{"title":"Structure determination using high-order spatial correlations in single-particle X-ray scattering","authors":"Wenyang Zhao , Osamu Miyashita , Miki Nakano , Florence Tama , F. Maia (Editor)","doi":"10.1107/S2052252523009831","DOIUrl":null,"url":null,"abstract":"<div><p>A method is described for determining the 3D structure of a sample from X-ray free-electron laser single-particle diffraction patterns by analyzing different orders of spatial correlations of diffraction intensities.</p></div><div><p>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 <em>ab initio</em> 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.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 1","pages":"Pages 92-108"},"PeriodicalIF":2.9000,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833384/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"IUCrJ","FirstCategoryId":"88","ListUrlMain":"https://www.sciencedirect.com/org/science/article/pii/S2052252524000149","RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
Abstract
A method is described for determining the 3D structure of a sample from X-ray free-electron laser single-particle diffraction patterns by analyzing different orders of spatial correlations of diffraction intensities.
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.
利用 X 射线自由电子激光器(XFEL)进行单粒子成像是在接近生理条件下观察纳米级生物样品的一项前景广阔的技术。然而,由于样品在每个衍射图样中的方向是未知的,因此需要先进的算法来重建三维衍射强度体积,进而重建样品的密度模型。大多数方法通过确定每个衍射图样的方向来进行三维重建,而基于相关性的方法则利用所有衍射图样衍射强度的平均空间相关性,因此非常适合处理单个衍射图样信噪比较差的实验数据。本文提出了一种通过分析衍射图样中的双倍、三倍和四倍空间相关性来确定样品三维结构的方法。这种从头开始的方法可以重建不规则非对称三维样品的基本形状,而不需要任何关于样品的先验知识。研究并修正了背景和噪声对相关性的影响,以确保在模拟实验条件下重建的成功。此外,还证明了使用基于相关性的方法处理不完整部分衍射图样的可行性。所提出的方法是对现有三维重建算法的有益补充,将进一步推动 XFEL 单粒子成像技术的发展和应用。
期刊介绍:
IUCrJ is a new fully open-access peer-reviewed journal from the International Union of Crystallography (IUCr).
The journal will publish high-profile articles on all aspects of the sciences and technologies supported by the IUCr via its commissions, including emerging fields where structural results underpin the science reported in the article. Our aim is to make IUCrJ the natural home for high-quality structural science results. Chemists, biologists, physicists and material scientists will be actively encouraged to report their structural studies in IUCrJ.