Alignment methods for nanotomography with deep subpixel accuracy.

As the resolution of X-ray tomography improves, the limited long-term stability and accuracy of nanoimaging tools does not allow computing artifact-free three-dimensional (3D) reconstructions without an additional step of numerical alignment of the measured projections. However, the common iterative alignment methods are significantly more computationally demanding than a simple tomographic reconstruction of the acquired volume. Here, we address this issue and present an alignment toolkit, which exploits methods with deep-subpixel accuracy combined with a multi-resolution scheme. This leads to robust and accurate alignment with significantly reduced computational and memory requirements. The performance of the presented methods is demonstrated on simulated and measured datasets for tomography and also laminography acquisition geometries. A GPU accelerated implementation of our alignment framework is publicly available.

[1]  Manuel Guizar-Sicairos,et al.  Efficient subpixel image registration algorithms. , 2008, Optics letters.

[2]  M. Guizar‐Sicairos,et al.  Ab initio nonrigid X-ray nanotomography , 2019, Nature Communications.

[3]  Jan Sijbers,et al.  Fast Fourier-Based Phase Unwrapping on the Graphics Processing Unit in Real-Time Imaging Applications , 2015, J. Imaging.

[4]  W. Baumeister,et al.  Towards automatic electron tomography. II. Implementation of autofocus and low-dose procedures , 1993 .

[5]  D. Vine,et al.  X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning , 2017, Scientific Reports.

[6]  O. Bunk,et al.  X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution , 2014, Scientific Reports.

[7]  O. Bunk,et al.  Quantitative region-of-interest tomography using variable field of view. , 2018, Optics express.

[8]  Jiang Li,et al.  High-Speed Image Registration Algorithm with Subpixel Accuracy , 2015, IEEE Signal Processing Letters.

[9]  J Frank,et al.  A marker-free alignment method for electron tomography. , 1995, Ultramicroscopy.

[10]  J. Baruchel,et al.  On the implementation of computed laminography using synchrotron radiation. , 2011, The Review of scientific instruments.

[11]  M. Ge,et al.  Multi-slice ptychography with large numerical aperture multilayer Laue lenses , 2018 .

[12]  Chenxi Wei,et al.  Automatic projection image registration for nanoscale X-ray tomographic reconstruction , 2018, Journal of synchrotron radiation.

[13]  Jan Sijbers,et al.  The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography. , 2015, Ultramicroscopy.

[14]  Chao Yang,et al.  Automatic alignment and reconstruction of images for soft X-ray tomography. , 2012, Journal of structural biology.

[15]  M. van Heel,et al.  Fourier shell correlation threshold criteria. , 2005, Journal of structural biology.

[16]  Lukas Helfen,et al.  Efficient Volume Reconstruction for Parallel-Beam Computed Laminography by Filtered Backprojection on Multi-Core Clusters , 2013, IEEE Transactions on Image Processing.

[17]  Kai He,et al.  Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection , 2017, Scientific Reports.

[18]  J. Dengler A multi-resolution approach to the 3D reconstruction from an electron microscope tilt series solving the alignment problem without gold particles , 1989 .

[19]  Jan Sijbers,et al.  Fast and flexible X-ray tomography using the ASTRA toolbox. , 2016, Optics express.

[20]  S. Marchesini,et al.  Chemical composition mapping with nanometre resolution by soft X-ray microscopy , 2014, Nature Photonics.

[21]  O. Bunk,et al.  High-throughput ptychography using Eiger: scanning X-ray nano-imaging of extended regions. , 2014, Optics express.

[22]  J. Miao,et al.  Correlative 3D x-ray fluorescence and ptychographic tomography of frozen-hydrated green algae , 2018, Science Advances.

[23]  Jörg Raabe,et al.  Three-dimensional imaging of integrated circuits with macro- to nanoscale zoom , 2019, Nature Electronics.

[24]  O. Bunk,et al.  Nanostructure surveys of macroscopic specimens by small-angle scattering tensor tomography , 2015, Nature.

[25]  M. Guizar‐Sicairos,et al.  Three-dimensional magnetization structures revealed with X-ray vector nanotomography , 2017, Nature.

[26]  Franz Pfeiffer,et al.  X-ray ptychography , 2017, Nature Photonics.

[27]  David J. Fleet,et al.  Performance of optical flow techniques , 1994, International Journal of Computer Vision.

[28]  Y. Ching,et al.  Image Alignment for Tomography Reconstruction from Synchrotron X-Ray Microscopic Images , 2014, PloS one.

[29]  O. Bunk,et al.  Quantitative interior x-ray nanotomography by a hybrid imaging technique , 2015 .

[30]  J. Rodenburg,et al.  A phase retrieval algorithm for shifting illumination , 2004 .

[31]  F. Noo,et al.  Direct determination of geometric alignment parameters for cone-beam scanners. , 2009, Physics in medicine and biology.

[32]  Chun-Chieh Wang,et al.  Fast Projection Matching for X-ray Tomography , 2017, Scientific Reports.

[33]  M. Stampanoni,et al.  Regridding reconstruction algorithm for real-time tomographic imaging , 2012, Journal of synchrotron radiation.

[34]  F. Pfeiffer,et al.  Six-dimensional real and reciprocal space small-angle X-ray scattering tomography , 2015, Nature.

[35]  F. Beckmann,et al.  Automated determination of the center of rotation in tomography data. , 2006, Journal of the Optical Society of America. A, Optics, image science, and vision.

[36]  R. Guckenberger Determination of a common origin in the micrographs of tilt series in three-dimensional electron microscopy , 1982 .

[37]  C. David,et al.  Towards optimized illumination for high-resolution ptychography. , 2019, Optics express.

[38]  D Ress,et al.  Automatic acquisition of fiducial markers and alignment of images in tilt series for electron tomography. , 1999, Journal of electron microscopy.

[39]  D. DeRosier,et al.  The reconstruction of a three-dimensional structure from projections and its application to electron microscopy , 1970, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.

[40]  David N. Mastronarde,et al.  Automated tilt series alignment and tomographic reconstruction in IMOD. , 2017, Journal of structural biology.

[41]  J. S. Jørgensen,et al.  Automated angular and translational tomographic alignment and application to phase-contrast imaging. , 2017, Journal of the Optical Society of America. A, Optics, image science, and vision.

[42]  O. Bunk,et al.  Ptychographic X-ray computed tomography at the nanoscale , 2010, Nature.

[43]  D A Agard,et al.  Toward fully automated high-resolution electron tomography. , 1996, Journal of structural biology.

[44]  Edward H. Adelson,et al.  PYRAMID METHODS IN IMAGE PROCESSING. , 1984 .

[45]  O. Bunk,et al.  Phase tomography from x-ray coherent diffractive imaging projections. , 2011, Optics express.

[46]  P. Cloetens,et al.  High-resolution three-dimensional imaging of flat objects by synchrotron-radiation computed laminography , 2005 .

[47]  J. Miao,et al.  Electron tomography at 2.4-ångström resolution , 2012, Nature.

[48]  Renmin Han,et al.  A novel fully automatic scheme for fiducial marker-based alignment in electron tomography. , 2015, Journal of structural biology.

[49]  C. Werner,et al.  Satellite radar interferometry: Two-dimensional phase unwrapping , 1988 .

[50]  D. Vine,et al.  Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae , 2015, Proceedings of the National Academy of Sciences.

[51]  Wah Chiu,et al.  GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging , 2017, Scientific Reports.

[52]  Xie Huimin,et al.  Performance of sub-pixel registration algorithms in digital image correlation , 2006 .

[53]  Manuel Guizar-Sicairos,et al.  High-speed tensor tomography: iterative reconstruction tensor tomography (IRTT) algorithm , 2019, Acta crystallographica. Section A, Foundations and advances.