Advanced denoising for X-ray ptychography
Abstract
The success of ptychographic imaging experiments strongly depends on achieving high signal-to-noise ratio. This is particularly important in nanoscale imaging experiments when diffraction signals are very weak and the experiments are accompanied by significant parasitic scattering (background), outliers or correlated noise sources. It is also critical when rare events, such as cosmic rays, or bad frames caused by electronic glitches or shutter timing malfunction take place. In this paper, we propose a novel iterative algorithm with rigorous analysis that exploits the direct forward model for parasitic noise and sample smoothness to achieve a thorough characterization and removal of structured and random noise. We present a formal description of the proposed algorithm and prove its convergence under mild conditions. Numerical experiments from simulations and real data (both soft and hard X-ray beamlines) demonstrate that the proposed algorithms produce better results when compared to state-of-the-art methods.
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1504305
- Alternate Identifier(s):
- OSTI ID: 1564021
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Optics Express
- Additional Journal Information:
- Journal Name: Optics Express Journal Volume: 27 Journal Issue: 8; Journal ID: ISSN 1094-4087
- Publisher:
- Optical Society of America
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 47 OTHER INSTRUMENTATION
Citation Formats
Chang, Huibin, Enfedaque, Pablo, Zhang, Jie, Reinhardt, Juliane, Enders, Bjoern, Yu, Young-Sang, Shapiro, David, Schroer, Christian G., Zeng, Tieyong, and Marchesini, Stefano. Advanced denoising for X-ray ptychography. United States: N. p., 2019.
Web. doi:10.1364/OE.27.010395.
Chang, Huibin, Enfedaque, Pablo, Zhang, Jie, Reinhardt, Juliane, Enders, Bjoern, Yu, Young-Sang, Shapiro, David, Schroer, Christian G., Zeng, Tieyong, & Marchesini, Stefano. Advanced denoising for X-ray ptychography. United States. https://doi.org/10.1364/OE.27.010395
Chang, Huibin, Enfedaque, Pablo, Zhang, Jie, Reinhardt, Juliane, Enders, Bjoern, Yu, Young-Sang, Shapiro, David, Schroer, Christian G., Zeng, Tieyong, and Marchesini, Stefano. Mon .
"Advanced denoising for X-ray ptychography". United States. https://doi.org/10.1364/OE.27.010395.
@article{osti_1504305,
title = {Advanced denoising for X-ray ptychography},
author = {Chang, Huibin and Enfedaque, Pablo and Zhang, Jie and Reinhardt, Juliane and Enders, Bjoern and Yu, Young-Sang and Shapiro, David and Schroer, Christian G. and Zeng, Tieyong and Marchesini, Stefano},
abstractNote = {The success of ptychographic imaging experiments strongly depends on achieving high signal-to-noise ratio. This is particularly important in nanoscale imaging experiments when diffraction signals are very weak and the experiments are accompanied by significant parasitic scattering (background), outliers or correlated noise sources. It is also critical when rare events, such as cosmic rays, or bad frames caused by electronic glitches or shutter timing malfunction take place. In this paper, we propose a novel iterative algorithm with rigorous analysis that exploits the direct forward model for parasitic noise and sample smoothness to achieve a thorough characterization and removal of structured and random noise. We present a formal description of the proposed algorithm and prove its convergence under mild conditions. Numerical experiments from simulations and real data (both soft and hard X-ray beamlines) demonstrate that the proposed algorithms produce better results when compared to state-of-the-art methods.},
doi = {10.1364/OE.27.010395},
journal = {Optics Express},
number = 8,
volume = 27,
place = {United States},
year = {2019},
month = {4}
}
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https://doi.org/10.1364/OE.27.010395
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Works referencing / citing this record:
Probe retrieval in ptychographic coherent diffractive imaging
journal, March 2009
- Thibault, Pierre; Dierolf, Martin; Bunk, Oliver
- Ultramicroscopy, Vol. 109, Issue 4
An improved ptychographical phase retrieval algorithm for diffractive imaging
journal, September 2009
- Maiden, Andrew M.; Rodenburg, John M.
- Ultramicroscopy, Vol. 109, Issue 10
Beamstop-based low-background ptychography to image weakly scattering objects
journal, February 2017
- Reinhardt, Juliane; Hoppe, Robert; Hofmann, Georg
- Ultramicroscopy, Vol. 173
Resolution beyond the 'information limit' in transmission electron microscopy
journal, April 1995
- Nellist, P. D.; McCallum, B. C.; Rodenburg, J. M.
- Nature, Vol. 374, Issue 6523
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
Chemical composition mapping with nanometre resolution by soft X-ray microscopy
journal, September 2014
- Shapiro, David A.; Yu, Young-Sang; Tyliszczak, Tolek
- Nature Photonics, Vol. 8, Issue 10
Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography
journal, March 2018
- Yu, Young-Sang; Farmand, Maryam; Kim, Chunjoong
- Nature Communications, Vol. 9, Issue 1
Electron ptychography of 2D materials to deep sub-ångström resolution
journal, July 2018
- Jiang, Yi; Chen, Zhen; Han, Yimo
- Nature, Vol. 559, Issue 7714
A phase retrieval algorithm for shifting illumination
journal, November 2004
- Rodenburg, J. M.; Faulkner, H. M. L.
- Applied Physics Letters, Vol. 85, Issue 20
Ptychography with broad-bandwidth radiation
journal, April 2014
- Enders, B.; Dierolf, M.; Cloetens, P.
- Applied Physics Letters, Vol. 104, Issue 17
Soft x-ray ptychography studies of nanoscale magnetic and structural correlations in thin SmCo5 films
journal, February 2016
- Shi, X.; Fischer, P.; Neu, V.
- Applied Physics Letters, Vol. 108, Issue 9
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
Relaxed averaged alternating reflections for diffraction imaging
journal, November 2004
- Luke, D. Russell
- Inverse Problems, Vol. 21, Issue 1
Alternating direction methods for classical and ptychographic phase retrieval
journal, October 2012
- Wen, Zaiwen; Yang, Chao; Liu, Xin
- Inverse Problems, Vol. 28, Issue 11
Augmented projections for ptychographic imaging
journal, October 2013
- Marchesini, Stefano; Schirotzek, Andre; Yang, Chao
- Inverse Problems, Vol. 29, Issue 11
Maximum-likelihood refinement for coherent diffractive imaging
journal, June 2012
- Thibault, P.; Guizar-Sicairos, M.
- New Journal of Physics, Vol. 14, Issue 6
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
Post-sample aperture for low background diffraction experiments at X-ray free-electron lasers
journal, October 2017
- Wiedorn, Max O.; Awel, Salah; Morgan, Andrew J.
- Journal of Synchrotron Radiation, Vol. 24, Issue 6
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
Augmented Lagrangian Method, Dual Methods, and Split Bregman Iteration for ROF, Vectorial TV, and High Order Models
journal, January 2010
- Wu, Chunlin; Tai, Xue-Cheng
- SIAM Journal on Imaging Sciences, Vol. 3, Issue 3
Nanosurveyor: a framework for real-time data processing
journal, January 2017
- Daurer, Benedikt J.; Krishnan, Hari; Perciano, Talita
- Advanced Structural and Chemical Imaging, Vol. 3, Issue 1
Background noise removal in x-ray ptychography
journal, January 2017
- Wang, Chunpeng; Xu, Zijian; Liu, Haigang
- Applied Optics, Vol. 56, Issue 8
Phase retrieval by iterated projections
journal, January 2003
- Elser, Veit
- Journal of the Optical Society of America A, Vol. 20, Issue 1
Iterative least-squares solver for generalized maximum-likelihood ptychography
journal, January 2018
- Odstrčil, Michal; Menzel, Andreas; Guizar-Sicairos, Manuel
- Optics Express, Vol. 26, Issue 3
Distributed Optimization and Statistical Learning via the Alternating Direction Method of Multipliers
book, January 2011
- Boyd, Stephen; Parikh, Neal; Chu, Eric
Advanced denoising for X-ray ptychography
text, January 2019
- Chang, Huibin; Enfedaque, Pablo; Zhang, Jie
- Deutsches Elektronen-Synchrotron, DESY, Hamburg
A reweighted $l^2$ method for image restoration with Poisson and mixed Poisson-Gaussian noise
journal, July 2015
- Li, Jia; Shen, Zuowei; Yin, Rujie
- Inverse Problems and Imaging, Vol. 9, Issue 3
Ptychographic Nano-Analytical Microscope (PtyNAMi) at PETRA III: signal-to-background optimization for imaging with high sensitivity
conference, September 2019
- Schroer, Christian G.; Seyrich, Martin; Schropp, Andreas
- X-Ray Nanoimaging: Instruments and Methods IV
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