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Proceedings Paper

A new workflow for x-ray fluorescence tomography: MAPStoTomoPy
Author(s): Young Pyo Hong; Si Chen; Chris Jacobsen
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Paper Abstract

X-ray fluorescence tomography involves the acquisition of a series of 2D x-ray fluorescence datasets between which a specimen is rotated. At the Advanced Photon Source at Argonne National Laboratory, the workflow at beamlines 2-ID-E and 21-ID-D (the Bionanoprobe, a cryogenic microscope system) has included the use of the program MAPS for obtaining elemental concentrations from 2D images, and the program TomoPy which was developed to include several tomographic reconstruction methods for x-ray transmission data. In the past, fluorescence projection images from an individual chemical element were hand-assembled into a 3D dataset for reconstruction using interactive tools such as ImageJ. We describe here the program MAPSToTomoPy, which provides a graphical user interface (GUI) to control a workflow between MAPS and TomoPy, with tools for visualizing the sinograms of projection image sequences from particular elements and to use these to help correct misalignments of the rotation axis. The program also provides an integrated output of the 3D distribution of the detected elements for subsequent 3D visualization packages.

Paper Details

Date Published: 18 September 2015
PDF: 8 pages
Proc. SPIE 9592, X-Ray Nanoimaging: Instruments and Methods II, 95920W (18 September 2015); doi: 10.1117/12.2194162
Show Author Affiliations
Young Pyo Hong, Northwestern Univ. (United States)
Si Chen, Argonne National Lab. (United States)
Chris Jacobsen, Argonne National Lab. (United States)
Northwestern Univ. (United States)


Published in SPIE Proceedings Vol. 9592:
X-Ray Nanoimaging: Instruments and Methods II
Barry Lai, Editor(s)

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