Cargando…
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...
Autores principales: | , , , , |
---|---|
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 |
_version_ | 1784721803430592512 |
---|---|
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. |
format | Online Article Text |
id | pubmed-9172041 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT assalauovadameli classificationofdiffractionpatternsusingaconvolutionalneuralnetworkinsingleparticleimagingexperimentsperformedatxrayfreeelectronlasers AT ignatenkoalexandr classificationofdiffractionpatternsusingaconvolutionalneuralnetworkinsingleparticleimagingexperimentsperformedatxrayfreeelectronlasers AT isenseefabian classificationofdiffractionpatternsusingaconvolutionalneuralnetworkinsingleparticleimagingexperimentsperformedatxrayfreeelectronlasers AT trofimovadarya classificationofdiffractionpatternsusingaconvolutionalneuralnetworkinsingleparticleimagingexperimentsperformedatxrayfreeelectronlasers AT vartanyantsivana classificationofdiffractionpatternsusingaconvolutionalneuralnetworkinsingleparticleimagingexperimentsperformedatxrayfreeelectronlasers |