A new workflow for x-ray fluorescence tomography: MAPStoTomoPy

Young Pyo Hong; Si Chen; Chris Jacobsen

doi:10.1117/12.2194162

18 September 2015 A new workflow for x-ray fluorescence tomography: MAPStoTomoPy

Young Pyo Hong, Si Chen, Chris Jacobsen

Proceedings Volume 9592, X-Ray Nanoimaging: Instruments and Methods II; 95920W (2015) https://doi.org/10.1117/12.2194162
Event: SPIE Optical Engineering + Applications, 2015, San Diego, California, United States

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.

Citation Download Citation

Young Pyo Hong, Si Chen, and Chris Jacobsen "A new workflow for x-ray fluorescence tomography: MAPStoTomoPy", Proc. SPIE 9592, X-Ray Nanoimaging: Instruments and Methods II, 95920W (18 September 2015); https://doi.org/10.1117/12.2194162

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