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Free log-likelihood as an unbiased metric for coherent diffraction imaging

Coherent Diffraction Imaging (CDI), a technique where an object is reconstructed from a single (2D or 3D) diffraction pattern, recovers the lost diffraction phases without a priori knowledge of the extent (support) of the object. The uncertainty of the object support can lead to over-fitting and pre...

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Autores principales: Favre-Nicolin, Vincent, Leake, Steven, Chushkin, Yuriy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7021796/
https://www.ncbi.nlm.nih.gov/pubmed/32060293
http://dx.doi.org/10.1038/s41598-020-57561-2
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author Favre-Nicolin, Vincent
Leake, Steven
Chushkin, Yuriy
author_facet Favre-Nicolin, Vincent
Leake, Steven
Chushkin, Yuriy
author_sort Favre-Nicolin, Vincent
collection PubMed
description Coherent Diffraction Imaging (CDI), a technique where an object is reconstructed from a single (2D or 3D) diffraction pattern, recovers the lost diffraction phases without a priori knowledge of the extent (support) of the object. The uncertainty of the object support can lead to over-fitting and prevents an unambiguous metric evaluation of solutions. We propose to use a ‘free’ log-likelihood indicator, where a small percentage of points are masked from the reconstruction algorithms, as an unbiased metric to evaluate the validity of computed solutions, independent of the sample studied. We also show how a set of solutions can be analysed through an eigen-decomposition to yield a better estimate of the real object. Example analysis on experimental data is presented both for a test pattern dataset, and the diffraction pattern from a live cyanobacteria cell. The method allows the validation of reconstructions on a wide range of materials (hard condensed or biological), and should be particularly relevant for 4th generation synchrotrons and X-ray free electron lasers, where large, high-throughput datasets require a method for unsupervised data evaluation.
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spelling pubmed-70217962020-02-24 Free log-likelihood as an unbiased metric for coherent diffraction imaging Favre-Nicolin, Vincent Leake, Steven Chushkin, Yuriy Sci Rep Article Coherent Diffraction Imaging (CDI), a technique where an object is reconstructed from a single (2D or 3D) diffraction pattern, recovers the lost diffraction phases without a priori knowledge of the extent (support) of the object. The uncertainty of the object support can lead to over-fitting and prevents an unambiguous metric evaluation of solutions. We propose to use a ‘free’ log-likelihood indicator, where a small percentage of points are masked from the reconstruction algorithms, as an unbiased metric to evaluate the validity of computed solutions, independent of the sample studied. We also show how a set of solutions can be analysed through an eigen-decomposition to yield a better estimate of the real object. Example analysis on experimental data is presented both for a test pattern dataset, and the diffraction pattern from a live cyanobacteria cell. The method allows the validation of reconstructions on a wide range of materials (hard condensed or biological), and should be particularly relevant for 4th generation synchrotrons and X-ray free electron lasers, where large, high-throughput datasets require a method for unsupervised data evaluation. Nature Publishing Group UK 2020-02-14 /pmc/articles/PMC7021796/ /pubmed/32060293 http://dx.doi.org/10.1038/s41598-020-57561-2 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Favre-Nicolin, Vincent
Leake, Steven
Chushkin, Yuriy
Free log-likelihood as an unbiased metric for coherent diffraction imaging
title Free log-likelihood as an unbiased metric for coherent diffraction imaging
title_full Free log-likelihood as an unbiased metric for coherent diffraction imaging
title_fullStr Free log-likelihood as an unbiased metric for coherent diffraction imaging
title_full_unstemmed Free log-likelihood as an unbiased metric for coherent diffraction imaging
title_short Free log-likelihood as an unbiased metric for coherent diffraction imaging
title_sort free log-likelihood as an unbiased metric for coherent diffraction imaging
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7021796/
https://www.ncbi.nlm.nih.gov/pubmed/32060293
http://dx.doi.org/10.1038/s41598-020-57561-2
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