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Title: 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.

Authors:
ORCiD logo; ; ; ; ; ; ; ; ; ORCiD logo
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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1364/OE.27.010395

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Cited by: 2 works
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Works referencing / citing this record:

Probe retrieval in ptychographic coherent diffractive imaging
journal, March 2009


An improved ptychographical phase retrieval algorithm for diffractive imaging
journal, September 2009


Beamstop-based low-background ptychography to image weakly scattering objects
journal, February 2017


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
  • DOI: 10.1038/374630a0

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
  • DOI: 10.1038/nature21698

Chemical composition mapping with nanometre resolution by soft X-ray microscopy
journal, September 2014


Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography
journal, March 2018


Electron ptychography of 2D materials to deep sub-ångström resolution
journal, July 2018


A phase retrieval algorithm for shifting illumination
journal, November 2004

  • Rodenburg, J. M.; Faulkner, H. M. L.
  • Applied Physics Letters, Vol. 85, Issue 20
  • DOI: 10.1063/1.1823034

Ptychography with broad-bandwidth radiation
journal, April 2014

  • Enders, B.; Dierolf, M.; Cloetens, P.
  • Applied Physics Letters, Vol. 104, Issue 17
  • DOI: 10.1063/1.4874304

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
  • DOI: 10.1063/1.4942776

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
  • DOI: 10.1073/pnas.0905846107

Relaxed averaged alternating reflections for diffraction imaging
journal, November 2004


Alternating direction methods for classical and ptychographic phase retrieval
journal, October 2012


Augmented projections for ptychographic imaging
journal, October 2013


Maximum-likelihood refinement for coherent diffractive imaging
journal, June 2012


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
  • DOI: 10.1107/s1600576716008074

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
  • DOI: 10.1107/s1600577517011961

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
  • DOI: 10.1107/s2053273318001924

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
  • DOI: 10.1137/090767558

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
  • DOI: 10.1186/s40679-017-0039-0

Background noise removal in x-ray ptychography
journal, January 2017

  • Wang, Chunpeng; Xu, Zijian; Liu, Haigang
  • Applied Optics, Vol. 56, Issue 8
  • DOI: 10.1364/ao.56.002099

Phase retrieval by iterated projections
journal, January 2003


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
  • DOI: 10.1364/oe.26.003108

Advanced denoising for X-ray ptychography
text, January 2019

  • Chang, Huibin; Enfedaque, Pablo; Zhang, Jie
  • Deutsches Elektronen-Synchrotron, DESY, Hamburg
  • DOI: 10.3204/pubdb-2019-02182

A reweighted $l^2$ method for image restoration with Poisson and mixed Poisson-Gaussian noise
journal, July 2015


Ptychographic Nano-Analytical Microscope (PtyNAMi) at PETRA III: signal-to-background optimization for imaging with high sensitivity
conference, September 2019

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  • X-Ray Nanoimaging: Instruments and Methods IV
  • DOI: 10.1117/12.2529096

A Monte Carlo ray-tracing simulation of coherent X-ray diffractive imaging
journal, January 2020

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