skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

This content will become publicly available on August 26, 2020

Title: Optimization-based simultaneous alignment and reconstruction in multi-element tomography

Abstract

As x-ray microscopy is pushed into the nanoscale with the advent of more bright and coherent x-ray sources, associated improvement in spatial resolution becomes highly vulnerable to geometrical errors and uncertainties during data collection. We address a form of error in tomography experiments, namely, the drift between projections during the tomographic scan. Our proposed method can simultaneously recover the drift, while tomographically reconstructing the specimen based on a joint iterative optimization scheme. This approach utilizes the correlation provided from different view angles and different signals. Finally, while generally applicable, we demonstrate our method on x-ray fluorescence tomography from a tissue specimen and compare the reconstruction quality with conventional methods.

Authors:
 [1];  [2]; ORCiD logo [3];  [4];  [5]; ORCiD logo [5];  [2]
  1. (Wendy) [Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division; Argonne National Lab. (ANL), Argonne, IL (United States). X-ray Science Division
  2. Argonne National Lab. (ANL), Argonne, IL (United States). X-ray Science Division
  3. Argonne National Lab. (ANL), Argonne, IL (United States). X-ray Science Division; Northwestern Univ., Evanston, IL (United States). Dept. of Electrical and Computer Engineering
  4. Northwestern Univ., Evanston, IL (United States). Dept. of Radiation Oncology
  5. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1574379
Alternate Identifier(s):
OSTI ID: 1558704
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Optics Letters
Additional Journal Information:
Journal Volume: 44; Journal Issue: 17; Journal ID: ISSN 0146-9592
Publisher:
Optical Society of America (OSA)
Country of Publication:
United States
Language:
English
Subject:
47 OTHER INSTRUMENTATION

Citation Formats

Di, Zichao, Chen, Si, Gursoy, Doga, Paunesku, Tatjana, Leyffer, Sven, Wild, Stefan M., and Vogt, Stefan. Optimization-based simultaneous alignment and reconstruction in multi-element tomography. United States: N. p., 2019. Web. doi:10.1364/OL.44.004331.
Di, Zichao, Chen, Si, Gursoy, Doga, Paunesku, Tatjana, Leyffer, Sven, Wild, Stefan M., & Vogt, Stefan. Optimization-based simultaneous alignment and reconstruction in multi-element tomography. United States. doi:10.1364/OL.44.004331.
Di, Zichao, Chen, Si, Gursoy, Doga, Paunesku, Tatjana, Leyffer, Sven, Wild, Stefan M., and Vogt, Stefan. Mon . "Optimization-based simultaneous alignment and reconstruction in multi-element tomography". United States. doi:10.1364/OL.44.004331.
@article{osti_1574379,
title = {Optimization-based simultaneous alignment and reconstruction in multi-element tomography},
author = {Di, Zichao and Chen, Si and Gursoy, Doga and Paunesku, Tatjana and Leyffer, Sven and Wild, Stefan M. and Vogt, Stefan},
abstractNote = {As x-ray microscopy is pushed into the nanoscale with the advent of more bright and coherent x-ray sources, associated improvement in spatial resolution becomes highly vulnerable to geometrical errors and uncertainties during data collection. We address a form of error in tomography experiments, namely, the drift between projections during the tomographic scan. Our proposed method can simultaneously recover the drift, while tomographically reconstructing the specimen based on a joint iterative optimization scheme. This approach utilizes the correlation provided from different view angles and different signals. Finally, while generally applicable, we demonstrate our method on x-ray fluorescence tomography from a tissue specimen and compare the reconstruction quality with conventional methods.},
doi = {10.1364/OL.44.004331},
journal = {Optics Letters},
number = 17,
volume = 44,
place = {United States},
year = {2019},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on August 26, 2020
Publisher's Version of Record

Save / Share:

Works referenced in this record:

X-ray fluorescence microprobe imaging in biology and medicine
journal, January 2006

  • Paunesku, Tatjana; Vogt, Stefan; Maser, Jörg
  • Journal of Cellular Biochemistry, Vol. 99, Issue 6
  • DOI: 10.1002/jcb.21047

Fluorescent Computer Tomography: A Model For Correction Of X-ray Absorption
journal, December 1991

  • Hogan, J. P.; Gonsalves, R. A.; Krieger, A. S.
  • IEEE Transactions on Nuclear Science, Vol. 38, Issue 6
  • DOI: 10.1109/TNS.1991.574221

Iterative Reconstruction in X-ray Fluorescence Tomography Based on Radon Inversion
journal, February 2011

  • Miqueles, E. X.; De Pierro, A. R.
  • IEEE Transactions on Medical Imaging, Vol. 30, Issue 2
  • DOI: 10.1109/TMI.2010.2085011

Nanoscale quantification of intracellular element concentration by X-ray fluorescence microscopy combined with X-ray phase contrast nanotomography
journal, January 2018

  • Gramaccioni, Chiara; Yang, Yang; Procopio, Alessandra
  • Applied Physics Letters, Vol. 112, Issue 5
  • DOI: 10.1063/1.5008834

Nondestructive three-dimensional elemental microanalysis by combined helical x-ray microtomographies
journal, March 2004

  • Golosio, Bruno; Somogyi, Andrea; Simionovici, Alexandre
  • Applied Physics Letters, Vol. 84, Issue 12
  • DOI: 10.1063/1.1686892

Reconstructing x-ray fluorescence microtomograms
journal, September 2001

  • Schroer, Christian G.
  • Applied Physics Letters, Vol. 79, Issue 12
  • DOI: 10.1063/1.1402643

A Scanning X-Ray Microscope Using Synchrotron Radiation
journal, November 1972


Elemental X-ray imaging using the Maia detector array: The benefits and challenges of large solid-angle
journal, July 2010

  • Ryan, C. G.; Kirkham, R.; Hough, R. M.
  • Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 619, Issue 1-3
  • DOI: 10.1016/j.nima.2009.11.035

Optimizing detector geometry for trace element mapping by X-ray fluorescence
journal, May 2015


Multimodal hard x-ray imaging with resolution approaching 10 nm for studies in material science
journal, March 2018


Multiresolution Parameter Choice Method for Total Variation Regularized Tomography
journal, January 2016

  • Niinimäki, Kati; Lassas, Matti; Hämäläinen, Keijo
  • SIAM Journal on Imaging Sciences, Vol. 9, Issue 3
  • DOI: 10.1137/15M1034076

Adaptive Graph-Based Total Variation for Tomographic Reconstructions
journal, May 2018

  • Mahmood, Faisal; Shahid, Nauman; Skoglund, Ulf
  • IEEE Signal Processing Letters, Vol. 25, Issue 5
  • DOI: 10.1109/LSP.2018.2816582

Hyperspectral image reconstruction for x-ray fluorescence tomography
journal, January 2015

  • Gürsoy, Doǧa; Biçer, Tekin; Lanzirotti, Antonio
  • Optics Express, Vol. 23, Issue 7
  • DOI: 10.1364/OE.23.009014

Electron microscope tomography: transcription in three dimensions
journal, April 1983


An automatic method of detecting and tracking fiducial markers for alignment in electron tomography
journal, November 2010

  • Cao, M.; Takaoka, A.; Zhang, H. -B.
  • Journal of Electron Microscopy, Vol. 60, Issue 1
  • DOI: 10.1093/jmicro/dfq076

A novel fully automatic scheme for fiducial marker-based alignment in electron tomography
journal, December 2015


Alternative automatic alignment method for specimen tilt-series images based on back-projected volume data cross-correlations
journal, May 2014


Analytical registration of vertical image drifts in parallel beam tomographic data
journal, January 2017

  • Storm, Malte; Beckmann, Felix; Rau, Christoph
  • Optics Letters, Vol. 42, Issue 23
  • DOI: 10.1364/OL.42.004982

Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection
journal, September 2017


Automated angular and translational tomographic alignment and application to phase-contrast imaging
journal, January 2017

  • Ramos, T.; Jørgensen, J. S.; Andreasen, J. W.
  • Journal of the Optical Society of America A, Vol. 34, Issue 10
  • DOI: 10.1364/JOSAA.34.001830

Automatic projection image registration for nanoscale X-ray tomographic reconstruction
journal, October 2018


Quantitative interior x-ray nanotomography by a hybrid imaging technique
journal, January 2015


Simultaneous Sensing Error Recovery and Tomographic Inversion Using an Optimization-Based Approach
journal, January 2019

  • Austin, Anthony P.; Wendy, Zichao; Leyffer, Sven
  • SIAM Journal on Scientific Computing, Vol. 41, Issue 3
  • DOI: 10.1137/18M121993X

Acceleration of maximum-likelihood image restoration for fluorescence microscopy and other noncoherent imagery
journal, January 1991

  • Holmes, Timothy J.; Liu, Yi-Hwa
  • Journal of the Optical Society of America A, Vol. 8, Issue 6
  • DOI: 10.1364/JOSAA.8.000893

Developments with maximum-likelihood x-ray computed tomography: initial testing with real data
journal, January 1994


A survey of truncated-Newton methods
journal, December 2000


TomoPy: a framework for the analysis of synchrotron tomographic data
journal, August 2014

  • Gürsoy, Dogˇa; De Carlo, Francesco; Xiao, Xianghui
  • Journal of Synchrotron Radiation, Vol. 21, Issue 5
  • DOI: 10.1107/S1600577514013939