Structure determination using high-order spatial correlations in single-particle X-ray scattering
Single-particle imaging using X-ray free-electron lasers (XFELs) is a promising technique for observing nanoscale biological samples under near-physiological conditions. However, as the sample's orientation in each diffraction pattern is unknown, advanced algorithms are required to reconstruct...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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International Union of Crystallography
2024-01-01
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| Series: | IUCrJ |
| Subjects: | |
| Online Access: | http://scripts.iucr.org/cgi-bin/paper?S2052252523009831 |
| _version_ | 1797360692362215424 |
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| author | Wenyang Zhao Osamu Miyashita Miki Nakano Florence Tama |
| author_facet | Wenyang Zhao Osamu Miyashita Miki Nakano Florence Tama |
| author_sort | Wenyang Zhao |
| collection | DOAJ |
| description | Single-particle imaging using X-ray free-electron lasers (XFELs) is a promising technique for observing nanoscale biological samples under near-physiological conditions. However, as the sample's orientation in each diffraction pattern is unknown, advanced algorithms are required to reconstruct the 3D diffraction intensity volume and subsequently the sample's density model. While most approaches perform 3D reconstruction via determining the orientation of each diffraction pattern, a correlation-based approach utilizes the averaged spatial correlations of diffraction intensities over all patterns, making it well suited for processing experimental data with a poor signal-to-noise ratio of individual patterns. Here, a method is proposed to determine the 3D structure of a sample by analyzing the double, triple and quadruple spatial correlations in diffraction patterns. This ab initio method can reconstruct the basic shape of an irregular unsymmetric 3D sample without requiring any prior knowledge of the sample. The impact of background and noise on correlations is investigated and corrected to ensure the success of reconstruction under simulated experimental conditions. Additionally, the feasibility of using the correlation-based approach to process incomplete partial diffraction patterns is demonstrated. The proposed method is a variable addition to existing algorithms for 3D reconstruction and will further promote the development and adoption of XFEL single-particle imaging techniques. |
| first_indexed | 2024-03-08T15:42:11Z |
| format | Article |
| id | doaj.art-e5fe81cc97df4c28b7cd20f100d36a5b |
| institution | Directory Open Access Journal |
| issn | 2052-2525 |
| language | English |
| last_indexed | 2024-03-08T15:42:11Z |
| publishDate | 2024-01-01 |
| publisher | International Union of Crystallography |
| record_format | Article |
| series | IUCrJ |
| spelling | doaj.art-e5fe81cc97df4c28b7cd20f100d36a5b2024-01-09T14:58:15ZengInternational Union of CrystallographyIUCrJ2052-25252024-01-011119210810.1107/S2052252523009831zf5022Structure determination using high-order spatial correlations in single-particle X-ray scatteringWenyang Zhao0Osamu Miyashita1Miki Nakano2Florence Tama3Computational Structural Biology Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, JapanComputational Structural Biology Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, JapanComputational Structural Biology Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, JapanComputational Structural Biology Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, JapanSingle-particle imaging using X-ray free-electron lasers (XFELs) is a promising technique for observing nanoscale biological samples under near-physiological conditions. However, as the sample's orientation in each diffraction pattern is unknown, advanced algorithms are required to reconstruct the 3D diffraction intensity volume and subsequently the sample's density model. While most approaches perform 3D reconstruction via determining the orientation of each diffraction pattern, a correlation-based approach utilizes the averaged spatial correlations of diffraction intensities over all patterns, making it well suited for processing experimental data with a poor signal-to-noise ratio of individual patterns. Here, a method is proposed to determine the 3D structure of a sample by analyzing the double, triple and quadruple spatial correlations in diffraction patterns. This ab initio method can reconstruct the basic shape of an irregular unsymmetric 3D sample without requiring any prior knowledge of the sample. The impact of background and noise on correlations is investigated and corrected to ensure the success of reconstruction under simulated experimental conditions. Additionally, the feasibility of using the correlation-based approach to process incomplete partial diffraction patterns is demonstrated. The proposed method is a variable addition to existing algorithms for 3D reconstruction and will further promote the development and adoption of XFEL single-particle imaging techniques.http://scripts.iucr.org/cgi-bin/paper?S20522525230098313d reconstructionssingle-particle imagingx-ray free-electron lasersspatial correlationsstructure determinationsingle-particle x-ray scatteringdiffraction patternsdetector noise |
| spellingShingle | Wenyang Zhao Osamu Miyashita Miki Nakano Florence Tama Structure determination using high-order spatial correlations in single-particle X-ray scattering IUCrJ 3d reconstructions single-particle imaging x-ray free-electron lasers spatial correlations structure determination single-particle x-ray scattering diffraction patterns detector noise |
| title | Structure determination using high-order spatial correlations in single-particle X-ray scattering |
| title_full | Structure determination using high-order spatial correlations in single-particle X-ray scattering |
| title_fullStr | Structure determination using high-order spatial correlations in single-particle X-ray scattering |
| title_full_unstemmed | Structure determination using high-order spatial correlations in single-particle X-ray scattering |
| title_short | Structure determination using high-order spatial correlations in single-particle X-ray scattering |
| title_sort | structure determination using high order spatial correlations in single particle x ray scattering |
| topic | 3d reconstructions single-particle imaging x-ray free-electron lasers spatial correlations structure determination single-particle x-ray scattering diffraction patterns detector noise |
| url | http://scripts.iucr.org/cgi-bin/paper?S2052252523009831 |
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