Fast Projection Matching for X-ray Tomography

Automatic marker-based alignment method for a nano-resolution full-field transmission X-ray microscope

Driven by the development of X-ray optics, the spatial resolution of the full-field transmission X-ray microscope (TXM) has reached tens of nanometers and plays an important role in promoting the development of biomedicine and materials science. However, due to the thermal drift and the radial/axial motion error of the rotation stage, TXM computed tomography (CT) data are often associated with random image jitter errors along the horizontal and vertical directions during CT measurement. A nano-resolution 3D structure information reconstruction is almost impossible without a prior appropriate alignment process. To solve this problem, a fully automatic gold particle marker-based alignment approach without human intervention was proposed in this study. It can automatically detect, isolate, and register gold particles for projection image alignment with high efficiency and accuracy, facilitating a high-quality tomographic reconstruction. Simulated and experimental results confirmed the reliability and robustness of this method.

First principal observation documenting the three-dimensional uptake of cadmium and spatial distribution of cadmium hydroxyapatite mineral in bone char

The 3-D matrix scale ion-exchange mechanism was explored for high-capacity cadmium (Cd) removal using bone chars (BC) chunks (1-2 mm) made at 500 °C (500BCE) and 700 °C (700BCE) in aqueous solutions. The Cd incorporation into the carbonated hydroxyapatite (CHAp) mineral of BC was examined using a set of synchrotron-based techniques. The Cd removal from solution and incorporation into mineral lattice were higher in 500BCE than 700BCE, and the diffusion depth was modulated by the initial Cd concentration and charring temperature. A higher carbonate level of BC, more pre-leached Ca sites, and external phosphorus input enhanced Cd removal. The 500BCE showed a higher CO32-/PO43- ratio and specific surface area (SSA) than the 700BCE, providing more vacant sites by dissolution of Ca2+. In situ observations revealed the refilling of sub-micron pore space in the mineral matrix because of Cd incorporation.The X-ray nanodiffraction (XND) analyses revealed that Cd was mainly removed from water by incorporation into the mineral lattice of 500BCE via ion exchange, rather than surface sorption and precipitation, and the mineral phase was transformed from hydroxyapatite (HAp) to cadmium hydroxyapatite (Cd-HAp). The Rietveld's refinement of X-ray diffraction (XRD) data resolved up to 91% of the crystal displacement of Ca2+ by Cd2+. The A specific phase and stoichiometry of the new Cd-HAp mineral was dependent on the level of ion exchange. This mechanistic study confirmed that 3-D ion exchange was the most important path for heavy metal removal from aqueous solution and immobilization in BC mineral matrix, and put forward a novel and sustainable remediation strategy for Cd removal in wastewater and soil clean-up.

Removal and concurrent reduction of Cr(VI) by thermoacidophilic Cyanidiales: a novel extreme biomaterial enlightened for acidic and neutral conditions

Thermoacidophilic Cyanidiales maintain a competitive edge in inhabiting extreme environments enriched with metals. Here, species of Cyanidioschyzon merolae (Cm), Cyanidium caldarium (Cc), and Galdieria partita (Gp) were exploited to remove hexavalent chromium [Cr(VI)]. Cm and Gp could remove 168.1 and 93.7 mg g^-1 of Cr(VI) at pH 2.0 and 7.0, respectively, wherein 89% and 62% of sorbed Cr on Cm and Gp occurred as trivalent chromium [Cr(III)]. Apart from surface-sorbed Cr(VI), the in vitro Cr(III) bound with polysaccharide and in vivo chromium(III) hydroxide [Cr(OH)₃] attested to the reduction capability of Cyanidiales. The distribution of Cr species varied as a function of sorbed Cr amount, yet a relatively consistent proportion of Cr(OH)₃, irrespective of Cr sorption capacity, was found only on Cm and Cc at pH 2.0. In conjunction with TXM (transmission X-ray microscopy) images that showed less impaired cell integrity and possible intracellular Cr distribution on Cm and Cc at pH 2.0, the in vivo Cr(OH)₃ might be the key to promoting the Cr sorption capacity (≥ 152 mg g^-1). Cyanidiales are promising candidates for the green and sustainable remediation of Cr(VI) due to their great removal capacity, the spontaneous reduction under oxic conditions, and in vivo accumulation.

Insights to the 3D internal morphology and metal oxidation states of single atmospheric aerosol particles by synchrotron-based methodology

The morphology and metal oxidation states of atmospheric aerosols are pertinent to their formation processes and ensuing interactions with surrounding gases, vapors and other environments upon deposition, such as human respiratory tract, soil and water. Although much progress has been made in recent years through single-particle techniques, considerably less is known with respect to the three-dimensional (3D) internal morphology of single atmospheric aerosol particles due to the limited penetration depth of electron microscopy. In this study, for the first time, a novel synchrotron-based transmission X-ray microscopy (TXM) methodology has been developed to visualize the 3D internal chemical mixing state and structure of single particles. The results show that the TXM is more applicable to the imaging of solid particles containing high-density elements, e.g., iron (Fe), aluminum (Al), silicone (Si), carbon (C) and sulfur (S), and/or solid particles of sizes larger than about 100 nm. In addition, the TXM is capable to reveal the fine 3D topographic features of single particles. The derived 3D internal and external information would be difficult to discern in the 2D images from electron microscopy. The TXM 3D images illustrate that aerosol particles exhibit complex internal mixing state and structure, e.g., homogeneously-, heterogeneously-mixed, multiple inclusions, fibrous, porous, and core-shell configuration. When coupled with the synchrotron-based X-ray fluorescence spectrometry (XRF) and absorption near-edge spectroscopy (XANES) of an X-ray nanoprobe in the energy range of 4-15 keV, the 3D morphology of single particles is further supplemented with the spatial distribution and oxidation sates of selected elements, including Fe, vanadium (V), manganese (Mn), chromium (Cr) and arsenic (As). The presented cross-platform, synchrotron-based methodology shows promise in complementing existing single-particle techniques and providing new insights to the heterogeneity of single-particle micro-physicochemical states relevant to the aerosol chemistry, optical properties, and their environmental and health impacts.

Geometry Calibration of a Modular Stereo Cone-Beam X-ray CT System

Compared to single source systems, stereo X-ray CT systems allow acquiring projection data within a reduced amount of time, for an extended field-of-view, or for dual X-ray energies. To exploit the benefit of a dual X-ray system, its acquisition geometry needs to be calibrated. Unfortunately, in modular stereo X-ray CT setups, geometry misalignment occurs each time the setup is changed, which calls for an efficient calibration procedure. Although many studies have been dealing with geometry calibration of an X-ray CT system, little research targets the calibration of a dual cone-beam X-ray CT system. In this work, we present a phantom-based calibration procedure to accurately estimate the geometry of a stereo cone-beam X-ray CT system. With simulated as well as real experiments, it is shown that the calibration procedure can be used to accurately estimate the geometry of a modular stereo X-ray CT system thereby reducing the misalignment artifacts in the reconstruction volumes.

Black carbon enriches short-range-order ferrihydrite in Amazonian Dark Earth: Interplay mechanism and environmental implications

Our study underpins the mechanism of organo-mineral interaction between black carbon (BC, biochar) and associated minerals in the historical BC-rich Amazonian Dark Earth (ADE) by using synchrotron-based microscopic (TXM), microspectroscopic (μFTIR) and spectroscopic (XAS and μ-diffraction) approaches. The BC-rich ADE contained over 100% more poorly crystalline minerals than the adjacent tropical soil. Linear combination fitting of k-spacing in the X-ray Absorption Spectra (XAS) revealed that ferrihydrite contributed to 81.1% of the Fe-minerals in BC. A small but distinct peak was observed at 5.7 Å^-1 in the extended X-ray absorption fine structure k oscillation of BC, revealing the presence of FeC (including Fe-O-C) covalent bonds. No FeC path was yielded by the XAS fitting when an obvious peak downshift of the first (FeFe¹) shell was observed, suggesting that the availability of inner-sphere FeC complexation was limited to the BC surface and interphase region. The main minerals for organo-mineral complexation were short-range-order (SRO) ferrihydrite on BC instead of corner-sharing FeO₆ octahedra. Compared to ADE, the coordination number of the first (FeFe¹) and second (FeFe²) shell was higher in BC, revealing a higher degree of order in coordination between the neighboring Fe mineral crystals. Black C limited the progressive aging of amorphous Fe phases and greatly enriched SRO ferrihydrite in the redox-fluctuating and high-leaching environment. The transformation of SRO ferrihydrite into the more crystalline Fe oxides was controlled by the local pH environment. A strong signal from the complexed phenolic group (aryl-OH, 1241 cm^-1) and a distinct band of inner-sphere complexation (Fe-aryl C, 1380-1384 cm^-1) were identified in the FTIR spectra. The enrichment of poorly crystalline minerals can have positive feedback on the long-term stabilization of BC. The scale-up application of biochar to agricultural and ecological systems may have a long-lasting impact on the enrichment and transformation of the SRO minerals in the soil.

Joint Iterative Fast Projection Matching for Fully Automatic Marker-free Alignment of Nano-tomography Reconstructions

Highly accurate, fully automatic marker-free image alignment plays an important role in nano-tomographic reconstruction, particularly in cases where the spatial resolution of the tomographic system is on the nanometer scale. However, highly accurate marker-free methods such as the projection matching method are computationally complex and time-consuming. Achieving alignment accuracy with reduced computational complexity remains a challenging problem. In this study, we propose an efficient method to achieve marker-free fully automatic alignment. Our method implements three main alignment procedures. First, the frequency-domain common line alignment method is used to correct the in-plane rotational errors of each projection. Second, real-space common line alignment method is used to correct the vertical errors of the projections. Finally, a single layer joint-iterative reconstruction and re-projection method is used to correct the horizontal projection errors. This combined alignment approach significantly reduces the computational complexity of the classical projection matching method, and increases the rate of convergence towards determining the accurate alignment. The total processing time can be reduced by up to 4 orders of magnitude as compared to the classical projection matching method. This suggests that the algorithm can be used to process image alignment of nano-tomographic reconstructions on a conventional personal computer in a reasonable time-frame.

Alignment methods for nanotomography with deep subpixel accuracy

As the resolution of X-ray tomography improves, the limited long-term stability and accuracy of nanoimaging tools does not allow computing artifact-free three-dimensional (3D) reconstructions without an additional step of numerical alignment of the measured projections. However, the common iterative alignment methods are significantly more computationally demanding than a simple tomographic reconstruction of the acquired volume. Here, we address this issue and present an alignment toolkit, which exploits methods with deep-subpixel accuracy combined with a multi-resolution scheme. This leads to robust and accurate alignment with significantly reduced computational and memory requirements. The performance of the presented methods is demonstrated on simulated and measured datasets for tomography and also laminography acquisition geometries. A GPU accelerated implementation of our alignment framework is publicly available.

Multi-Scale Microstructure Investigation for a PM2.5 Air-Filter Efficiency Study of Non-Woven Polypropylene

A N95 face-piece respirator and a 3M air filter composed of non-woven polypropylene filter material were investigated for their multi-scale microstructure and resulting filtration performance. Filtration mechanisms of each system are found and quantified. Both media showed a gradually decrease of the most penetrating particle size with respect to an increase in face velocity or surface charge density. Increasing the face velocity and porosity dramatically degraded the collection efficiency in the 3M filter rather than in the N95 system. We exploited three-dimensional X-ray tomography to characterize the morphological and geometrical properties of the fiber arrangement and deposition of aerosol on the fiber surface. Tuning the most predominant material parameters to achieve a precedence in lower pressure drop or higher collection efficiency in a specifically captured particle size range is of great requisite to a peculiar application of the filter media.

Jitter correction for transmission X-ray microscopy via measurement of geometric moments

Transmission X-ray microscopes (TXMs) have become one of the most powerful tools for imaging 3D structures of nano-scale samples using the computed tomography (CT) principle. As a major error source, sample jitter caused by mechanical instability of the rotation stage produces shifted 2D projections, from which reconstructed images contain severe motion artifacts. In this paper, a jitter correction algorithm is proposed, that has high accuracy and computational efficiency for TXM experiments with or without nano-particle markers. Geometric moments (GMs) are measured on segmented projections for each angle and fitted to sinusoidal curves in the angular direction. Sample jitter is estimated from the difference between the measured and the fitted GMs for image correction. On a digital phantom, the proposed method removes jitter errors at different noise levels. Physical experiments on chlorella cells show that the proposed GM method achieves better spatial resolution and higher computational efficiency than the re-projection method, a state-of-the-art algorithm using iterative correction. It even outperforms the approach of manual alignment, the current gold standard, on faithfully maintaining fine structures on the CT images. Our method is practically attractive in that it is computationally efficient and lowers experimental costs in current TXM studies without using expensive nano-particles markers.

Use 3-D tomography to reveal structural modification of bentonite-enriched clay by nonionic surfactants: Application of organo-clay composites to detoxify aflatoxin B1 in chickens

Although nonionic surfactants are relatively eco-friendly compared with cationic and anionic surfactants, few studies have investigated their application in modified clay. Herein we prepared organo-clay composites (OCCs) by mixing bentonite-enriched clay (BEC) with nonionic surfactants (Brij 30 and Igepal CO-890) and determined if these modifications would enable chickens to detoxify aflatoxin B1 (AFB1). For the first time, in situ three-dimensional (3-D) microstructures of modified BEC was characterized in suspension using transmission X-ray microscopy. Although X-ray diffraction patterns indicated the expansion in the spacing between planes of atoms (basal spacing) of surfactant-modified BEC, 3-D images indicated shrinkage in its microscale porous framework with increasing surfactant additions from 1 to 30 wt%. Such declining trends in porous dimensions caused by the dehydration in interlayer galleries of clays positively correlated with sorption amounts of AFB1 on OCCs. After chickens had consumed amended feeds for 11 weeks, AFB1 concentrations in liver, kidney, and plasma were significantly lower than in the control treatment. Thus, we suggest using BEC with 1 wt% surfactant addition, an amendment to chicken feeds, to detoxify AFB1. Modifying BEC with nonionic surfactants show the promise in mitigating AFB1 accumulation in chickens, which should improve food safety and reduce environmental contamination.

Calcitriol exerts a mineralization-inductive effect comparable to that of vitamin C in cultured human periodontium cells

This study inspected whether calcitriol could exert a mineralization-inductive effect comparable to that of vitamin C in cultured human periodontium cells (hPDCs). The mRNA expression of the mineralization-related biomarkers core-binding factor subunit alpha-1 (Cbfa1), collagen 1 α1 (Col-I), alkaline phosphatase (ALP), osteopontin (OPN), bone sialoprotein (BSP), osteocalcin (OCN), vitamin D receptor (VDR), cementum protein 1 (CEMP-1), cementum attachment protein (CAP), interleukin 6 (IL-6), transforming growth factor-β1 (TGF-β1) and osteoprotegerin (OPG) was surveyed after incubation of hPDCs with vitamin C and calcitriol for 2 weeks. Translational expression information from ALP activity and CEMP-1 and CAP immunofluorescence assays was acquired from hPDCs at the second and third weeks. Extracellular calcifications were confirmed by von Kossa staining, Alizarin Red staining and synchrotron transmission X-ray microscopy (TXM) at the fourth and fifth weeks. It was found that both vitamin C and calcitriol not only increased mineralization-related mRNA fold-changes but also enhanced ALP activity, CEMP-1 immunofluorescence, von Kossa and Alizarin Red staining and TXM-associated calcifications. Generally, 10^-8 M calcitriol displayed greater mineralization significance than 10^-7 M calcitriol in the assays tested. However, vitamin C stimulated lower Cbfa1, Col-1, ALP, OPN, BSP, OCN, VDR, CEMP-1 and IL-6 mRNA fold-changes than 10^-8 M calcitriol. Finally, TXM analysis indicated that a 10^-8 M calcitriol treatment stimulated greater calcifications than vitamin C treatment. Therefore, the analytical results confirmed the osteo-inductive potential of vitamin C in cultured hPDCs. In contrast, 10^-8 M calcitriol could potentially function as a substitute because it stimulates a greater mineralization effect than vitamin C or 10^-7 M calcitriol.

On the effect of computed tomography resolution to distinguish between abdominal aortic aneurysm wall tissue and calcification: A proof of concept

PURPOSE

The purpose of this study is to determine the optimal target CT spatial resolution for accurately imaging abdominal aortic aneurysm (AAA) wall characteristics, distinguishing between tissue and calcification components, for an accurate assessment of rupture risk.

MATERIALS AND METHODS

Ruptured and non-ruptured AAA-wall samples were acquired from eight patients undergoing open surgical aneurysm repair upon institutional review board approval and informed consent was obtained from all patients. Physical measurements of AAA-wall cross-section were made using scanning electron microscopy. Samples were scanned using high resolution micro-CT scanning. A resolution range of 15.5-155μm was used to quantify the influence of decreasing resolution on wall area measurements, in terms of tissue and calcification. A statistical comparison between the reference resolution (15.5μm) and multi-detector CT resolution (744μm) was also made.

RESULTS

Electron microscopy examination of ruptured AAAs revealed extremely thin outer tissue structure <200μm in radial distribution which is supporting the aneurysm wall along with large areas of adjacent medial calcifications far greater in area than the tissue layer. The spatial resolution of 155μm is a significant predictor of the reference AAA-wall tissue and calcification area measurements (r=0.850; p<0.001; r=0.999; p<0.001 respectively). The tissue and calcification area at 155μm is correct within 8.8%±1.86 and 26.13%±9.40 respectively with sensitivity of 87.17% when compared to the reference.

CONCLUSION

The inclusion of AAA-wall measurements, through the use of high resolution-CT will elucidate the variations in AAA-wall tissue and calcification distributions across the wall which may help to leverage an improved assessment of AAA rupture risk.