Laue-DIALS:多色 X 射线衍射数据开源软件。

IF 2.3 2区 物理与天体物理 Q3 CHEMISTRY, PHYSICAL
Structural Dynamics-Us Pub Date : 2024-10-02 eCollection Date: 2024-09-01 DOI:10.1063/4.0000265
Rick A Hewitt, Kevin M Dalton, Derek A Mendez, Harrison K Wang, Margaret A Klureza, Dennis E Brookner, Jack B Greisman, David McDonagh, Vukica Šrajer, Nicholas K Sauter, Aaron S Brewster, Doeke R Hekstra
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引用次数: 0

摘要

大多数 X 射线源本身都具有多色性。多色("粉色")X 射线是进行衍射实验的有效方法,因为可以使用更多的光子,而且在曝光过程中无需旋转样品即可探测大面积的倒易空间--这是时间分辨应用的理想条件。然而,此类数据的分析非常复杂,大多数 X 射线设备都会丢弃大于 99% 的 X 射线光子,以获取单色数据。分析多色衍射数据的主要挑战包括晶格搜索、索引和波长分配、根据波长效应校正测量强度以及谐波解卷积。最近,我们介绍了一种名为 Careless 的算法,该算法可以执行谐波解卷积,并在获得综合衍射强度和分配波长时,根据波长变化校正测量强度。在此,我们介绍 Laue-DIALS,这是一个开源软件管道,可对多色衍射数据进行索引和整合。Laue-DIALS 基于 dxtbx 工具箱,该工具箱支持常用于处理单色数据的 DIALS 软件。因此,Laue-DIALS 具有许多相同的优势:开源、模块化和可扩展的架构,为未来的发展提供了坚实的基础。我们展示的基准测试结果表明,Laue-DIALS 与 Careless 一起,为多色衍射数据分析提供了一种合适的方法,包括时间分辨应用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Laue-DIALS: Open-source software for polychromatic x-ray diffraction data.

Most x-ray sources are inherently polychromatic. Polychromatic ("pink") x-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during exposure-ideal conditions for time-resolved applications. Analysis of such data is complicated, however, causing most x-ray facilities to discard >99% of x-ray photons to obtain monochromatic data. Key challenges in analyzing polychromatic diffraction data include lattice searching, indexing and wavelength assignment, correction of measured intensities for wavelength-dependent effects, and deconvolution of harmonics. We recently described an algorithm, Careless, that can perform harmonic deconvolution and correct measured intensities for variation in wavelength when presented with integrated diffraction intensities and assigned wavelengths. Here, we present Laue-DIALS, an open-source software pipeline that indexes and integrates polychromatic diffraction data. Laue-DIALS is based on the dxtbx toolbox, which supports the DIALS software commonly used to process monochromatic data. As such, Laue-DIALS provides many of the same advantages: an open-source, modular, and extensible architecture, providing a robust basis for future development. We present benchmark results showing that Laue-DIALS, together with Careless, provides a suitable approach to the analysis of polychromatic diffraction data, including for time-resolved applications.

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来源期刊
Structural Dynamics-Us
Structural Dynamics-Us CHEMISTRY, PHYSICALPHYSICS, ATOMIC, MOLECU-PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
CiteScore
5.50
自引率
3.60%
发文量
24
审稿时长
16 weeks
期刊介绍: Structural Dynamics focuses on the recent developments in experimental and theoretical methods and techniques that allow a visualization of the electronic and geometric structural changes in real time of chemical, biological, and condensed-matter systems. The community of scientists and engineers working on structural dynamics in such diverse systems often use similar instrumentation and methods. The journal welcomes articles dealing with fundamental problems of electronic and structural dynamics that are tackled by new methods, such as: Time-resolved X-ray and electron diffraction and scattering, Coherent diffractive imaging, Time-resolved X-ray spectroscopies (absorption, emission, resonant inelastic scattering, etc.), Time-resolved electron energy loss spectroscopy (EELS) and electron microscopy, Time-resolved photoelectron spectroscopies (UPS, XPS, ARPES, etc.), Multidimensional spectroscopies in the infrared, the visible and the ultraviolet, Nonlinear spectroscopies in the VUV, the soft and the hard X-ray domains, Theory and computational methods and algorithms for the analysis and description of structuraldynamics and their associated experimental signals. These new methods are enabled by new instrumentation, such as: X-ray free electron lasers, which provide flux, coherence, and time resolution, New sources of ultrashort electron pulses, New sources of ultrashort vacuum ultraviolet (VUV) to hard X-ray pulses, such as high-harmonic generation (HHG) sources or plasma-based sources, New sources of ultrashort infrared and terahertz (THz) radiation, New detectors for X-rays and electrons, New sample handling and delivery schemes, New computational capabilities.
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