Removing Stripes, Scratches, and Curtaining with Nonrecoverable Compressed Sensing

Schwartz, Jonathan; Jiang, Yi; Wang, Yongjie; Aiello, Anthony; Bhattacharya, Pallab; Yuan, Hui; Mi, Zetian; Bassim, Nabil; Hovden, Robert

doi:10.1017/S1431927619000254

Title: Removing Stripes, Scratches, and Curtaining with Nonrecoverable Compressed Sensing

Journal Article · Thu Mar 14 00:00:00 EDT 2019 · Microscopy and Microanalysis

DOI:https://doi.org/10.1017/S1431927619000254· OSTI ID:1572085

^[1]; Jiang, Yi ^[2]; Wang, Yongjie ^[1]; Aiello, Anthony ^[1]; Bhattacharya, Pallab ^[1]; Yuan, Hui ^[3]; Mi, Zetian ^[1]; Bassim, Nabil ^[3]; Hovden, Robert ^[1]

Univ. of Michigan, Ann Arbor, MI (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)
McMaster Univ., Hamilton, ON (Canada)

Highly-directional image artifacts such as ion mill curtaining, mechanical scratches, or image striping from beam instability degrade the interpretability of micrographs. These unwanted, aperiodic features extend the image along a primary direction and occupy a small wedge of information in Fourier space. Deleting this wedge of data replaces stripes, scratches, or curtaining, with more complex streaking and blurring artifacts—known within the tomography community as “missing wedge” artifacts. Here, we overcome this problem by recovering the missing region using total variation minimization, which leverages image sparsity-based reconstruction techniques—colloquially referred to as compressed sensing (CS)—to reliably restore images corrupted by stripe-like features. Our approach removes beam instability, ion mill curtaining, mechanical scratches, or any stripe features and remains robust at low signal-to-noise. In conclusion, the success of this approach is achieved by exploiting CS's inability to recover directional structures that are highly localized and missing in Fourier Space.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1572085

Journal Information:: Microscopy and Microanalysis, Vol. 25, Issue 3; ISSN 1431-9276

Publisher:: Microscopy Society of America (MSA)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 13 works

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References (30)

Compressed sensing Donoho, D. L. IEEE Transactions on Information Theory, Vol. 52, Issue 4 https://doi.org/10.1109/TIT.2006.871582	journal	April 2006
CT Image Reconstruction from Sparse Projections Using Adaptive TpV Regularization Qi, Hongliang; Chen, Zijia; Zhou, Linghong Computational and Mathematical Methods in Medicine, Vol. 2015 https://doi.org/10.1155/2015/354869	journal	January 2015
3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography Midgley, P. A.; Weyland, M. Ultramicroscopy, Vol. 96, Issue 3-4 https://doi.org/10.1016/S0304-3991(03)00105-0	journal	September 2003
Stripe and ring artifact removal with combined wavelet—Fourier filtering Münch, Beat; Trtik, Pavel; Marone, Federica Optics Express, Vol. 17, Issue 10 https://doi.org/10.1364/OE.17.008567	journal	January 2009
Robust destriping method with unidirectional total variation and framelet regularization Chang, Yi; Fang, Houzhang; Yan, Luxin Optics Express, Vol. 21, Issue 20 https://doi.org/10.1364/OE.21.023307	journal	January 2013
Plasma Focused Ion Beam Curtaining Artifact Correction by Fourier-Based Linear Opti-mization Model Schankula, Christopher W.; Anand, Christopher K.; Bassim, Nabil D. Microscopy and Microanalysis, Vol. 24, Issue S1 https://doi.org/10.1017/S1431927618003434	journal	August 2018
A new approach to the investigation of nanoparticles: Electron tomography with compressed sensing Thomas, John Meurig; Leary, Rowan; Midgley, Paul A. Journal of Colloid and Interface Science, Vol. 392 https://doi.org/10.1016/j.jcis.2012.09.068	journal	February 2013
Structured Compressed Sensing: From Theory to Applications Duarte, Marco F.; Eldar, Yonina C. IEEE Transactions on Signal Processing, Vol. 59, Issue 9 https://doi.org/10.1109/TSP.2011.2161982	journal	September 2011
Destriping CMODIS data by power filtering IEEE Transactions on Geoscience and Remote Sensing, Vol. 41, Issue 9 https://doi.org/10.1109/TGRS.2003.817206	journal	September 2003
FIB∕SEM Structural Analysis Of Through-Silicon-Vias Bender, H.; Drijbooms, C.; Radisic, A. FRONTIERS OF CHARACTERIZATION AND METROLOGY FOR NANOELECTRONICS: 2011, AIP Conference Proceedings https://doi.org/10.1063/1.3657903	conference	January 2011
Stripe Noise Reduction in MODIS Data by Combining Histogram Matching With Facet Filter Rakwatin, Preesan; Takeuchi, Wataru; Yasuoka, Yoshifumi IEEE Transactions on Geoscience and Remote Sensing, Vol. 45, Issue 6 https://doi.org/10.1109/TGRS.2007.895841	journal	June 2007
Cryo-FIB-nanotomography for quantitative analysis of particle structures in cement suspensions Holzer, L.; Gasser, Ph.; Kaech, A. Journal of Microscopy, Vol. 227, Issue 3 https://doi.org/10.1111/j.1365-2818.2007.01804.x	journal	September 2007
Strip Integration in Radio Astronomy Bracewell, Rn Australian Journal of Physics, Vol. 9, Issue 2 https://doi.org/10.1071/PH560198	journal	January 1956
Toward Optimal Destriping of MODIS Data Using a Unidirectional Variational Model Bouali, Marouan; Ladjal, Saïd IEEE Transactions on Geoscience and Remote Sensing, Vol. 49, Issue 8 https://doi.org/10.1109/TGRS.2011.2119399	journal	August 2011
Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information Candes, E.J.; Romberg, J.; Tao, T. IEEE Transactions on Information Theory, Vol. 52, Issue 2, p. 489-509 https://doi.org/10.1109/TIT.2005.862083	journal	February 2006
DeStripe: frequency-based algorithm for removing stripe noises from AFM images Chen, Shu-wen W.; Pellequer, Jean-Luc BMC Structural Biology, Vol. 11, Issue 1 https://doi.org/10.1186/1472-6807-11-7	journal	January 2011
Removal of curtaining effects by a variational model with directional forward differences Fitschen, Jan Henrik; Ma, Jianwei; Schuff, Sebastian Computer Vision and Image Understanding, Vol. 155 https://doi.org/10.1016/j.cviu.2016.12.008	journal	February 2017
Destriping multisensor imagery with moment matching Gadallah, F. L.; Csillag, F.; Smith, E. J. M. International Journal of Remote Sensing, Vol. 21, Issue 12 https://doi.org/10.1080/01431160050030592	journal	January 2000
Sampling limits for electron tomography with sparsity-exploiting reconstructions Jiang, Yi; Padgett, Elliot; Hovden, Robert Ultramicroscopy, Vol. 186 https://doi.org/10.1016/j.ultramic.2017.12.010	journal	March 2018
Compressed sensing electron tomography Leary, Rowan; Saghi, Zineb; Midgley, Paul A. Ultramicroscopy, Vol. 131 https://doi.org/10.1016/j.ultramic.2013.03.019	journal	August 2013
Stripe artifact elimination based on nonsubsampled contourlet transform for light sheet fluorescence microscopy Liang, Xiao; Zang, Yali; Dong, Di Journal of Biomedical Optics, Vol. 21, Issue 10 https://doi.org/10.1117/1.JBO.21.10.106005	journal	October 2016
Sparse Approximate Solutions to Linear Systems Natarajan, B. K. SIAM Journal on Computing, Vol. 24, Issue 2 https://doi.org/10.1137/S0097539792240406	journal	April 1995
Wavelet analysis for the elimination of striping noise in satellite images Infante, Sergio Omar Optical Engineering, Vol. 40, Issue 7 https://doi.org/10.1117/1.1383996	journal	July 2001
Three-Dimensional Orientation Microscopy in a Focused Ion Beam–Scanning Electron Microscope: A New Dimension of Microstructure Characterization Zaefferer, S.; Wright, S. I.; Raabe, D. Metallurgical and Materials Transactions A, Vol. 39, Issue 2 https://doi.org/10.1007/s11661-007-9418-9	journal	January 2008
Sparse MRI: The application of compressed sensing for rapid MR imaging Lustig, Michael; Donoho, David; Pauly, John M. Magnetic Resonance in Medicine, Vol. 58, Issue 6 https://doi.org/10.1002/mrm.21391	journal	January 2007
An Introduction To Compressive Sampling Candes, E. J.; Wakin, M. B. IEEE Signal Processing Magazine, Vol. 25, Issue 2 https://doi.org/10.1109/MSP.2007.914731	journal	March 2008
Stripe and ring artifact removal with combined wavelet--Fourier filtering Münch, B.; Trtik, P.; Marone, F. Optical Society of America (OSA) https://doi.org/10.5167/uzh-27018	text	January 2009
Structured Compressed Sensing: From Theory to Applications Duarte, Marco F.; Eldar, Yonina C. arXiv https://doi.org/10.48550/arxiv.1106.6224	text	January 2011
Removal of Curtaining Effects by a Variational Model with Directional Forward Differences Fitschen, Jan Henrik; Ma, Jianwei; Schuff, Sebastian arXiv https://doi.org/10.48550/arxiv.1507.00112	preprint	January 2015
Robust Uncertainty Principles: Exact Signal Reconstruction from Highly Incomplete Frequency Information Candes, Emmanuel; Romberg, Justin; Tao, Terence arXiv https://doi.org/10.48550/arxiv.math/0409186	preprint	January 2004

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