Fast and noise-tolerant determination of the center of rotation in tomography

Vacek, Everett; Jacobsen, Chris

doi:10.1107/S1600577521012777

Title: Fast and noise-tolerant determination of the center of rotation in tomography

Journal Article · 18 January 2022 · Journal of Synchrotron Radiation (Online)

DOI: https://doi.org/10.1107/S1600577521012777 · OSTI ID:1841050

Vacek, Everett;

High-quality tomographic reconstruction is not possible without the accurate localization of the center of rotation. Poor localization leads to artifacts in the data and can even cause reconstructions to fail. There are many approaches to solving this problem, some of which involve the collection of full sinograms, or even provisional tomographic reconstructions, in order to determine the center of rotation. Here, a simple method based on the expected symmetry of the Fourier transform of summed projections approximately 180° apart is presented; unlike cross-correlation methods, it requires only a single Fourier transform to compute, and uses mainly low spatial frequency information which is less susceptible to noise. This approach is shown to be fast, and robust against poor signal-to-noise as well as to projection images acquired at angles that are not exactly 180° apart. This rapid method can be useful as a first step in the processing of tomographic data.

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

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

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1841050

Journal Information:: Journal of Synchrotron Radiation (Online), Journal Name: Journal of Synchrotron Radiation (Online) Journal Issue: 2 Vol. 29; ISSN 1600-5775; ISSN JSYRES

Publisher:: International Union of Crystallography (IUCr)Copyright Statement

Country of Publication:: Denmark

Language:: English

References (35)

Modelling the Power Spectra of Natural Images: Statistics and Information van der Schaaf, A.; van Hateren, J. H. Vision Research, Vol. 36, Issue 17 https://doi.org/10.1016/0042-6989(96)00002-8	journal	September 1996
The tuning fork artifact in computerized tomography Shepp, L. A.; Hilal, S. K.; Schulz, R. A. Computer Graphics and Image Processing, Vol. 10, Issue 3 https://doi.org/10.1016/0146-664X(79)90004-2	journal	July 1979
A multi-resolution approach to the 3D reconstruction from an electron microscope tilt series solving the alignment problem without gold particles Dengler, Joachim Ultramicroscopy, Vol. 30, Issue 3 https://doi.org/10.1016/0304-3991(89)90063-6	journal	July 1989
Double-tilt electron tomography Penczek, Pawel; Marko, Michael; Buttle, Karolyn Ultramicroscopy, Vol. 60, Issue 3 https://doi.org/10.1016/0304-3991(95)00078-X	journal	October 1995
The relevance of dose-fractionation in tomography of radiation-sensitive specimens McEwen, Bruce F.; Downing, Kenneth H.; Glaeser, Robert M. Ultramicroscopy, Vol. 60, Issue 3 https://doi.org/10.1016/0304-3991(95)00082-8	journal	October 1995
Alignment of electron tomographic series by correlation without the use of gold particles Owen, Cameron H.; Landis, William J. Ultramicroscopy, Vol. 63, Issue 1 https://doi.org/10.1016/0304-3991(95)00154-9	journal	April 1996
Tilted view reconstruction in optical microscopy. Three-dimensional reconstruction of Drosophila melanogaster embryo nuclei Shaw, P. J.; Agard, D. A.; Hiraoka, Y. Biophysical Journal, Vol. 55, Issue 1 https://doi.org/10.1016/S0006-3495(89)82783-3	journal	January 1989
Automatic alignment and reconstruction of images for soft X-ray tomography Parkinson, Dilworth Y.; Knoechel, Christian; Yang, Chao Journal of Structural Biology, Vol. 177, Issue 2 https://doi.org/10.1016/j.jsb.2011.11.027	journal	February 2012
GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging Pryor, Alan; Yang, Yongsoo; Rana, Arjun Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-09847-1	journal	September 2017
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
Correction of center of rotation and projection angle in synchrotron X-ray computed tomography Cheng, Chang-Chieh; Ching, Yu-Tai; Ko, Pai-Hung Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-28149-8	journal	June 2018
Correction of artefacts in optical projection tomography Walls, Johnathon R.; Sled, John G.; Sharpe, James Physics in Medicine and Biology, Vol. 50, Issue 19 https://doi.org/10.1088/0031-9155/50/19/015	journal	September 2005
TomoBank: a tomographic data repository for computational x-ray science De Carlo, Francesco; Gürsoy, Doğa; Ching, Daniel J. Measurement Science and Technology, Vol. 29, Issue 3 https://doi.org/10.1088/1361-6501/aa9c19	journal	February 2018
The Reconstruction of a Three-Dimensional Structure from Projections and its Application to Electron Microscopy Crowther, R. A.; DeRosier, D. J.; Klug, A. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 317, Issue 1530 https://doi.org/10.1098/rspa.1970.0119	journal	June 1970
Alignment of low-dose X-ray fluorescence tomography images using differential phase contrast Hong, Young Pyo; Gleber, Sophie-Charlotte; O'Halloran, Thomas V. Journal of Synchrotron Radiation, Vol. 21, Issue 1 https://doi.org/10.1107/S1600577513029512	journal	December 2013
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 convolutional neural network approach to calibrating the rotation axis for X-ray computed tomography Yang, Xiaogang; De Carlo, Francesco; Phatak, Charudatta Journal of Synchrotron Radiation, Vol. 24, Issue 2 https://doi.org/10.1107/S1600577516020117	journal	January 2017
Calculation of the rotational centers in computed tomography sinograms Azevedo, S. G.; Schneberk, D. J.; Fitch, J. P. IEEE Transactions on Nuclear Science, Vol. 37, Issue 4 https://doi.org/10.1109/23.55866	journal	January 1990
On estimating signal-to-noise ratio using the sample correlation coefficient (Corresp.) Bershad, N.; Rockmore, A. IEEE Transactions on Information Theory, Vol. 20, Issue 1 https://doi.org/10.1109/TIT.1974.1055159	journal	January 1974
Reconstruction Algorithm for Fan Beam with a Displaced Center-of-Rotation Gullberg, Grant T.; Crawford, Carl R.; Tsui, Benjamin M. W. IEEE Transactions on Medical Imaging, Vol. 5, Issue 1 https://doi.org/10.1109/TMI.1986.4307735	journal	March 1986
The Fourier reconstruction of a head section Shepp, L. A.; Logan, B. F. IEEE Transactions on Nuclear Science, Vol. 21, Issue 3 https://doi.org/10.1109/TNS.1974.6499235	journal	June 1974
Micro computed tomography: removal of translational stage backlash Hogan, John P.; Gonsalves, Robert A.; Krieger, Allen S. IEEE Transactions on Nuclear Science, Vol. 40, Issue 4 https://doi.org/10.1109/TNS.1993.8526784	journal	August 1993
Spatiotemporal computed tomography of dynamic processes Münch, Beat Optical Engineering, Vol. 50, Issue 12 https://doi.org/10.1117/1.3660298	journal	December 2011
A robust procedure for determination of center of rotation in tomography Brunetti, Antonio; De Carlo, Francesco Optical Science and Technology, the SPIE 49th Annual Meeting, SPIE Proceedings https://doi.org/10.1117/12.560440	conference	October 2004
Measurement of center of rotation for projection in x-ray two-dimensional computed tomography system Li, Baolei; Zhang, Yaojun; Mo, Yang Sixth International Symposium on Precision Engineering Measurements and Instrumentation, SPIE Proceedings https://doi.org/10.1117/12.885217	conference	December 2010
Novel Properties Of The Fourier Decomposition Of The Sinogram Edholm, Paul R.; Lewitt, Robert M.; Lindholm, Bernt Physics and Engineering of Computerized Multidimensional Imaging and Processing, SPIE Proceedings https://doi.org/10.1117/12.966672	conference	April 1988
Color and spatial structure in natural scenes Burton, G. J.; Moorhead, Ian R. Applied Optics, Vol. 26, Issue 1 https://doi.org/10.1364/AO.26.000157	journal	January 1987
Correction for specimen movement and rotation errors for in-vivo Optical Projection Tomography Birk, Udo Jochen; Rieckher, Matthias; Konstantinides, Nikos Biomedical Optics Express, Vol. 1, Issue 1 https://doi.org/10.1364/BOE.1.000087	journal	January 2010
Automated determination of the center of rotation in tomography data Donath, Tilman; Beckmann, Felix; Schreyer, Andreas Journal of the Optical Society of America A, Vol. 23, Issue 5 https://doi.org/10.1364/JOSAA.23.001048	journal	January 2006
Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy Huang, Xiaojing; Miao, Huijie; Steinbrener, Jan Optics Express, Vol. 17, Issue 16 https://doi.org/10.1364/OE.17.013541	journal	January 2009
Reliable method for calculating the center of rotation in parallel-beam tomography Vo, Nghia T.; Drakopoulos, Michael; Atwood, Robert C. Optics Express, Vol. 22, Issue 16 https://doi.org/10.1364/OE.22.019078	journal	January 2014
Efficient subpixel image registration algorithms Guizar-Sicairos, Manuel; Thurman, Samuel T.; Fienup, James R. Optics Letters, Vol. 33, Issue 2 https://doi.org/10.1364/OL.33.000156	journal	January 2008
Influence of Electron Noise on Three-dimensional Image Reconstruction Hegerl, R.; Hoppe, W. Zeitschrift für Naturforschung A, Vol. 31, Issue 12 https://doi.org/10.1515/zna-1976-1241	journal	December 1976
An Algorithm for the Evaluation of Finite Trigonometric Series Goertzel, Gerald The American Mathematical Monthly, Vol. 65, Issue 1 https://doi.org/10.2307/2310304	journal	January 1958
scikit-image: image processing in Python van der Walt, Stéfan; Schönberger, Johannes L.; Nunez-Iglesias, Juan PeerJ, Vol. 2 https://doi.org/10.7717/peerj.453	journal	January 2014

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73 NUCLEAR PHYSICS AND RADIATION PHYSICS
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tomography alignment
x-ray tomography

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