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 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.

A discrete tomography algorithm for improving the quality of three-dimensional X-ray diffraction grain maps

2006 ◽  
Vol 39 (4) ◽  
pp. 582-588 ◽  
Author(s):  
A. Alpers ◽  
H. F. Poulsen ◽  
E. Knudsen ◽  
G. T. Herman
Keyword(s):  
Monte Carlo ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Simulation Studies ◽  
Discrete Structure ◽  
X Ray Diffraction ◽  
Discrete Tomography ◽  
X Ray ◽  
Restoration Method

A discrete tomography algorithm is presented for the reconstruction of grain maps based on X-ray diffraction data. This is the first algorithm for this task, inherently exploiting the discrete structure of grain maps. Gibbs potentials serve to characterize the statistics of the local morphology of the grain boundaries. A Monte Carlo based algorithm is applied as a restoration method for improving the quality of grain maps produced by a classical (non-discrete) tomography algorithm (ART). The quality of the restored maps is demonstrated and quantified by simulation studies. The robustness of the algorithm with respect to the choice of Gibbs potentials is investigated.

Three-Dimensional Algebraic Reconstruction From Three Mutually Orthogonal Projections

1985 ◽  
Vol 43 ◽  
pp. 306-307
Author(s):  
Ximen Jiye ◽  
Shao Zhifeng
Keyword(s):  
Electron Microscopy ◽  
Approximate Solution ◽  
Three Dimensional ◽  
Reconstruction Technique ◽  
Algebraic Reconstruction Technique ◽  
Reconstruction Problem ◽  
Orthogonal Projections ◽  
3 Dimensional ◽  
Dimensional Reconstruction ◽  
Algebraic Reconstruction

The classic reconstruction problem is that of reconstructing a 3D object from its 2D projections /1-5/. It is also well known that the principal difficulty in solving this problem in electron microscopy is that a very large number of independent projections are normally required. Recently it has been shown /3,4/ that if we restrict our attention to binary or Boolean objects, far fewer projections are needed in order to obtain an approximate solution. 2-dimensional solutions of ID projections were demonstrated using only four views and 3-dimensional reconstruction of 2D projections were obtained by dividing the projections into identifiable slices.In the present paper, an algebraic reconstruction technique (ART) has been studied which uses three mutually orthogonal projections.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

Semi-automated methods for 3-D reconstruction of macromolecular complexes

1995 ◽  
Vol 53 ◽  
pp. 42-43
Author(s):  
B. Carragher ◽  
M. Whittaker
Keyword(s):  
Three Dimensional ◽  
Time Saving ◽  
Macromolecular Complexes ◽  
Symmetry Properties ◽  
Dimensional Reconstruction ◽  
Experienced Operator ◽  
Projection Images ◽  
The Individual ◽  
Natural Symmetry

Techniques for three-dimensional reconstruction of macromolecular complexes from electron micrographs have been successfully used for many years. These include methods which take advantage of the natural symmetry properties of the structure (for example helical or icosahedral) as well as those that use single axis or other tilting geometries to reconstruct from a set of projection images. These techniques have traditionally relied on a very experienced operator to manually perform the often numerous and time consuming steps required to obtain the final reconstruction. While the guidance and oversight of an experienced and critical operator will always be an essential component of these techniques, recent advances in computer technology, microprocessor controlled microscopes and the availability of high quality CCD cameras have provided the means to automate many of the individual steps.During the acquisition of data automation provides benefits not only in terms of convenience and time saving but also in circumstances where manual procedures limit the quality of the final reconstruction.

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