Seed-skewness algorithm for X-ray diffraction signal detection in time-resolved synchrotron Laue photocrystallography

Abstract

A one‐dimensional seed‐skewness algorithm adapted for X‐ray diffraction signal detection is presented and discussed. The method, primarily designed for photocrystallographic time‐resolved Laue data processing, was shown to work well for the type of data collected at the Advanced Photon Source and European Synchrotron Radiation Facility. Nevertheless, it is also applicable in the case of standard single‐crystal X‐ray diffraction data. The reported algorithm enables reasonable separation of signal from the background in single one‐dimensional data vectors as well as the capability to determine small changes of reflection shapes and intensities resulting from exposure of the sample to laser light. Otherwise, the procedure is objective, and relies only on skewness computation and its subsequent minimization. The new algorithm was proved to yield comparable results to the Kruskal–Wallis test method [Kalinowski, J. A. et al. (2012). J. Synchrotron Rad.19, 637], while the processing takes a similar amount of time. Importantly, in contrast to the Kruskal–Wallis test, the reported seed‐skewness approach does not need redundant input data, which allows for faster data collections and wider applications. Furthermore, as far as the structure refinement is concerned, the reported algorithm leads to the excited‐state geometry closest to the one modelled using the quantum‐mechanics/molecular‐mechanics approach reported previously [Jarzembska, K. N. et al. (2014). Inorg. Chem.53, 10594], when the t and s algorithm parameters are set to the recommended values of 0.2 and 3.0, respectively.

Advances in Diffraction Studies of Light-Induced Transient Species in Molecular Crystals and Selected Complementary Techniques

“…In order to evaluate whether a pixel contains signal in a given frame, a Kruskal-Wallis test is applied recursively. Quite recently an alternative signal-detection method, the so-called seed-skewness algorithm [65][66][67], has been implemented and shown to yield comparable results in terms of extracting weak signal on a frame, while keeping the background filtering procedure at the same level of efficacy [68]. In either case, if a pixel does not contain signal, it is discarded from further processing, and treated as a part of a background mask.…”

Instrument-model refinement in normalized reciprocal-vector space for X-ray Laue diffraction

“…The data for the second compound, Cu(dppe)(dmdpp)PF 6 (dmdpp = 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline) (monoclinic space group P2 1 =n), were collected at the ID09 beamline (Wulff et al, 2002) at the European Synchrotron Radiation Facility (ESRF). Both data sets were initially integrated using our new one-dimensional seed-skewness method (Szarejko et al, 2020), which resulted in a set of reflection intensities and positions. All data sets examined in this study are summarized in Table 1, including their abbreviations used hereafter.…”

“…This constitutes a major improvement in the small-molecule X-ray Laue diffraction processing pipeline. The algorithm is implemented in our new Laue data processing software (Szarejko et al, 2020;Jarzembska et al, 2019). The current version of the program (including the source code), interfaced also with the LaueUtil suite (Kalinowski et al, 2011(Kalinowski et al, , 2012, is available from the authors upon request (the program code will be available publicly open source shortly).…”

On the Nature of Luminescence Thermochromism of Multinuclear Copper(I) Benzoate Complexes in the Crystalline State

“…, which are then used to estimate "monochromatic" structure factor amplitudes not spurred by the wavelength dependence present in the original Laue diffraction data. The diffraction spot intensities from the Laue experiment were integrated with our new locally-written software [40], and later indexed by the modified version of the LAUEUTIL software package [41,42]. The resulting intensity ratios were averaged with the SORTAV program [43,44].…”