Liu Jing, Engblom Stefan, Nettelblad Carl
J Opt Soc Am A Opt Image Sci Vis. 2020 Oct 1;37(10):1673-1686. doi: 10.1364/JOSAA.390384.
Modern Flash X-ray diffraction Imaging (FXI) acquires diffraction signals from single biomolecules at a high repetition rate from X-ray Free Electron Lasers (XFELs), easily obtaining millions of 2D diffraction patterns from a single experiment. Due to the stochastic nature of FXI experiments and the massive volumes of data, retrieving 3D electron densities from raw 2D diffraction patterns is a challenging and time-consuming task. We propose a semi-automatic data analysis pipeline for FXI experiments, which includes four steps: hit-finding and preliminary filtering, pattern classification, 3D Fourier reconstruction, and post-analysis. We also include a recently developed bootstrap methodology in the post-analysis step for uncertainty analysis and quality control. To achieve the best possible resolution, we further suggest using background subtraction, signal windowing, and convex optimization techniques when retrieving the Fourier phases in the post-analysis step. As an application example, we quantified the 3D electron structure of the PR772 virus using the proposed data analysis pipeline. The retrieved structure was above the detector edge resolution and clearly showed the pseudo-icosahedral capsid of the PR772.
现代闪光X射线衍射成像（FXI）以高重复率从X射线自由电子激光（XFEL）获取单个生物分子的衍射信号，单次实验就能轻松获得数百万个二维衍射图案。由于FXI实验的随机性和海量数据，从原始二维衍射图案中检索三维电子密度是一项具有挑战性且耗时的任务。我们提出了一种用于FXI实验的半自动数据分析流程，包括四个步骤：命中查找和初步过滤、图案分类、三维傅里叶重建以及后期分析。我们还在后期分析步骤中纳入了一种最近开发的自助法，用于不确定性分析和质量控制。为了获得尽可能高的分辨率，我们进一步建议在后期分析步骤中检索傅里叶相位时使用背景扣除、信号开窗和凸优化技术。作为一个应用示例，我们使用所提出的数据分析流程对PR772病毒的三维电子结构进行了量化。检索到的结构高于探测器边缘分辨率，并清晰显示了PR772的准二十面体衣壳。
