A new workflow for x-ray fluorescence tomography: MAPStoTomoPy

Young Pyo Hong*, Si Chen, Chris Jacobsen

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations


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.

Original languageEnglish (US)
Title of host publicationX-Ray Nanoimaging
Subtitle of host publicationInstruments and Methods II
EditorsBarry Lai
ISBN (Electronic)9781628417586
StatePublished - 2015
EventX-Ray Nanoimaging: Instruments and Methods II - San Diego, United States
Duration: Aug 12 2015Aug 13 2015

Publication series

NameProceedings of SPIE - The International Society for Optical Engineering
ISSN (Print)0277-786X
ISSN (Electronic)1996-756X


OtherX-Ray Nanoimaging: Instruments and Methods II
Country/TerritoryUnited States
CitySan Diego


  • Software
  • Tomography
  • X-ray Imaging

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Computer Science Applications
  • Applied Mathematics
  • Electrical and Electronic Engineering


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