**5** Publications

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Acta Crystallogr D Struct Biol 2021 Apr 30;77(Pt 4):447-456. Epub 2021 Mar 30.

Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, United Kingdom.

In this paper, several approaches to be used to accelerate algorithms for fitting an atomic structure into a given 3D density map determined by cryo-EM are discussed. Rotation and translation of the atomic structure to find similarity scores are used and implemented with discrete Fourier transforms. Several rotations can be combined into groups to accelerate processing. The finite resolution of experimental and simulated maps allows a reduction in the number of rotations and translations needed in order to estimate similarity-score values.

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http://dx.doi.org/10.1107/S2059798321001212 | DOI Listing |

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8025886 | PMC |

April 2021

J Synchrotron Radiat 2016 11 17;23(Pt 6):1447-1461. Epub 2016 Oct 17.

Henry Moseley X-ray Imaging Facility, Photon Science Institute, Alan Turing Building, The University of Manchester, Manchester M13 9PL, UK.

Ring artefacts are the most disturbing artefacts when reconstructed volumes are segmented. A lot of effort has already been put into better X-ray optics, scintillators and detectors in order to minimize the appearance of these artefacts. However, additional processing is often required after standard flat-field correction. Several methods exist to suppress artefacts. One group of methods is based on minimization of the Tikhonov functional. An analytical formula for processing of a single sinogram was developed. In this paper a similar approach is used and a formula for processing two-dimensional projections is found. Thus suppression of ring artefacts is organized as a two-dimensional convolution of `averaged' projections with a given filter. Several approaches are discussed in order to find elements of the filter in a faster and accurate way. Examples of experimental datasets processed by the proposed method are considered.

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http://dx.doi.org/10.1107/S160057751601479X | DOI Listing |

November 2016

J Synchrotron Radiat 2011 May 2;18(Pt 3):427-35. Epub 2011 Apr 2.

Department of Mathematics, Faculty of Physics, Moscow State University, Leninskie Gory, Moscow 119991, Russia.

There are many objects for which the attenuation varies significantly as they are rotated during computerized X-ray tomography, for example plate samples. This can lead to significant ring artefacts in the subsequent tomographic reconstructions. In this paper a new method is presented that can successfully suppress such ring artefacts and is applicable to both parallel and cone-beam geometries. Rapid correction is achieved via an analytical formula which involves only a matrix-vector multiplication, for which the matrix is known and depends on a regularization parameter. The efficacy of the method is demonstrated for a paleontological sample (calcified shark cartilage) and a carbon-carbon composite/Ti-SiC metal matrix composite test sample.

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http://dx.doi.org/10.1107/S0909049511006005 | DOI Listing |

May 2011

J Synchrotron Radiat 2010 Sep 22;17(5):689-99. Epub 2010 Jul 22.

Henry Moseley X-ray Imaging Facility, School of Materials, University of Manchester, Grosvenor Street, Manchester M13 9PL, UK.

The first processing step in synchrotron-based micro-tomography is the normalization of the projection images against the background, also referred to as a white field. Owing to time-dependent variations in illumination and defects in detection sensitivity, the white field is different from the projection background. In this case standard normalization methods introduce ring and wave artefacts into the resulting three-dimensional reconstruction. In this paper the authors propose a new adaptive technique accounting for these variations and allowing one to obtain cleaner normalized data and to suppress ring and wave artefacts. The background is modelled by the product of two time-dependent terms representing the illumination and detection stages. These terms are written as unknown functions, one scaled and shifted along a fixed direction (describing the illumination term) and one translated by an unknown two-dimensional vector (describing the detection term). The proposed method is applied to two sets (a stem Salix variegata and a zebrafish Danio rerio) acquired at the parallel beam of the micro-tomography station 2-BM at the Advanced Photon Source showing significant reductions in both ring and wave artefacts. In principle the method could be used to correct for time-dependent phenomena that affect other tomographic imaging geometries such as cone beam laboratory X-ray computed tomography.

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http://dx.doi.org/10.1107/S0909049510024908 | DOI Listing |

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924793 | PMC |

September 2010

J Synchrotron Radiat 2010 Jul 14;17(4):540-9. Epub 2010 May 14.

Department of Mathematics, Faculty of Physics, Moscow State University, Leninskie Gory, Moscow, Russia.

Ring artefacts in X-ray computerized tomography reconstructions are considered. The authors propose a ring artefact removal method based on a priori information regarding the sinogram including smoothness along the horizontal coordinate, symmetry of the first and the final rows and consideration of small perturbations during acquisition. The method does not require prior reconstruction of the original or corrected sinograms. Its numerical implementation is based on quadratic programming. Its efficacy is examined with regard to experimental data sets collected on graphite and bone.

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http://dx.doi.org/10.1107/S0909049510010964 | DOI Listing |

July 2010