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Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasers

Single particle imaging (SPI) at X-ray free-electron lasers is particularly well suited to determining the 3D structure of particles at room temperature. For a successful reconstruction, diffraction patterns originating from a single hit must be isolated from a large number of acquired patterns. It...

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Autores principales: Assalauova, Dameli, Ignatenko, Alexandr, Isensee, Fabian, Trofimova, Darya, Vartanyants, Ivan A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9172041/
https://www.ncbi.nlm.nih.gov/pubmed/35719305
http://dx.doi.org/10.1107/S1600576722002667
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author Assalauova, Dameli
Ignatenko, Alexandr
Isensee, Fabian
Trofimova, Darya
Vartanyants, Ivan A.
author_facet Assalauova, Dameli
Ignatenko, Alexandr
Isensee, Fabian
Trofimova, Darya
Vartanyants, Ivan A.
author_sort Assalauova, Dameli
collection PubMed
description Single particle imaging (SPI) at X-ray free-electron lasers is particularly well suited to determining the 3D structure of particles at room temperature. For a successful reconstruction, diffraction patterns originating from a single hit must be isolated from a large number of acquired patterns. It is proposed that this task could be formulated as an image-classification problem and solved using convolutional neural network (CNN) architectures. Two CNN configurations are developed: one that maximizes the F1 score and one that emphasizes high recall. The CNNs are also combined with expectation-maximization (EM) selection as well as size filtering. It is observed that the CNN selections have lower contrast in power spectral density functions relative to the EM selection used in previous work. However, the reconstruction of the CNN-based selections gives similar results. Introducing CNNs into SPI experiments allows the reconstruction pipeline to be streamlined, enables researchers to classify patterns on the fly, and, as a consequence, enables them to tightly control the duration of their experiments. Incorporating non-standard artificial-intelligence-based solutions into an existing SPI analysis workflow may be beneficial for the future development of SPI experiments.
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spelling pubmed-91720412022-06-17 Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasers Assalauova, Dameli Ignatenko, Alexandr Isensee, Fabian Trofimova, Darya Vartanyants, Ivan A. J Appl Crystallogr Research Papers Single particle imaging (SPI) at X-ray free-electron lasers is particularly well suited to determining the 3D structure of particles at room temperature. For a successful reconstruction, diffraction patterns originating from a single hit must be isolated from a large number of acquired patterns. It is proposed that this task could be formulated as an image-classification problem and solved using convolutional neural network (CNN) architectures. Two CNN configurations are developed: one that maximizes the F1 score and one that emphasizes high recall. The CNNs are also combined with expectation-maximization (EM) selection as well as size filtering. It is observed that the CNN selections have lower contrast in power spectral density functions relative to the EM selection used in previous work. However, the reconstruction of the CNN-based selections gives similar results. Introducing CNNs into SPI experiments allows the reconstruction pipeline to be streamlined, enables researchers to classify patterns on the fly, and, as a consequence, enables them to tightly control the duration of their experiments. Incorporating non-standard artificial-intelligence-based solutions into an existing SPI analysis workflow may be beneficial for the future development of SPI experiments. International Union of Crystallography 2022-04-22 /pmc/articles/PMC9172041/ /pubmed/35719305 http://dx.doi.org/10.1107/S1600576722002667 Text en © Dameli Assalauova et al. 2022 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Research Papers
Assalauova, Dameli
Ignatenko, Alexandr
Isensee, Fabian
Trofimova, Darya
Vartanyants, Ivan A.
Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasers
title Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasers
title_full Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasers
title_fullStr Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasers
title_full_unstemmed Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasers
title_short Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasers
title_sort classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at x-ray free-electron lasers
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9172041/
https://www.ncbi.nlm.nih.gov/pubmed/35719305
http://dx.doi.org/10.1107/S1600576722002667
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