo simulations were
performed using the SIERRA code previously validated using 30 mm diameter PMMA phantom. The results
obtained indicate that: a) the mean absorbed dose for ULX is less than or equal to that from a W-anode micro-CT
tube operating at 30-40 kVp with 0.5 or 1.0 mm Al; b) for filter thickness above 100 μm, Sn-Sn results in the
highest dose, followed by Ag-Ag and Mo-Mo; c) the multilayer x-ray mirror with FWHM ≤ 10 keV produces
significantly lower dose than metallic foil filters. We conclude that ULX can provide better dose utilization than a
microfocal x-ray tube for in vivo microtomography applications.
X-ray Microtomography bridges the 3D analysis gap between conventional x-ray tomography and TEM tomography.
The use of a laboratory-based microfocus source opens up the opportunity to gain additional benefits from in-line phase
contrast for enhancing the visibility of fine features, cracks, voids and boundaries in individual views. Coupled with
phase retrieval methods, such images can be used as input to conventional reconstruction algorithms for three
dimensional visualization. Working at high resolution brings challenges of physical stability of the system. Software
approaches to overcoming these difficulties have enabled submicron resolution 3D reconstructions.
We perform a theoretical analysis of the mathematical stability and locality of several modes of amplitude and phase
contrast computed tomography (CT) suitable for reconstruction of the 3D distribution of complex refractive index in
samples displaying weak absorption contrast. We present a general formalism for CT reconstruction in linear shift-invariant
optical systems. Examples of such systems include propagation-based and analyser-based CT. We obtain
general formulae for CT reconstruction from analyser-based projection data. We also propose a new tomographic
algorithm for the reconstruction of the 3D distribution of complex refractive index in a sample from a single
propagation-based projection image per view angle, where the images display both absorption and phase contrast. The
method assumes that the real and imaginary parts of the refractive index are proportional to each other. Using singular-value
decompositions of the relevant operators we show that, in contrast to conventional amplitude-contrast CT, phase-contrast
(diffraction) tomography is mathematically well-posed. The presented results are pertinent to biomedical
imaging and non-destructive testing of samples exhibiting weak absorption contrast.
Conventional radiography is based on absorption contrast and geometrical (ray) optics. After an outline of the relevant theory, this article reports results displaying both phase- and absorption-contrast, collected with a technique which utilizes a micro-focus x-ray source to achieve a high degree of spatial coherence, and relatively large object-to-image distances to enable (wave) interference effects (Fresnel diffraction) to occur and manifest themselves as phase contrast in the image plane. Both soft tissue (chicken knee) and hard tissue (finger bone) samples are investigated for a range of source sizes and object-to-image distances, encompassing conditions somewhat analogous to conventional radiography. Variation in image contrast and resolution as a function of these variables is observed and discussed.
We report the results of quantitative hard X-ray phase- contrast microscopy and tomography using synchrotron radiation, in-line imaging geometry and a non-interferometric phase retrieval technique based on the Transport of Intensity equation. This quantitative imaging method is fast, simple, robust, does not require sophisticated X-ray optical elements and can potentially provide submicron spatial resolution over a field of view of the order of centimeters. In the present experiment a spatial resolution of approximately 0.8 micron has been achieved in images of a polystyrene sphere using 19.6 keV X-rays. We demonstrate that appropriate processing of phase-contrast images obtained in the in-line geometry can reveal important new information about the internal structure of weakly absorbing organic samples. We present some preliminary results of a phase-contrast tomographic reconstruction with and without phase retrieval in each X-ray projection. We believe that this method of quantitative X-ray phase-contrast imaging will find applications in biology and medicine, particularly for high-contrast imaging of soft tissues.
X-ray focusing using square channel capillary arrays is reviewed. We review our theoretical understanding of these devices and go on to examine their potential in the context of x-ray astronomy as an approach to the construction of a lobster-eye telescope. We show that a reasonably small device has the potential, in principle, to improve the sensitivity of wide field of view x-ray telescopes by an order of magnitude. We go on to briefly review our experimental work and indicate that these devices are getting close to realizing their theoretical potential.
X-ray focusing using square channel capillary arrays is reviewed. We present some experimental results obtained using a variety of array configurations and we deduce that channel misalignment and surface roughness are the prime factors limiting the performance of these devices. We present results obtained using a stacked array of commercial precision bore square tubing and deduce that the reflectivity from these unetched surfaces is superior to that from etched micro-channel plate blanks. The improved surface quality implied by this reflectivity result is confirmed using atomic force microscopy. We also present results of a new drawing technique that we have developed.
X-ray optical devices based on arrays of capillaries and single tapered capillaries can focus and concentrate x rays by the reflection of near-grazing-incidence rays at the interior walls of the channels. Capillary arrays are true imaging devices and can be used as focusing, condensing,and collimating optics, suitable for x-ray microcopy and astronomy. Rays which enter channels and are reflected once or twice, via total external reflection, may be redirected towards the image. Theoretical calculations of the focusing performance of arrays consisting of capillaries of square and circular cross-section are given. Experimental investigations have been made using microchannel plate (MCP) detector blanks and various x-ray sources.
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