scholarly journals Quantitative three-dimensional nondestructive imaging of whole anaerobic ammonium-oxidizing bacteria

2019 ◽  
Author(s):  
M-W. Peng ◽  
Y. Guan ◽  
J-H. Liu ◽  
L. Chen ◽  
H. Wang ◽  
...  
Keyword(s):  
Total Variation ◽  
Nitrogen Cycle ◽  
Three Dimensional ◽  
Anammox Bacteria ◽  
Reconstruction Technique ◽  
Algebraic Reconstruction Technique ◽  
X Ray ◽  
Shape Adaptation ◽  
Global Nitrogen Cycle ◽  
Simultaneous Algebraic Reconstruction Technique

AbstractAnaerobic ammonium-oxidizing (anammox) bacteria play a key role in the global nitrogen cycle and the treatment of nitrogenous wastewater. These functions are closely related to the unique biophysical structure of anammox bacteria. However, the research on the biophysical ultrastructure of intact anammox bacteria is lacking. In this study, in-situ three-dimensional nondestructive ultrastructure imaging of whole anammox cell was performed using synchrotron soft X-ray nano-computed tomography and the total variation-based simultaneous algebraic reconstruction technique (TV-SART). Statistical and quantitative analyses of the ultrastructures of intact anammox bacteria were performed. The linear absorption coefficient values of the ultrastructures of anammox bacteria were calculated and the asymmetric structure of the anammox bacteria was quantified. On this basis, the shape adaptation of the anammox bacteria responses to Fe2+ were explored, and the underlying regulation mechanism of Fe2+ on anammox bacteria was explored. Furthermore, a promising method to study the biophysical properties of cells in different environments and engineering processes was proposed.Graphical AbstractStatement of SignificanceAnaerobic ammonium-oxidizing (anammox) bacteria play key role in global nitrogen cycle, and this physiological function depends on the unique morphology of anammox bacteria. In this study, synchrotron soft-X ray imaging technique coupled with simultaneous algebraic reconstruction technique with total variation (SART-TV) algorithm were performed to quantify the three-dimensional ultrastructure of the whole anammox bacteria for the first time. On this basis, the shape adaptation and mechanism of the anammox bacteria responses to Fe2+ were explored and a promising method for detecting the physiological properties of anammox bacteria was proposed.

scholarly journals Quantitative three-dimensional nondestructive imaging of whole anaerobic ammonium-oxidizing bacteria

2020 ◽  
Vol 27 (3) ◽  
pp. 753-761
Author(s):  
Meng-Wen Peng ◽  
Yong Guan ◽  
Jian-Hong Liu ◽  
Liang Chen ◽  
Han Wang ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Morphological Structure ◽  
Anammox Bacteria ◽  
Reconstruction Technique ◽  
X Ray ◽  
Shape Adaptation ◽  
Nondestructive Imaging ◽  
Quantitative Analyses ◽  
X Ray Absorption

Anaerobic ammonium-oxidizing (anammox) bacteria play a key role in the global nitrogen cycle and in nitrogenous wastewater treatment. The anammox bacteria ultrastructure is unique and distinctly different from that of other prokaryotic cells. The morphological structure of an organism is related to its function; however, research on the ultrastructure of intact anammox bacteria is lacking. In this study, in situ three-dimensional nondestructive ultrastructure imaging of a whole anammox cell was performed using synchrotron soft X-ray tomography (SXT) and the total variation-based simultaneous algebraic reconstruction technique (TV-SART). Statistical and quantitative analyses of the intact anammox bacteria were performed. High soft X-ray absorption composition inside anammoxosome was detected and verified to be relevant to iron-binding protein. On this basis, the shape adaptation of the anammox bacteria response to iron was explored.

X-ray topo-tomography studies of linear dislocations in silicon single crystals

2018 ◽  
Vol 51 (6) ◽  
pp. 1616-1622 ◽  
Author(s):  
Victor Asadchikov ◽  
Alexey Buzmakov ◽  
Felix Chukhovskii ◽  
Irina Dyachkova ◽  
Denis Zolotov ◽  
...  
Keyword(s):  
Numerical Analysis ◽  
High Resolution ◽  
Single Crystals ◽  
Complete Characterization ◽  
Reconstruction Technique ◽  
Algebraic Reconstruction Technique ◽  
X Ray ◽  
Laboratory Setup ◽  
Simultaneous Algebraic Reconstruction Technique

This article describes complete characterization of the polygonal dislocation half-loops (PDHLs) introduced by scratching and subsequent bending of an Si(111) crystal. The study is based on the X-ray topo-tomography technique using both a conventional laboratory setup and the high-resolution X-ray image-detecting systems at the synchrotron facilities at KIT (Germany) and ESRF (France). Numerical analysis of PDHL images is performed using the Takagi–Taupin equations and the simultaneous algebraic reconstruction technique (SART) tomographic algorithm.

A modified discrete tomography for improving the reconstruction of unknown multi-gray-level material in the `missing wedge' situation

2018 ◽  
Vol 25 (6) ◽  
pp. 1847-1859 ◽  
Author(s):  
Jianhong Liu ◽  
Zhiting Liang ◽  
Yong Guan ◽  
Wenbin Wei ◽  
Haobo Bai ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Iteration Process ◽  
Reconstruction Technique ◽  
Morphological Operations ◽  
Algebraic Reconstruction Technique ◽  
Discrete Tomography ◽  
Boundary Extraction ◽  
X Ray ◽  
Dimensional Reconstruction

Full angular rotational projections cannot always be acquired in tomographic reconstructions because of the limited space in the experimental setup, leading to the `missing wedge' situation. In this paper, a recovering `missing wedge' discrete algebraic reconstruction technique algorithm (rmwDART) has been proposed to solve the `missing wedge' problem and improve the quality of the three-dimensional reconstruction without prior knowledge of the material component's number or the material's values. By using oversegmentation, boundary extraction and mathematical morphological operations, `missing wedge' artifact areas can be located. Then, in the iteration process, by updating the located areas and regions, high-quality reconstructions can be obtained from the simulations, and the reconstructed images based on the rmwDART algorithm can be obtained from soft X-ray nano-computed tomography experiments. The results showed that there is the potential for discrete tomography.

scholarly journals SART-Type Image Reconstruction from Overlapped Projections

2011 ◽  
Vol 2011 ◽  
pp. 1-7
Author(s):  
Hengyong Yu ◽  
Changguo Ji ◽  
Ge Wang
Keyword(s):  
Image Reconstruction ◽  
Reconstruction Algorithm ◽  
Reconstruction Technique ◽  
Algebraic Reconstruction Technique ◽  
Multiple Sources ◽  
X Ray ◽  
Type Reconstruction ◽  
Soft Threshold ◽  
Simultaneous Algebraic Reconstruction Technique ◽  
Data Acquisition Process

To maximize the time-integrated X-ray flux from multiple X-ray sources and shorten the data acquisition process, a promising way is to allow overlapped projections from multiple sources being simultaneously on without involving the source multiplexing technology. The most challenging task in this configuration is to perform image reconstruction effectively and efficiently from overlapped projections. Inspired by the single-source simultaneous algebraic reconstruction technique (SART), we hereby develop a multisource SART-type reconstruction algorithm regularized by a sparsity-oriented constraint in the soft-threshold filtering framework to reconstruct images from overlapped projections. Our numerical simulation results verify the correctness of the proposed algorithm and demonstrate the advantage of image reconstruction from overlapped projections.

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