Joint ptycho-tomography reconstruction through alternating direction method of multipliers
Abstract
We present the extension of ptychography forthree-dimensional object reconstruction in a tomography setting. We describe the alternating direction method of multipliers (ADMM) as a generic reconstruction framework to efficiently solve the nonlinear optimization problem. In this framework, the ADMM breaks the joint reconstruction problem into two well-defined subproblems: ptychographic phase retrieval and tomographic reconstruction. In this paper, we use the gradient descent algorithm to solve both problems and demonstrate the efficiency of the proposed approach through numerical simulations. Further, we show that the proposed joint approach relaxes existing requirements for lateral probe overlap in conventional ptychography. Thus, it can allow more flexible data acquisition.
- Authors:
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); Swedish Research Council (SRC)
- OSTI Identifier:
- 1499836
- Alternate Identifier(s):
- OSTI ID: 1510486
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Published Article
- Journal Name:
- Optics Express
- Additional Journal Information:
- Journal Name: Optics Express Journal Volume: 27 Journal Issue: 6; Journal ID: ISSN 1094-4087
- Publisher:
- Optical Society of America (OSA)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING
Citation Formats
Aslan, Selin, Nikitin, Viktor, Ching, Daniel J., Bicer, Tekin, Leyffer, Sven, and Gürsoy, Doğa. Joint ptycho-tomography reconstruction through alternating direction method of multipliers. United States: N. p., 2019.
Web. doi:10.1364/OE.27.009128.
Aslan, Selin, Nikitin, Viktor, Ching, Daniel J., Bicer, Tekin, Leyffer, Sven, & Gürsoy, Doğa. Joint ptycho-tomography reconstruction through alternating direction method of multipliers. United States. https://doi.org/10.1364/OE.27.009128
Aslan, Selin, Nikitin, Viktor, Ching, Daniel J., Bicer, Tekin, Leyffer, Sven, and Gürsoy, Doğa. Thu .
"Joint ptycho-tomography reconstruction through alternating direction method of multipliers". United States. https://doi.org/10.1364/OE.27.009128.
@article{osti_1499836,
title = {Joint ptycho-tomography reconstruction through alternating direction method of multipliers},
author = {Aslan, Selin and Nikitin, Viktor and Ching, Daniel J. and Bicer, Tekin and Leyffer, Sven and Gürsoy, Doğa},
abstractNote = {We present the extension of ptychography forthree-dimensional object reconstruction in a tomography setting. We describe the alternating direction method of multipliers (ADMM) as a generic reconstruction framework to efficiently solve the nonlinear optimization problem. In this framework, the ADMM breaks the joint reconstruction problem into two well-defined subproblems: ptychographic phase retrieval and tomographic reconstruction. In this paper, we use the gradient descent algorithm to solve both problems and demonstrate the efficiency of the proposed approach through numerical simulations. Further, we show that the proposed joint approach relaxes existing requirements for lateral probe overlap in conventional ptychography. Thus, it can allow more flexible data acquisition.},
doi = {10.1364/OE.27.009128},
journal = {Optics Express},
number = 6,
volume = 27,
place = {United States},
year = {Thu Mar 14 00:00:00 EDT 2019},
month = {Thu Mar 14 00:00:00 EDT 2019}
}
https://doi.org/10.1364/OE.27.009128
Web of Science
Works referenced in this record:
Phase retrieval with transverse translation diversity: a nonlinear optimization approach
journal, January 2008
- Guizar-Sicairos, Manuel; Fienup, James R.
- Optics Express, Vol. 16, Issue 10
Three-dimensional iterative multislice reconstruction for ptychographic X-ray computed tomography
journal, January 2018
- Shimomura, Kei; Hirose, Makoto; Higashino, Takaya
- Optics Express, Vol. 26, Issue 24
Parallel ptychographic reconstruction
journal, January 2014
- Nashed, Youssef S. G.; Vine, David J.; Peterka, Tom
- Optics Express, Vol. 22, Issue 26
Multi-slice ptychographic tomography
journal, February 2018
- Li, Peng; Maiden, Andrew
- Scientific Reports, Vol. 8, Issue 1
Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae
journal, February 2015
- Deng, Junjing; Vine, David J.; Chen, Si
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 8
Maximum-likelihood refinement for coherent diffractive imaging
journal, June 2012
- Thibault, P.; Guizar-Sicairos, M.
- New Journal of Physics, Vol. 14, Issue 6
On the Fast Fourier Transform of Functions with Singularities
journal, October 1995
- Beylkin, G.
- Applied and Computational Harmonic Analysis, Vol. 2, Issue 4
Experimental robustness of Fourier ptychography phase retrieval algorithms
journal, January 2015
- Yeh, Li-Hao; Dong, Jonathan; Zhong, Jingshan
- Optics Express, Vol. 23, Issue 26
XDesign : an open-source software package for designing X-ray imaging phantoms and experiments
journal, February 2017
- Ching, Daniel J.; Gürsoy, Dogˇa
- Journal of Synchrotron Radiation, Vol. 24, Issue 2
Phase Retrieval via Matrix Completion
journal, January 2013
- Candès, Emmanuel J.; Eldar, Yonina C.; Strohmer, Thomas
- SIAM Journal on Imaging Sciences, Vol. 6, Issue 1
Augmented projections for ptychographic imaging
journal, October 2013
- Marchesini, Stefano; Schirotzek, Andre; Yang, Chao
- Inverse Problems, Vol. 29, Issue 11
Direct coupling of tomography and ptychography
journal, January 2017
- Gürsoy, Doğa
- Optics Letters, Vol. 42, Issue 16
Transmission microscopy without lenses for objects of unlimited size
journal, February 2007
- Rodenburg, J. M.; Hurst, A. C.; Cullis, A. G.
- Ultramicroscopy, Vol. 107, Issue 2-3
Density mapping of hardened cement paste using ptychographic X-ray computed tomography
journal, February 2013
- Trtik, Pavel; Diaz, Ana; Guizar-Sicairos, Manuel
- Cement and Concrete Composites, Vol. 36
3D x-ray imaging of continuous objects beyond the depth of focus limit
journal, January 2018
- Gilles, M. A.; Nashed, Y. S. G.; Du, M.
- Optica, Vol. 5, Issue 9
Total Variation--Based Phase Retrieval for Poisson Noise Removal
journal, January 2018
- Chang, Huibin; Lou, Yifei; Duan, Yuping
- SIAM Journal on Imaging Sciences, Vol. 11, Issue 1
High-Resolution Scanning X-ray Diffraction Microscopy
journal, July 2008
- Thibault, P.; Dierolf, M.; Menzel, A.
- Science, Vol. 321, Issue 5887
Non-destructive and quantitative imaging of a nano-structured microchip by ptychographic hard X-ray scanning microscopy: NON-DESTRUCTIVE AND QUANTITATIVE X-RAY IMAGING
journal, December 2010
- Schropp, A.; Boye, P.; Goldschmidt, A.
- Journal of Microscopy, Vol. 241, Issue 1
X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution
journal, January 2014
- Holler, M.; Diaz, A.; Guizar-Sicairos, M.
- Scientific Reports, Vol. 4, Issue 1
Global Convergence of ADMM in Nonconvex Nonsmooth Optimization
journal, June 2018
- Wang, Yu; Yin, Wotao; Zeng, Jinshan
- Journal of Scientific Computing, Vol. 78, Issue 1
Partially coherent ptychography by gradient decomposition of the probe
journal, April 2018
- Chang, Huibin; Enfedaque, Pablo; Lou, Yifei
- Acta Crystallographica Section A Foundations and Advances, Vol. 74, Issue 3
Cryo-scanning x-ray diffraction microscopy of frozen-hydrated yeast: CRYO-SCANNING X-RAY DIFFRACTION MICROSCOPY
journal, December 2012
- Lima, E.; Diaz, A.; Guizar-Sicairos, M.
- Journal of Microscopy, Vol. 249, Issue 1
SHARP : a distributed GPU-based ptychographic solver
journal, July 2016
- Marchesini, Stefano; Krishnan, Hari; Daurer, Benedikt J.
- Journal of Applied Crystallography, Vol. 49, Issue 4
Phase retrieval by iterated projections
journal, January 2003
- Elser, Veit
- Journal of the Optical Society of America A, Vol. 20, Issue 1
Proximal Heterogeneous Block Implicit-Explicit Method and Application to Blind Ptychographic Diffraction Imaging
journal, January 2015
- Hesse, Robert; Luke, D. Russell; Sabach, Shoham
- SIAM Journal on Imaging Sciences, Vol. 8, Issue 1
Nanoscale x-ray imaging of circuit features without wafer etching
journal, March 2017
- Deng, Junjing; Hong, Young Pyo; Chen, Si
- Physical Review B, Vol. 95, Issue 10
Hard X-ray imaging of bacterial cells: nano-diffraction and ptychographic reconstruction
journal, January 2012
- Wilke, R. N.; Priebe, M.; Bartels, M.
- Optics Express, Vol. 20, Issue 17
On the $O(1/n)$ Convergence Rate of the Douglas–Rachford Alternating Direction Method
journal, January 2012
- He, Bingsheng; Yuan, Xiaoming
- SIAM Journal on Numerical Analysis, Vol. 50, Issue 2
Fourier ptychographic reconstruction using Wirtinger flow optimization
journal, January 2015
- Bian, Liheng; Suo, Jinli; Zheng, Guoan
- Optics Express, Vol. 23, Issue 4
Variational Phase Retrieval with Globally Convergent Preconditioned Proximal Algorithm
journal, January 2018
- Chang, Huibin; Marchesini, Stefano; Lou, Yifei
- SIAM Journal on Imaging Sciences, Vol. 11, Issue 1
Quantitative biological imaging by ptychographic x-ray diffraction microscopy
journal, December 2009
- Giewekemeyer, K.; Thibault, P.; Kalbfleisch, S.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 2
Three-dimensional mass density mapping of cellular ultrastructure by ptychographic X-ray nanotomography
journal, December 2015
- Diaz, Ana; Malkova, Barbora; Holler, Mirko
- Journal of Structural Biology, Vol. 192, Issue 3
Distributed Optimization and Statistical Learning via the Alternating Direction Method of Multipliers
book, January 2011
- Boyd, Stephen; Parikh, Neal; Chu, Eric
Probe retrieval in ptychographic coherent diffractive imaging
journal, March 2009
- Thibault, Pierre; Dierolf, Martin; Bunk, Oliver
- Ultramicroscopy, Vol. 109, Issue 4
Rotation-as-fast-axis scanning-probe x-ray tomography: the importance of angular diversity for fly-scan modes
journal, January 2018
- Ching, Daniel J.; Hidayetoğlu, Mert; Biçer, Tekin
- Applied Optics, Vol. 57, Issue 30
A phase retrieval algorithm for shifting illumination
journal, November 2004
- Rodenburg, J. M.; Faulkner, H. M. L.
- Applied Physics Letters, Vol. 85, Issue 20
An instrument for 3D x-ray nano-imaging
journal, July 2012
- Holler, M.; Raabe, J.; Diaz, A.
- Review of Scientific Instruments, Vol. 83, Issue 7
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
Quantitative x-ray phase nanotomography
journal, January 2012
- Diaz, Ana; Trtik, Pavel; Guizar-Sicairos, Manuel
- Physical Review B, Vol. 85, Issue 2
Emerging In Situ and Operando Nanoscale X-Ray Imaging Techniques for Energy Storage Materials
journal, February 2015
- Nelson Weker, Johanna; Toney, Michael F.
- Advanced Functional Materials, Vol. 25, Issue 11
Multi-slice ptychography with large numerical aperture multilayer Laue lenses
journal, January 2018
- Öztürk, Hande; Yan, Hanfei; He, Yan
- Optica, Vol. 5, Issue 5
Real-Time Data Analysis and Autonomous Steering of Synchrotron Light Source Experiments
conference, October 2017
- Bicer, Tekin; Gursoy, Doga; Kettimuthu, Rajkumar
- 2017 IEEE 13th International Conference on e-Science (e-Science)
Continuous motion scan ptychography: characterization for increased speed in coherent x-ray imaging
journal, January 2015
- Deng, Junjing; Nashed, Youssef S. G.; Chen, Si
- Optics Express, Vol. 23, Issue 5
New theory of partial coherence in the space–frequency domain Part I: spectra and cross spectra of steady-state sources
journal, January 1982
- Wolf, Emil
- Journal of the Optical Society of America, Vol. 72, Issue 3
X-Ray Interactions: Photoabsorption, Scattering, Transmission, and Reflection at E = 50-30,000 eV, Z = 1-92
journal, July 1993
- Henke, B. L.; Gullikson, E. M.; Davis, J. C.
- Atomic Data and Nuclear Data Tables, Vol. 54, Issue 2, p. 181-342
Beugung im inhomogenen Primärstrahlwellenfeld. I. Prinzip einer Phasenmessung von Elektronenbeungungsinterferenzen
journal, July 1969
- Hoppe, W.
- Acta Crystallographica Section A, Vol. 25, Issue 4
Fast-updating and nonrepeating Lissajous image reconstruction method for capturing increased dynamic information
journal, January 2011
- Hoy, Christopher L.; Durr, Nicholas J.; Ben-Yakar, Adela
- Applied Optics, Vol. 50, Issue 16
Three-Dimensional Structure Analysis and Percolation Properties of a Barrier Marine Coating
journal, January 2013
- Chen, Bo; Guizar-Sicairos, Manuel; Xiong, Gang
- Scientific Reports, Vol. 3, Issue 1
Phase retrieval algorithms: a comparison
journal, January 1982
- Fienup, J. R.
- Applied Optics, Vol. 21, Issue 15
Ptychographic X-ray computed tomography at the nanoscale
journal, September 2010
- Dierolf, Martin; Menzel, Andreas; Thibault, Pierre
- Nature, Vol. 467, Issue 7314
Convergence Analysis of Alternating Direction Method of Multipliers for a Family of Nonconvex Problems
journal, January 2016
- Hong, Mingyi; Luo, Zhi-Quan; Razaviyayn, Meisam
- SIAM Journal on Optimization, Vol. 26, Issue 1
Proximal alternating linearized minimization for nonconvex and nonsmooth problems
journal, July 2013
- Bolte, Jérôme; Sabach, Shoham; Teboulle, Marc
- Mathematical Programming, Vol. 146, Issue 1-2
Trace: a high-throughput tomographic reconstruction engine for large-scale datasets
journal, January 2017
- Bicer, Tekin; Gürsoy, Doğa; Andrade, Vincent De
- Advanced Structural and Chemical Imaging, Vol. 3, Issue 1
In situ X-ray ptychography imaging of high-temperature CO 2 acceptor particle agglomerates
journal, June 2014
- Høydalsvik, Kristin; Bø Fløystad, Jostein; Zhao, Tiejun
- Applied Physics Letters, Vol. 104, Issue 24
Chemical Contrast in Soft X-Ray Ptychography
journal, November 2011
- Beckers, Mike; Senkbeil, Tobias; Gorniak, Thomas
- Physical Review Letters, Vol. 107, Issue 20
Ptychography & lensless X-ray imaging
journal, January 2008
- Dierolf, Martin; Bunk, Oliver; Kynde, Søren
- Europhysics News, Vol. 39, Issue 1
Multiplier and gradient methods
journal, November 1969
- Hestenes, Magnus R.
- Journal of Optimization Theory and Applications, Vol. 4, Issue 5
Further improvements to the ptychographical iterative engine
journal, January 2017
- Maiden, Andrew; Johnson, Daniel; Li, Peng
- Optica, Vol. 4, Issue 7
Reconstruction of an object from the modulus of its Fourier transform
journal, January 1978
- Fienup, J. R.
- Optics Letters, Vol. 3, Issue 1, p. 27-29
Hard-X-Ray Lensless Imaging of Extended Objects
journal, January 2007
- Rodenburg, J. M.; Hurst, A. C.; Cullis, A. G.
- Physical Review Letters, Vol. 98, Issue 3
Molar concentration from sequential 2-D water-window X-ray ptychography and X-ray fluorescence in hydrated cells
journal, April 2016
- Jones, M. W. M.; Elgass, K. D.; Junker, M. D.
- Scientific Reports, Vol. 6, Issue 1
Splitting Methods in Communication, Imaging, Science, and Engineering
book, January 2017
- Glowinski, Roland; Osher, Stanley J.; Yin, Wotao
- Scientific Computation
High-resolution non-destructive three-dimensional imaging of integrated circuits
journal, March 2017
- Holler, Mirko; Guizar-Sicairos, Manuel; Tsai, Esther H. R.
- Nature, Vol. 543, Issue 7645
Alternating direction methods for classical and ptychographic phase retrieval
journal, October 2012
- Wen, Zaiwen; Yang, Chao; Liu, Xin
- Inverse Problems, Vol. 28, Issue 11
Phase Retrieval via Wirtinger Flow: Theory and Algorithms
journal, April 2015
- Candes, Emmanuel J.; Li, Xiaodong; Soltanolkotabi, Mahdi
- IEEE Transactions on Information Theory, Vol. 61, Issue 4
Ten implementations of ptychography: TEN IMPLEMENTATIONS OF PTYCHOGRAPHY
journal, July 2017
- Li, Peng; Maiden, Andrew M.
- Journal of Microscopy, Vol. 269, Issue 3
On the numerical solution of heat conduction problems in two and three space variables
journal, February 1956
- Douglas, Jim; Rachford, H. H.
- Transactions of the American Mathematical Society, Vol. 82, Issue 2