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StreamSAXS: a Python-based workflow platform for processing streaming SAXS/WAXS data. StreamSAXS：基于 Python 的工作流平台，用于处理流 SAXS/WAXS 数据。
IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2024-09-01 Epub Date: 2024-07-15 DOI: 10.1107/S1600577524005149
Jiayi Wang, Zheng Dong, Yi Zhang, Wenqiang Hua, Zudeng Wang, Huilong Guo, Yiming Yang, Xiaoxue Bi
{"title":"StreamSAXS: a Python-based workflow platform for processing streaming SAXS/WAXS data.","authors":"Jiayi Wang, Zheng Dong, Yi Zhang, Wenqiang Hua, Zudeng Wang, Huilong Guo, Yiming Yang, Xiaoxue Bi","doi":"10.1107/S1600577524005149","DOIUrl":"10.1107/S1600577524005149","url":null,"abstract":"<p><p>StreamSAXS is a Python-based small- and wide-angle X-ray scattering (SAXS/WAXS) data analysis workflow platform with graphical user interface (GUI). It aims to provide an interactive and user-friendly tool for analysis of both batch data files and real-time data streams. Users can easily create customizable workflows through the GUI to meet their specific needs. One characteristic of StreamSAXS is its plug-in framework, which enables developers to extend the built-in workflow tasks. Another feature is the support for both already acquired and real-time data sources, allowing StreamSAXS to function as an offline analysis platform or be integrated into large-scale acquisition systems for end-to-end data management. This paper presents the core design of StreamSAXS and provides user cases demonstrating its utilization for SAXS/WAXS data analysis in offline and online scenarios.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Spexwavepy: an open-source Python package for X-ray wavefront sensing using speckle-based techniques. Spexwavepy：使用基于斑点的技术进行 X 射线波前传感的开源 Python 软件包。
IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2024-09-01 Epub Date: 2024-07-30 DOI: 10.1107/S1600577524005861
Lingfei Hu, Hongchang Wang, Kawal Sawhney
{"title":"Spexwavepy: an open-source Python package for X-ray wavefront sensing using speckle-based techniques.","authors":"Lingfei Hu, Hongchang Wang, Kawal Sawhney","doi":"10.1107/S1600577524005861","DOIUrl":"10.1107/S1600577524005861","url":null,"abstract":"<p><p>In situ wavefront sensing plays a critical role in the delivery of high-quality beams for X-ray experiments. X-ray speckle-based techniques stand out among other in situ techniques for their easy experimental setup and various data acquisition modes. Although X-ray speckle-based techniques have been under development for more than a decade, there are still no user-friendly software packages for new researchers to begin with. Here, we present an open-source Python package, spexwavepy, for X-ray wavefront sensing using speckle-based techniques. This Python package covers a variety of X-ray speckle-based techniques, provides plenty of examples with real experimental data and offers detailed online documentation for users. We hope it can help new researchers learn and apply the speckle-based techniques for X-ray wavefront sensing to synchrotron radiation and X-ray free-electron laser beamlines.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effectiveness of ab initio molecular dynamics in simulating EXAFS spectra from layered systems. 模拟层状系统 EXAFS 光谱的 ab initio 分子动力学的有效性。
IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2024-09-01 Epub Date: 2024-07-23 DOI: 10.1107/S1600577524005484
F d'Acapito, M A Rehman
{"title":"Effectiveness of ab initio molecular dynamics in simulating EXAFS spectra from layered systems.","authors":"F d'Acapito, M A Rehman","doi":"10.1107/S1600577524005484","DOIUrl":"10.1107/S1600577524005484","url":null,"abstract":"<p><p>The simulation of EXAFS spectra of thin films via ab initio methods is discussed. The procedure for producing the spectra is presented as well as an application to a two-dimensional material (WSe<sub>2</sub>) where the effectiveness of this method in reproducing the spectrum and the linear dichroic response is shown. A series of further examples in which the method has been employed for the structural determination of materials are given.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
In situ photodeposition of ultra-small palladium particles on TiO2. 在二氧化钛上原位光沉积超小型钯粒子。
IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2024-09-01 Epub Date: 2024-07-15 DOI: 10.1107/S1600577524004788
Elizaveta Kozyr, Sara Martí-Sánchez, Alina Skorynina, Jordi Arbiol, Carlos Escudero, Lorenzo Mino, Aram Bugaev
{"title":"In situ photodeposition of ultra-small palladium particles on TiO<sub>2</sub>.","authors":"Elizaveta Kozyr, Sara Martí-Sánchez, Alina Skorynina, Jordi Arbiol, Carlos Escudero, Lorenzo Mino, Aram Bugaev","doi":"10.1107/S1600577524004788","DOIUrl":"10.1107/S1600577524004788","url":null,"abstract":"<p><p>In situ and operando investigation of photocatalysts plays a fundamental role in understanding the processes of active phase formation and the mechanisms of catalytic reactions, which is crucial for the rational design of more efficient materials. Using a custom-made operando photocatalytic cell, an in situ procedure to follow the formation steps of Pd/TiO<sub>2</sub> photocatalyst by synchrotron-based X-ray absorption spectroscopy (XAS) is proposed. The procedure resulted in the formation of ∼1 nm Pd particles with a much narrower size distribution and homogeneous spreading over TiO<sub>2</sub> support compared with the samples generated in a conventional batch reactor. The combination of in situ XAS spectroscopy with high-angle annular dark-field scanning transmission electron microscopy demonstrated the formation of single-atom Pd(0) sites on TiO<sub>2</sub> as the initial step of the photodeposition process. Palladium hydride particles were observed for all investigated samples upon exposure to formic acid solutions.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
RefXAS: an open access database of X-ray absorption spectra. RefXAS：开放式 X 射线吸收光谱数据库。
IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2024-09-01 Epub Date: 2024-08-27 DOI: 10.1107/S1600577524006751
Sebastian Paripsa, Abhijeet Gaur, Frank Förste, Dmitry E Doronkin, Wolfgang Malzer, Christopher Schlesiger, Birgit Kanngießer, Edmund Welter, Jan Dierk Grunwaldt, Dirk Lützenkirchen-Hecht
{"title":"RefXAS: an open access database of X-ray absorption spectra.","authors":"Sebastian Paripsa, Abhijeet Gaur, Frank Förste, Dmitry E Doronkin, Wolfgang Malzer, Christopher Schlesiger, Birgit Kanngießer, Edmund Welter, Jan Dierk Grunwaldt, Dirk Lützenkirchen-Hecht","doi":"10.1107/S1600577524006751","DOIUrl":"10.1107/S1600577524006751","url":null,"abstract":"<p><p>Under DAPHNE4NFDI, the X-ray absorption spectroscopy (XAS) reference database, RefXAS, has been set up. For this purpose, we developed a method to enable users to submit a raw dataset, with its associated metadata, via a dedicated website for inclusion in the database. Implementation of the database includes an upload of metadata to the scientific catalogue and an upload of files via object storage, with automated query capabilities through a web server and visualization of the data and files. Based on the mode of measurements, quality criteria have been formulated for the automated check of any uploaded data. In the present work, the significant metadata fields for reusability, as well as reproducibility of results (FAIR data principles), are discussed. Quality criteria for the data uploaded to the database have been formulated and assessed. Moreover, the usability and interoperability of available XAS data/file formats have been explored. The first version of the RefXAS database prototype is presented, which features a human verification procedure, currently being tested with a new user interface designed specifically for curators; a user-friendly landing page; a full list of datasets; advanced search capabilities; a streamlined upload process; and, finally, a server-side automatic authentication and (meta-) data storage via MongoDB, PostgreSQL and (data-) files via relevant APIs.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142082368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A distributed software system for integrating data-intensive imaging methods in a hard X-ray nanoprobe beamline at the SSRF. 在 SSRF 的硬 X 射线纳米探针光束线中集成数据密集型成像方法的分布式软件系统。
IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2024-09-01 Epub Date: 2024-08-22 DOI: 10.1107/S1600577524006994
Peicheng Zhang, Zhisen Jiang, Yan He, Aiguo Li
{"title":"A distributed software system for integrating data-intensive imaging methods in a hard X-ray nanoprobe beamline at the SSRF.","authors":"Peicheng Zhang, Zhisen Jiang, Yan He, Aiguo Li","doi":"10.1107/S1600577524006994","DOIUrl":"10.1107/S1600577524006994","url":null,"abstract":"<p><p>The development of hard X-ray nanoprobe techniques has given rise to a number of experimental methods, like nano-XAS, nano-XRD, nano-XRF, ptychography and tomography. Each method has its own unique data processing algorithms. With the increase in data acquisition rate, the large amount of generated data is now a big challenge to these algorithms. In this work, an intuitive, user-friendly software system is introduced to integrate and manage these algorithms; by taking advantage of the loosely coupled, component-based design approach of the system, the data processing speed of the imaging algorithm is enhanced through optimization of the parallelism efficiency. This study provides meaningful solutions to tackle complexity challenges faced in synchrotron data processing.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142019257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Development of an advanced in-line multilayer deposition system at Diamond Light Source. 在钻石光源开发先进的在线多层沉积系统。
IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2024-09-01 Epub Date: 2024-08-09 DOI: 10.1107/S1600577524006854
Hongchang Wang, Arindam Majhi, Wai Jue Tan, Wadwan Singhapong, Christian Morawe, Kawal Sawhney
{"title":"Development of an advanced in-line multilayer deposition system at Diamond Light Source.","authors":"Hongchang Wang, Arindam Majhi, Wai Jue Tan, Wadwan Singhapong, Christian Morawe, Kawal Sawhney","doi":"10.1107/S1600577524006854","DOIUrl":"10.1107/S1600577524006854","url":null,"abstract":"<p><p>A state-of-the-art multilayer deposition system with a 4200 mm-long linear substrate translator housed within an ultra-high vacuum chamber has been developed. This instrument is engineered to produce single and multilayer coatings, accommodating mirrors up to 2000 mm in length through the utilization of eight rectangular cathodes. To ensure the quality and reliability of the coatings, the system incorporates various diagnostic tools for in situ thickness uniformity and stress measurement. Furthermore, the system features an annealing process capable of heating up to 700°C within the load-lock chamber. The entire operation, including pump down, deposition and venting processes, is automated through user-friendly software. In addition, all essential log data, power of sputtering source, working pressure and motion positions are automatically stored for comprehensive data analysis. Preliminary commissioning results demonstrate excellent lateral film thickness uniformity, achieving 0.26% along the translation direction over 1500 mm in dynamic mode. The multilayer deposition system is poised for use in fabricating periodic, lateral-graded and depth-graded multilayers, specifically catering to the beamlines for diverse scientific applications at Diamond Light Source.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Diamond sensors for hard X-ray energy and position resolving measurements at the European XFEL. 用于欧洲 XFEL 硬 X 射线能量和位置分辨测量的金刚石传感器。
IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2024-09-01 Epub Date: 2024-07-30 DOI: 10.1107/S1600577524006015
Tuba Çonka Yıldız, Wolfgang Freund, Jia Liu, Matthias Schreck, Dmitry Khakhulin, Hazem Yousef, Christopher Milne, Jan Grünert
{"title":"Diamond sensors for hard X-ray energy and position resolving measurements at the European XFEL.","authors":"Tuba Çonka Yıldız, Wolfgang Freund, Jia Liu, Matthias Schreck, Dmitry Khakhulin, Hazem Yousef, Christopher Milne, Jan Grünert","doi":"10.1107/S1600577524006015","DOIUrl":"10.1107/S1600577524006015","url":null,"abstract":"<p><p>The diagnostics of X-ray beam properties has a critical importance at the European X-ray Free-Electron Laser facility. Besides existing diagnostic components, utilization of a diamond sensor was proposed to achieve radiation-hard, non-invasive beam position and pulse energy measurements for hard X-rays. In particular, with very hard X-rays, diamond-based sensors become a useful complement to gas-based devices which lose sensitivity due to significantly reduced gas cross-sections. The measurements presented in this work were performed with diamond sensors consisting of an electronic-grade single-crystal chemical-vapor-deposition diamond with position-sensitive resistive electrodes in a duo-lateral configuration. The results show that the diamond sensor delivers pulse-resolved X-ray beam position data at 2.25 MHz with an uncertainty of less than 1% of the beam size. To our knowledge this is the first demonstration of pulse-resolved position measurements at the MHz rate using a transmissive diamond sensor at a free-electron laser facility. It can therefore be a valuable tool for X-ray free-electron lasers, especially for high-repetition-rate machines, enabling applications such as beam-based alignment and intra-pulse-train position feedback.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
MuscleX: data analysis software for fiber diffraction patterns from muscle. MuscleX：用于分析肌肉纤维衍射图样的数据分析软件。
IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2024-09-01 Epub Date: 2024-07-30 DOI: 10.1107/S1600577524006167
Jiranun Jiratrakanvong, Jinjian Shao, Jiaqi Li, Miguel Menendez Alvarez, Xintian Li, Prajwal Das, Grant Nikseresht, Nikhil Miskin, Ran Huo, Jules Nabon, Tristan Leduc, Eric Zhang, Weikang Ma, Gady Agam, Thomas C Irving
{"title":"MuscleX: data analysis software for fiber diffraction patterns from muscle.","authors":"Jiranun Jiratrakanvong, Jinjian Shao, Jiaqi Li, Miguel Menendez Alvarez, Xintian Li, Prajwal Das, Grant Nikseresht, Nikhil Miskin, Ran Huo, Jules Nabon, Tristan Leduc, Eric Zhang, Weikang Ma, Gady Agam, Thomas C Irving","doi":"10.1107/S1600577524006167","DOIUrl":"10.1107/S1600577524006167","url":null,"abstract":"<p><p>MuscleX is an integrated, open-source computer software suite for data reduction of X-ray fiber diffraction patterns from striated muscle and other fibrous systems. It is written in Python and runs on Linux, Microsoft Windows or macOS. Most modules can be run either from a graphical user interface or in a `headless mode' from the command line, suitable for incorporation into beamline control systems. Here, we provide an overview of the general structure of the MuscleX software package and describe the specific features of the individual modules as well as examples of applications.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
X-ray lens figure errors retrieved by deep learning from several beam intensity images. 通过深度学习从多个光束强度图像中检索 X 射线透镜图形误差。
IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2024-09-01 Epub Date: 2024-07-23 DOI: 10.1107/S1600577524004958
Manuel Sanchez Del Rio, Rafael Celestre, Juan Reyes-Herrera
{"title":"X-ray lens figure errors retrieved by deep learning from several beam intensity images.","authors":"Manuel Sanchez Del Rio, Rafael Celestre, Juan Reyes-Herrera","doi":"10.1107/S1600577524004958","DOIUrl":"10.1107/S1600577524004958","url":null,"abstract":"<p><p>The phase problem in the context of focusing synchrotron beams with X-ray lenses is addressed. The feasibility of retrieving the surface error of a lens system by using only the intensity of the propagated beam at several distances is demonstrated. A neural network, trained with a few thousand simulations using random errors, can predict accurately the lens error profile that accounts for all aberrations. It demonstrates the feasibility of routinely measuring the aberrations induced by an X-ray lens, or another optical system, using only a few intensity images.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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