Deep-learning-based image registration for nano-resolution tomographic reconstruction

Fu, Tianyu; Zhang, Kai; Wang, Yan; Li, Jizhou; Zhang, Jin; Yao, Chunxia; He, Qili; Wang, Shanfeng; Huang, Wanxia; Yuan, Qingxi; Pianetta, Piero; Liu, Yijin

doi:10.1107/s1600577521008481

Deep-learning-based image registration for nano-resolution tomographic reconstruction

Journal Article · Mon Sep 13 00:00:00 EDT 2021 · Journal of Synchrotron Radiation (Online)

DOI:https://doi.org/10.1107/s1600577521008481· OSTI ID:1871523

^[1]; ^[2]; ^[2]; ^[3]; Zhang, Jin ^[4]; Yao, Chunxia ^[1]; He, Qili ^[1]; Wang, Shanfeng ^[2]; Huang, Wanxia ^[2]; ^[2]; ^[3]; ^[3]

Chinese Academy of Sciences (CAS), Beijing (China); University of Chinese Academy of Sciences, Beijing (China)
Chinese Academy of Sciences (CAS), Beijing (China)
SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
Chinese Academy of Sciences (CAS), Beijing (China); University of Chinese Academy of Sciences, Beijing (China); SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

Nano-resolution full-field transmission X-ray microscopy has been successfully applied to a wide range of research fields thanks to its capability of non-destructively reconstructing the 3D structure with high resolution. Due to constraints in the practical implementations, the nano-tomography data is often associated with a random image jitter, resulting from imperfections in the hardware setup. Without a proper image registration process prior to the reconstruction, the quality of the result will be compromised. Here a deep-learning-based image jitter correction method is presented, which registers the projective images with high efficiency and accuracy, facilitating a high-quality tomographic reconstruction. This development is demonstrated and validated using synthetic and experimental datasets. We report the method is effective and readily applicable to a broad range of applications. Together with this paper, the source code is published and adoptions and improvements from our colleagues in this field are welcomed.

View Accepted Manuscript (DOE)

Research Organization:: SLAC National Accelerator Laboratory, Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1871523

Journal Information:: Journal of Synchrotron Radiation (Online), Journal Name: Journal of Synchrotron Radiation (Online) Journal Issue: 6 Vol. 28; ISSN 1600-5775

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

References (39)

Fast X‐ray Nanotomography with Sub‐10 nm Resolution as a Powerful Imaging Tool for Nanotechnology and Energy Storage Applications De Andrade, Vincent; Nikitin, Viktor; Wojcik, Michael Advanced Materials, Vol. 33, Issue 21 https://doi.org/10.1002/adma.202008653	journal	April 2021
Quantification of Heterogeneous Degradation in Li‐Ion Batteries Yang, Yang; Xu, Rong; Zhang, Kai Advanced Energy Materials, Vol. 9, Issue 25 https://doi.org/10.1002/aenm.201900674	journal	May 2019
Hard X-ray Nanotomography of Catalytic Solids at Work Gonzalez-Jimenez, Ines D.; Cats, Korneel; Davidian, Thomas Angewandte Chemie International Edition, Vol. 51, Issue 48 https://doi.org/10.1002/anie.201204930	journal	October 2012
Toward Fully Automated High-Resolution Electron Tomography Fung, Jennifer C.; Liu, Weiping; de Ruijter, W. J. Journal of Structural Biology, Vol. 116, Issue 1 https://doi.org/10.1006/jsbi.1996.0029	journal	January 1996
3D elemental sensitive imaging using transmission X-ray microscopy Liu, Yijin; Meirer, Florian; Wang, Junyue Analytical and Bioanalytical Chemistry, Vol. 404, Issue 5 https://doi.org/10.1007/s00216-012-5818-9	journal	February 2012
Micron-scale crack propagation in laser-irradiated enamel and dentine studied with nano-CT Aljdaimi, Abtesam; Devlin, Hugh; Dickinson, Mark Clinical Oral Investigations, Vol. 23, Issue 5 https://doi.org/10.1007/s00784-018-2654-0	journal	October 2018
Cryo X-ray microscopy with high spatial resolution in amplitude and phase contrast Schneider, Gerd Ultramicroscopy, Vol. 75, Issue 2 https://doi.org/10.1016/S0304-3991(98)00054-0	journal	November 1998
Charge Heterogeneity and Surface Chemistry in Polycrystalline Cathode Materials Tian, Chixia; Xu, Yahong; Nordlund, Dennis Joule, Vol. 2, Issue 3 https://doi.org/10.1016/j.joule.2017.12.008	journal	March 2018
A novel fully automatic scheme for fiducial marker-based alignment in electron tomography Han, Renmin; Wang, Liansan; Liu, Zhiyong Journal of Structural Biology, Vol. 192, Issue 3 https://doi.org/10.1016/j.jsb.2015.09.022	journal	December 2015
Automated tilt series alignment and tomographic reconstruction in IMOD Mastronarde, David N.; Held, Susannah R. Journal of Structural Biology, Vol. 197, Issue 2 https://doi.org/10.1016/j.jsb.2016.07.011	journal	February 2017
Chemomechanical interplay of layered cathode materials undergoing fast charging in lithium batteries Xia, Sihao; Mu, Linqin; Xu, Zhengrui Nano Energy, Vol. 53 https://doi.org/10.1016/j.nanoen.2018.09.051	journal	November 2018
Non-destructive characterization of lithium deposition at the Li/separator and Li/carbon matrix interregion by synchrotron X-ray tomography Dong, Kang; Osenberg, Markus; Sun, Fu Nano Energy, Vol. 62 https://doi.org/10.1016/j.nanoen.2019.05.022	journal	August 2019
Combined Computed Nanotomography and Nanoscopic X-ray Fluorescence Imaging of Cobalt Nanoparticles in Caenorhabditis elegans Cagno, Simone; Brede, Dag Anders; Nuyts, Gert Analytical Chemistry, Vol. 89, Issue 21 https://doi.org/10.1021/acs.analchem.7b02554	journal	October 2017
Three-Dimensional Analysis of Particle Distribution on Filter Layers inside N95 Respirators by Deep Learning Lee, Hye Ryoung; Liao, Lei; Xiao, Wang Nano Letters, Vol. 21, Issue 1 https://doi.org/10.1021/acs.nanolett.0c04230	journal	December 2020
Oxygen Release Induced Chemomechanical Breakdown of Layered Cathode Materials Mu, Linqin; Lin, Ruoqian; Xu, Rong Nano Letters, Vol. 18, Issue 5 https://doi.org/10.1021/acs.nanolett.8b01036	journal	April 2018
Soft X-ray microscopy at a spatial resolution better than 15 nm Chao, Weilun; Harteneck, Bruce D.; Liddle, J. Alexander Nature, Vol. 435, Issue 7046 https://doi.org/10.1038/nature03719	journal	June 2005
Synchrotron X-ray tomographic microscopy of fossil embryos Donoghue, Philip C. J.; Bengtson, Stefan; Dong, Xi-ping Nature, Vol. 442, Issue 7103 https://doi.org/10.1038/nature04890	journal	August 2006
Ultra-high aspect ratio high-resolution nanofabrication for hard X-ray diffractive optics Chang, Chieh; Sakdinawat, Anne Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms5243	journal	June 2014
Machine-learning-revealed statistics of the particle-carbon/binder detachment in lithium-ion battery cathodes Jiang, Zhisen; Li, Jizhou; Yang, Yang Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-16233-5	journal	May 2020
Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection Gürsoy, Doğa; Hong, Young P.; He, Kuan Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-12141-9	journal	September 2017
Visualizing percolation and ion transport in hybrid solid electrolytes for Li–metal batteries Zaman, Wahid; Hortance, Nicholas; Dixit, Marm B. Journal of Materials Chemistry A, Vol. 7, Issue 41 https://doi.org/10.1039/C9TA05118J	journal	January 2019
Applications of Hard X‐ray Full‐Field Transmission X‐ray Microscopy at SSRL Liu, Y.; Andrews, J. C.; Meirer, F. THE 10TH INTERNATIONAL CONFERENCE ON X‐RAY MICROSCOPY, AIP Conference Proceedings https://doi.org/10.1063/1.3625377	conference	January 2011
Efficient Removal of Impulse Noise from Highly Corrupted Digital Images by a Simple Neuro-Fuzzy Operator Yüksel, M. Emin; Baştürk, Alper AEU - International Journal of Electronics and Communications, Vol. 57, Issue 3 https://doi.org/10.1078/1434-8411-54100164	journal	January 2003
A High Resolution, Hard X-ray Bio-imaging Facility at SSRL Andrews, J. C.; Brennan, S.; Patty, C. Synchrotron Radiation News, Vol. 21, Issue 3 https://doi.org/10.1080/08940880802123043	journal	June 2008
Microscopy Instrumentation and Nanopositioning at NSLS-II: Current Status and Future Directions Nazaretski, E.; Xu, W.; Yan, H. Synchrotron Radiation News, Vol. 31, Issue 5 https://doi.org/10.1080/08940886.2018.1506233	journal	September 2018
Full-field transmission x-ray microscopy for bio-imaging Andrews, J. C.; Brennan, S.; Liu, Y. Journal of Physics: Conference Series, Vol. 186 https://doi.org/10.1088/1742-6596/186/1/012081	journal	September 2009
Automatic acquisition of fiducial markers and alignment of images in tilt series for electron tomography Ress, D.; Harlow, M. L.; Schwarz, M. Journal of Electron Microscopy, Vol. 48, Issue 3 https://doi.org/10.1093/oxfordjournals.jmicro.a023679	journal	January 1999
A 30 nm-resolution hard X-ray microscope with X-ray fluorescence mapping capability at BSRF Yuan, Qingxi; Zhang, Kai; Hong, Youli Journal of Synchrotron Radiation, Vol. 19, Issue 6 https://doi.org/10.1107/S0909049512032852	journal	September 2012
TomoPy: a framework for the analysis of synchrotron tomographic data Gürsoy, Dogˇa; De Carlo, Francesco; Xiao, Xianghui Journal of Synchrotron Radiation, Vol. 21, Issue 5 https://doi.org/10.1107/S1600577514013939	journal	August 2014
A high-precision instrument for mapping of rotational errors in rotary stages Xu, Weihe; Lauer, Kenneth; Chu, Yong Journal of Synchrotron Radiation, Vol. 21, Issue 6 https://doi.org/10.1107/S160057751401618X	journal	October 2014
Automatic projection image registration for nanoscale X-ray tomographic reconstruction Yu, Haiyan; Xia, Sihao; Wei, Chenxi Journal of Synchrotron Radiation, Vol. 25, Issue 6 https://doi.org/10.1107/S1600577518013929	journal	October 2018
Automatic 3D image registration for nano-resolution chemical mapping using synchrotron spectro-tomography Zhang, Jin; Hu, Jun; Jiang, Zhisen Journal of Synchrotron Radiation, Vol. 28, Issue 1 https://doi.org/10.1107/S1600577520014691	journal	January 2021
Distributed Optimization for Nonrigid Nano-Tomography Nikitin, Viktor; De Andrade, Vincent; Slyamov, Azat IEEE Transactions on Computational Imaging, Vol. 7 https://doi.org/10.1109/TCI.2021.3060915	journal	January 2021
Adaptive Type-2 Fuzzy Approach for Filtering Salt and Pepper Noise in Grayscale Images Singh, Vikas; Dev, Raghav; Dhar, Narendra K. IEEE Transactions on Fuzzy Systems, Vol. 26, Issue 5 https://doi.org/10.1109/TFUZZ.2018.2805289	journal	October 2018
Electron microscope tomography: transcription in three dimensions Olins, D.; Olins, A.; Levy, H. Science, Vol. 220, Issue 4596 https://doi.org/10.1126/science.6836293	journal	April 1983
ImageNet classification with deep convolutional neural networks Krizhevsky, Alex; Sutskever, Ilya; Hinton, Geoffrey E. Communications of the ACM, Vol. 60, Issue 6 https://doi.org/10.1145/3065386	journal	May 2017
Backpropagation Applied to Handwritten Zip Code Recognition LeCun, Y.; Boser, B.; Denker, J. S. Neural Computation, Vol. 1, Issue 4 https://doi.org/10.1162/neco.1989.1.4.541	journal	December 1989
Alignment methods for nanotomography with deep subpixel accuracy Odstrčil, Michal; Holler, Mirko; Raabe, Jörg Optics Express, Vol. 27, Issue 25 https://doi.org/10.1364/OE.27.036637	journal	January 2019
Image Alignment for Tomography Reconstruction from Synchrotron X-Ray Microscopic Images Cheng, Chang-Chieh; Chien, Chia-Chi; Chen, Hsiang-Hsin PLoS ONE, Vol. 9, Issue 1 https://doi.org/10.1371/journal.pone.0084675	journal	January 2014

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Automatic projection image registration for nanoscale X-ray tomographic reconstruction

Journal Article · Wed Oct 31 20:00:00 EDT 2018 · Journal of Synchrotron Radiation (Online) · OSTI ID:1476346

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73 NUCLEAR PHYSICS AND RADIATION PHYSICS
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image registration
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Deep-learning-based image registration for nano-resolution tomographic reconstruction

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