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. 2020 Nov 1;27(Pt 6):1734-1740.
doi: 10.1107/S1600577520010838. Epub 2020 Sep 14.

X-ray Spectral Imaging Program: XSIP

Peng Qi  1 , Nazanin Samadi  2 , Dean Chapman  3
Affiliations

X-ray Spectral Imaging Program: XSIP

Peng Qi et al. J Synchrotron Radiat. .

Abstract

Spectral K-edge subtraction imaging and wide-field energy-dispersive X-ray absorption spectroscopy imaging are novel, related, synchrotron imaging techniques for element absorption contrast imaging and element speciation imaging, respectively. These two techniques serve different goals but share the same X-ray optics principles with a bent Laue type monochromator and the same data processing algorithms. As there is a growing interest to implement these novel techniques in synchrotron facilities, Python-based software has been developed to automate the data processing procedures for both techniques. In this paper, the concept of the essential data processing algorithms are explained, the workflow of the software is described, and the main features and some related utilities are introduced.

Keywords: Python; spectral KES; wide-field energy-dispersive XAS.

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Figures

Figure 1
Figure 1
Overview of the XSIP workflow. The program starts by calling the ‘nei’ function with a number of user-defined parameters and ends with the outputs in forms of images and a PKL format file containing intermediate results during the data analysis.
Figure 2
Figure 2
An example edge image. (a) A 0.2 mm selenium film is used as the edge reference material. The arrow indicates the absorption edge at 12.658 keV. Data collected on 10 September 2015. (b) Energy mapping in the total image field of view.
Figure 3
Figure 3
The geometry for relating the diffraction angles and the pixel positions on the detector with (a) one reference energy and (b) two reference energies. The K-edge energy, the monochromator focal distance, the focus-to-detector distance, the Bragg plane indices and the crystal asymmetry angle are the determining factors.
Figure 4
Figure 4
An example of spectra curve fitting. (a) The mass attenuation coefficient of reference materials. (b) Measured absorption spectrum and fitted absorption spectrum with reference materials. The reference spectra are also shown in the figure with their fitted weight. The attenuation by Water is removed from the total attenuation for better demonstration.
Figure 5
Figure 5
Sinograms of the distribution of (a) selenate, (b) selenite, (c) selenomethionine and (d) water. The CT reconstruction of the density distributions of (e) selenate, (f) selenite, (g) selenomethionine and (h) water. Every Se compound solution is prepared with 100 mM concentration. 7 mg cm−3 selenomethionine was detected in the seedpod of Astragalus bisulcatus, which is placed in the center of the sample holder. The gray scale bar on the bottom left is shown for the corresponding Se compounds concentrations in (e), (f) and (g), and the gray scale bar on the bottom right for (h).
Figure 6
Figure 6
Screenshots of the XSIP GUI. (a) The ‘Spectral Imaging’ panel contains the main data analysis pipeline and several parameters to tune for best result. (b) The ‘Reconstruction’ panel contains the reconstruction tool and a display canvas for the sinogram and reconstruction results.
See this image and copyright information in PMC

References

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