Biao Deng

Fast and accurate X‐ray fluorescence computed tomography imaging with the ordered‐subsets expectation maximization algorithm

The ordered-subsets expectation maximization algorithm (OSEM) is introduced to X-ray fluorescence computed tomography (XFCT) and studied; here, simulations and experimental results are presented. The simulation results indicate that OSEM is more accurate than the filtered back-projection algorithm, and it can efficiently suppress the deterioration of image quality within a large range of angular sampling intervals. Experimental results of both an artificial phantom and cirrhotic liver show that with a satisfying image quality the angular sampling interval could be improved to save on the data-acquisition time when OSEM is employed. In addition, with an optimum number of subsets, the image reconstruction time of OSEM could be reduced to about half of the time required for one subset. Accordingly, it can be concluded that OSEM is a potential method for fast and accurate XFCT imaging.

X-ray biomedical imaging beamline at SSRF

Since May 6, 2009, the X-ray biomedical imaging beamline at Shanghai Synchrotron Radiation Facility (SSRF) has been formally opened to users. The beamline is composed of a wiggler source with the intensity of magnetic field of 2.0 Tesla, a double crystal monochromator (DCM) cooled with liquid nitrogen, a 6-axis filter for high heat load reducing on the downstream optics such as Be window and DCM. The photon energy range for the monochromatic beam is 8-72.5keV. Three sets of digital X-ray detectors are provided to users with the pixel size range being 0.37-13 mu m. Several imaging methods such as micro-CT, in-line phase contrast imaging could be applied in biomedicine, material science and paleontology studies. The spatial resolution of 0.8 mu m and the temporal resolution of 1 ms could be realized. By the end of 2012, the beamline has provided more than 13900 hours beamtime for users, while over half of the research proposals come from biomedicine field. Nearly 2000 person-times have come and done their experiments at the beamline. More than 470 user proposals have been perfomed and more than 110 papers from users have been published. Some typical experimental results on biomedical applications will be introduced.

Anisotropic shrinkage of insect air sacs revealed in vivo by X-ray microtomography.

Air sacs are thought to be the bellows for insect respiration. However, their exact mechanism of action as a bellows remains unclear. A direct way to investigate this problem is in vivo observation of the changes in their three-dimensional structures. Therefore, four-dimensional X-ray phase contrast microtomography is employed to solve this puzzle. Quantitative analysis of three-dimensional image series reveals that the compression of the air sac during respiration in bell crickets exhibits obvious anisotropic characteristics both longitudinally and transversely. Volumetric changes of the tracheal trunks in the prothorax further strengthen the evidence of this finding. As a result, we conclude that the shrinkage and expansion of the insect air sac is anisotropic, contrary to the hypothesis of isotropy, thereby providing new knowledge for further research on the insect respiratory system.

X-ray propagation-based equally sloped tomography for mouse brain

BACKGROUND The outstanding functional importance of the brain implies a strong need for brain imaging modalities. However, the current imaging approaches that target the brain in rodents remain suboptimal. OBJECTIVE AND METHODS In this paper, X-ray propagation-based phase contrast imaging combined with equally sloped tomography (PPCI-EST) was employed to nondestructively investigate the mouse brain. RESULTS The grey and white matters, which have extremely small differences in electron density, were clearly discriminated. The fine structures, including the corpus callosum (cc), the optic chiasma (ox) and the caudate putamen (CPu), were revealed. Compared to the filtered back projection reconstruction, the PPCI-EST significantly reduce projection number while maintaining sufficient image quality. CONCLUSIONS It could be a potential tool for fast and low-dose phase-contrast imaging to biomedical specimens.

Speckle-tracking X-ray phase-contrast imaging for samples with obvious edge-enhancement effect

Compared to the grating or crystal-based X-ray phase contrast imaging, the speckle-tracking method has the advantages of a simple setup and two-dimensional imaging. However, the edge-enhancement effect prevents the application of the speckle-tracking imaging to a large variety of samples. In this letter, an image reconstruction method is proposed to solve this problem. The experimental results from phantom, a biomedical sample, and a sample with a speckle-resembling structure demonstrated that the proposed method is efficacious in eliminating the effect of edge enhancement. The proposed method may greatly expand the application of the speckle-tracking method to most biomedical and material samples.

Quantitative multi-scale analysis of mineral distributions and fractal pore structures for a heterogeneous Junger Basin shale

Three dimensional (3D) characterization of shales has recently attracted wide attentions in relation to the growing importance of shale oil and gas. Obtaining a complete 3D compositional distribution of shale has proven to be challenging due to its multi-scale characteristics. A combined multi-energy X-ray micro-CT technique and data-constrained modelling (DCM) approach has been used to quantitatively investigate the multi-scale mineral and porosity distributions of a heterogeneous shale from the Junger Basin, northwestern China by sub-sampling. The 3D sub-resolution structures of minerals and pores in the samples are quantitatively obtained as the partial volume fraction distributions, with colours representing compositions. The shale sub-samples from two areas have different physical structures for minerals and pores, with the dominant minerals being feldspar and dolomite, respectively. Significant heterogeneities have been observed in the analysis. The sub-voxel sized pores form large interconnected clusters with fractal structures. The fractal dimensions of the largest clusters for both sub-samples were quantitatively calculated and found to be 2.34 and 2.86, respectively. The results are relevant in quantitative modelling of gas transport in shale reservoirs.

Simulation and experimental study of aspect ratio limitation in Fresnel zone plates for hard-x-ray optics.

For acquiring high-contrast and high-brightness images in hard-x-ray optics, Fresnel zone plates with high aspect ratios (zone height/zone width) have been constantly pursued. However, knowledge of aspect ratio limits remains limited. This work explores the achievable aspect ratio limit in polymethyl methacrylate (PMMA) by electron-beam lithography (EBL) under 100 keV, and investigates the lithographic factors for this limitation. Both Monte Carlo simulation and EBL on thick PMMA are applied to investigate the profile evolution with exposure doses over 100 nm wide dense zones. A high-resolution scanning electron microscope at low acceleration mode for charging free is applied to characterize the resultant zone profiles. It was discovered for what we believe is the first time that the primary electron-beam spreading in PMMA and the proximity effect due to extra exposure from neighboring areas could be the major causes of limiting the aspect ratio. Using the optimized lithography condition, a 100 nm zone plate with aspect ratio of 15/1 was fabricated and its focusing property was characterized at the Shanghai Synchrotron Radiation Facility. The aspect ratio limit found in this work should be extremely useful for guiding further technical development in nanofabrication of high-quality Fresnel zone plates.

Exact revision of the elliptically bent mirror theory

One of the main hurdles for nanometer focusing by a bending mirror lies in the theoretical surface errors by its approximations used for the traditional theory. The impacts of approximations and analytical corrections have been discussed, and the elliptically bent mirror theory has been described during exact mathematical analysis without any approximations. These approximations are harmful for the focusing system with bigger grazing angle, bigger mirror length, and bigger numerical aperture. The properties of equal-moment and single-moment bent mirrors have been described and discussed. Because of its obvious advantages, a single-moment bending mirror has high potential ability for nanometer focusing.

Monochromatic-beam-based dynamic X-ray microtomography based on OSEM-TV algorithm

Monochromatic-beam-based dynamic X-ray computed microtomography (CT) was developed to observe evolution of microstructure inside samples. However, the low flux density results in low efficiency in data collection. To increase efficiency, reducing the number of projections should be a practical solution. However, it has disadvantages of low image reconstruction quality using the traditional filtered back projection (FBP) algorithm. In this study, an iterative reconstruction method using an ordered subset expectation maximization-total variation (OSEM-TV) algorithm was employed to address and solve this problem. The simulated results demonstrated that normalized mean square error of the image slices reconstructed by the OSEM-TV algorithm was about 1/4 of that by FBP. Experimental results also demonstrated that the density resolution of OSEM-TV was high enough to resolve different materials with the number of projections less than 100. As a result, with the introduction of OSEM-TV, the monochromatic-beam-based dynamic X-ray microtomography is potentially practicable for the quantitative and non-destructive analysis to the evolution of microstructure with acceptable efficiency in data collection and reconstructed image quality.

Improving the efficiency of small-angle x-ray scattering computed tomography using the OSEM algorithm

Small-angle x-ray scattering computed tomography (SAXS-CT) is a nondestructive method for the nanostructure analysis of heterogeneous materials. However, the limits of a long data acquisition time and vast amounts of data prevent SAXS-CT from becoming a routine experimental method in the applications of synchrotron radiation. In this study, the ordered subsets expectation maximization (OSEM) algorithm is introduced to improve the efficiency of SAXS-CT. To demonstrate the practicability of this method, a systematic simulation and experiments were carried out. The simulation results on a numerical phantom show that the OSEM-based SAXS-CT can effectively eliminate streaking artifacts and improve the efficiency of data acquisition by at least 3 times compared with the filter backprojection algorithm. By compromising the reconstruction speed and image quality, the optimal reconstruction parameters are also given for the image reconstruction in the OSEM-based SAXS-CT experiments. An experiment on a bamboo sample verified the validity of the proposed method with limited projection data. A further experiment on polyethylene demonstrated that the OSEM-based SAXS-CT is able to reveal the local nanoscale information about the crystalline structure and distributional difference inside the sample. In conclusion, the OSEM-based SAXS-CT can significantly improve experimental efficiency, which may promote SAXS-CT becoming a conventional method.