Journal of Synchrotron Radiation最新文献_第2页

Long-term timing stabilization for pump-probe experiments at SACLA.

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2025-03-01 Epub Date: 2025-02-03 DOI: 10.1107/S1600577524011974

Tadashi Togashi, Shigeki Owada, Toshinori Yabuuchi, Makina Yabashi

引用次数: 0

Development of the Nanobeam X-ray Experiments instrument at PAL-XFEL.

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2025-03-01 Epub Date: 2025-02-12 DOI: 10.1107/S1600577525000426

Jangwoo Kim, HyoJung Hyun, Seonghan Kim, Sun Min Hwang, Myong Jin Kim, Dogeun Jang, Kyung Sook Kim, Jaeyong Shin, Sejin Kim, Junha Hwang, Sung Yun Lee, Eunyoung Park, Sangsoo Kim, Intae Eom, Changyong Song, Daewoong Nam

引用次数: 0

Novel fixed-target serial crystallography flip-holder for macromolecular crystallography beamlines at synchrotron radiation sources.

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2025-03-01 Epub Date: 2025-02-03 DOI: 10.1107/S1600577524011664

Do Heon Gu, Dong Tak Jeong, Cheolsoo Eo, Pil Won Seo, Jeong Sun Kim, Suk Youl Park

{"title":"Novel fixed-target serial crystallography flip-holder for macromolecular crystallography beamlines at synchrotron radiation sources.","authors":"Do Heon Gu, Dong Tak Jeong, Cheolsoo Eo, Pil Won Seo, Jeong Sun Kim, Suk Youl Park","doi":"10.1107/S1600577524011664","DOIUrl":"10.1107/S1600577524011664","url":null,"abstract":"Synchrotron serial crystallography (SSX) is an emerging method for determining crystal structure at room temperature using synchrotron radiation facilities. Despite the various approaches available, reducing sample consumption, removing mother liquid from crystal solution, soaking small molecules for protein-ligand complex structure and prevention of sample dehydration are still challenging problems to be overcome in SSX. Therefore, we have developed a new flip-type fixed-target SSX sample holder for conventional protein crystallography beamlines based on nylon mesh and kapton film. The potential of the flip-holder was evaluated in an SSX experiment with lysozyme crystals at room temperature. About 19600 diffraction images were collected during 40 minutes using a repetition rate of 10 Hz at the 11C beamline of the Pohang Accelerator Laboratory, and the crystal structure of lysozyme was determined at 1.89 Å resolution. This straightforward flip-holder can be used in synchrotron beamlines for routine crystallography.","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"315-320"},"PeriodicalIF":2.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143123917","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

Design and implementation of a user office system for the Canadian Light Source.

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2025-03-01 Epub Date: 2025-02-06 DOI: 10.1107/S1600577525000153

Kathryn Janzen, Michel Fodje

引用次数: 0

Multi-stage deep learning artifact reduction for parallel-beam computed tomography.

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2025-03-01 Epub Date: 2025-02-17 DOI: 10.1107/S1600577525000359

Jiayang Shi, Daniël M Pelt, K Joost Batenburg

{"title":"Multi-stage deep learning artifact reduction for parallel-beam computed tomography.","authors":"Jiayang Shi, Daniël M Pelt, K Joost Batenburg","doi":"10.1107/S1600577525000359","DOIUrl":"10.1107/S1600577525000359","url":null,"abstract":"Computed tomography (CT) using synchrotron radiation is a powerful technique that, compared with laboratory CT techniques, boosts high spatial and temporal resolution while also providing access to a range of contrast-formation mechanisms. The acquired projection data are typically processed by a computational pipeline composed of multiple stages. Artifacts introduced during data acquisition can propagate through the pipeline and degrade image quality in the reconstructed images. Recently, deep learning has shown significant promise in enhancing image quality for images representing scientific data. This success has driven increasing adoption of deep learning techniques in CT imaging. Various approaches have been proposed to incorporate deep learning into computational pipelines, but each has limitations in addressing artifacts effectively and efficiently in synchrotron CT, either in properly addressing the specific artifacts or in computational efficiency. Recognizing these challenges, we introduce a novel method that incorporates separate deep learning models at each stage of the tomography pipeline - projection, sinogram and reconstruction - to address specific artifacts locally in a data-driven way. Our approach includes bypass connections that feed both the outputs from previous stages and raw data to subsequent stages, minimizing the risk of error propagation. Extensive evaluations on both simulated and real-world datasets illustrate that our approach effectively reduces artifacts and outperforms comparison methods.","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"442-456"},"PeriodicalIF":2.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442481","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

Mixed gain detector configurations for time-resolved X-ray solution scattering.

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2025-03-01 Epub Date: 2025-02-06 DOI: 10.1107/S1600577524012219

Morten Lunn Haubro, Joseph Pon, Philip Adam Hart, Kristoffer Haldrup, Tim Brandt van Driel

{"title":"Mixed gain detector configurations for time-resolved X-ray solution scattering.","authors":"Morten Lunn Haubro, Joseph Pon, Philip Adam Hart, Kristoffer Haldrup, Tim Brandt van Driel","doi":"10.1107/S1600577524012219","DOIUrl":"10.1107/S1600577524012219","url":null,"abstract":"X-ray detection at X-ray free-electron lasers is challenging in part due to the XFEL's extremely short and intense X-ray pulses. Experimental measurements are further complicated by the large fluctuations inherent to the self-amplified spontaneous emission process producing the X-rays. At the Linac Coherent Light Source the ePix10ka2M detector offers multiple gain modes, and auto-ranging between these, to increase the dynamic range while retaining low noise. For diffuse scattering techniques, such as time-resolved X-ray solution scattering, where the shape of the scattering pattern largely does not change between exposures, a fixed mix of different gain modes offers many of the same advantages as auto-ranging. We find that configuring individual ASICs in separate gain modes does not impact the intensity linearity of the gain response and has a limited effect on the effective dynamic range in regions with different gain mode settings while avoiding the complexities of auto-ranging. Small (<5%) non-linear gain contributions arise when pixels on the same ASIC are configured in different gain modes. We present a configuration scheme that is designed to select the optimal mixed gain configuration to minimize effects of saturation in the high-/medium-gain region, while maximizing the number of pixels with higher gain to improve the signal-to-noise ratio.","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"355-364"},"PeriodicalIF":2.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366331","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

Present and future structural biology activities at DESY and the European XFEL.

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2025-03-01 Epub Date: 2025-02-18 DOI: 10.1107/S1600577525000669

Dominik Oberthür, Johanna Hakanpää, Spyros Chatziefthymiou, Guilllaume Pompidor, Richard Bean, Henry N Chapman, Edgar Weckert

{"title":"Present and future structural biology activities at DESY and the European XFEL.","authors":"Dominik Oberthür, Johanna Hakanpää, Spyros Chatziefthymiou, Guilllaume Pompidor, Richard Bean, Henry N Chapman, Edgar Weckert","doi":"10.1107/S1600577525000669","DOIUrl":"10.1107/S1600577525000669","url":null,"abstract":"Structural biology investigations using synchrotron radiation have a long history at the photon science facilities at DESY. Presently, EMBL and DESY operate state-of-the-art macromolecular crystallography and biological SAXS stations at the synchrotron radiation source PETRA III for the international user community. New experimental opportunities for experiments with femtosecond temporal resolution and for extremely small macromolecular crystals have become available with the advent of X-ray free-electron lasers (XFELs) such as the European XFEL. Within large international collaborations, groups at DESY and the European XFEL have contributed significantly to the development of experimental and data analysis methods to enable serial crystallography experiments at both XFELs and high-brilliance synchrotron radiation sources. The available portfolio of analytical infrastructure in photon science at DESY has attracted several campus partners to contribute to the development of instruments and methods and provide their own complementary experimental techniques, thereby establishing a fruitful scientific environment to make significant contributions to present and future societal challenges in the field of life sciences.","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"474-485"},"PeriodicalIF":2.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450586","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

Local structure of solid and liquid gold probed by reverse Monte Carlo analysis of X-ray absorption data. 通过对 X 射线吸收数据的反向蒙特卡罗分析探测固态和液态金的局部结构。

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2025-03-01 Epub Date: 2025-02-04 DOI: 10.1107/S1600577524011706

Nodoka Hara, Fabio Iesari, Toshihiro Okajima, Andrea Di Cicco

{"title":"Local structure of solid and liquid gold probed by reverse Monte Carlo analysis of X-ray absorption data.","authors":"Nodoka Hara, Fabio Iesari, Toshihiro Okajima, Andrea Di Cicco","doi":"10.1107/S1600577524011706","DOIUrl":"10.1107/S1600577524011706","url":null,"abstract":"The increase in computational capabilities of modern computers has allowed us to develop new accurate methods for EXAFS (extended X-ray absorption fine structure) data-analysis. In particular, the RMC-GNXAS package provides models of the three-dimensional structure applying the reverse Monte Carlo (RMC) method to EXAFS of condensed or molecular systems. Simulations of the EXAFS signals within RMC-GNXAS are based on accurate multiple-scattering (MS) simulations accounting for relativistic effects. The method is implemented to include MS signals related to pair and triplet distributions, using different data sets and long-range constraints provided by complementary techniques (diffraction). In this work we have validated this approach studying the local structure of solid and liquid Au, providing also a benchmark for analysis of functional materials based on heavy noble atoms such as Au. An accurate reconstruction of the pair and triplet distribution functions in solid and liquid Au was obtained and compared with literature data. We show that the inclusion of the contribution of MS signals related to three-body configurations is especially important in solid Au at low temperatures. In liquid Au, we obtained the pair distribution function and analyzed the bond-angle distribution. We applied common-neighbor analysis to identify the local symmetry of the atomic configurations. Liquid Au is found to follow the trend of other close-packing liquids for which the dominant structures are distorted or defective icosahedral configurations.","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"408-416"},"PeriodicalIF":2.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143191042","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

The current status and future prospects of the Synchrotron Radiation Protein Crystallography Core Facility at NSRRC: a focus on the TPS 05A, TPS 07A and TLS 15A1 beamlines.

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2025-03-01 Epub Date: 2025-02-06 DOI: 10.1107/S1600577525000177

Chung Kuang Chou, Chien Chang Tseng, Cheng Hung Chiang, Yi Hui Chen, Yi Chun Liu, Chen Ying Huang, Chun Hsiung Chao, Chun Hsiang Huang

{"title":"The current status and future prospects of the Synchrotron Radiation Protein Crystallography Core Facility at NSRRC: a focus on the TPS 05A, TPS 07A and TLS 15A1 beamlines.","authors":"Chung Kuang Chou, Chien Chang Tseng, Cheng Hung Chiang, Yi Hui Chen, Yi Chun Liu, Chen Ying Huang, Chun Hsiung Chao, Chun Hsiang Huang","doi":"10.1107/S1600577525000177","DOIUrl":"10.1107/S1600577525000177","url":null,"abstract":"The Synchrotron Radiation Protein Crystallography Core Facility (SPXF) at the National Synchrotron Radiation Research Center has been pivotal in advancing structural biology research in Taiwan. Since the 1990s, Taiwan has invested in the development of synchrotron light sources, including the Taiwan Light Source and the Taiwan Photon Source, which have profoundly enhanced protein structure analysis capability. Through the high-performance beamlines, SPXF has enabled significant scientific achievements, contributing to disease research and drug development. The facility's move towards automation and its integration of advanced techniques, such as in situ serial synchrotron crystallography, underscore its commitment to meeting the evolving needs of the research community. The SPXF continues to foster innovation and collaboration, providing world-class resources for both domestic and international users.","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"457-465"},"PeriodicalIF":2.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366294","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

Deep learning-based spatio-temporal fusion for high-fidelity ultra-high-speed X-ray radiography.

IF 2.5 3区物理与天体物理

Journal of Synchrotron Radiation Pub Date : 2025-03-01 Epub Date: 2025-02-12 DOI: 10.1107/S1600577525000323

Songyuan Tang, Tekin Bicer, Tao Sun, Kamel Fezzaa, Samuel J Clark

{"title":"Deep learning-based spatio-temporal fusion for high-fidelity ultra-high-speed X-ray radiography.","authors":"Songyuan Tang, Tekin Bicer, Tao Sun, Kamel Fezzaa, Samuel J Clark","doi":"10.1107/S1600577525000323","DOIUrl":"10.1107/S1600577525000323","url":null,"abstract":"Full-field ultra-high-speed (UHS) X-ray imaging experiments have been well established to characterize various processes and phenomena. However, the potential of UHS experiments through the joint acquisition of X-ray videos with distinct configurations has not been fully exploited. In this paper, we investigate the use of a deep learning-based spatio-temporal fusion (STF) framework to fuse two complementary sequences of X-ray images and reconstruct the target image sequence with high spatial resolution, high frame rate and high fidelity. We applied a transfer learning strategy to train the model and compared the peak signal-to-noise ratio (PSNR), average absolute difference (AAD) and structural similarity (SSIM) of the proposed framework on two independent X-ray data sets with those obtained from a baseline deep learning model, a Bayesian fusion framework and the bicubic interpolation method. The proposed framework outperformed the other methods with various configurations of the input frame separations and image noise levels. With three subsequent images from the low-resolution (LR) sequence of a four times lower spatial resolution and another two images from the high-resolution (HR) sequence of a 20 times lower frame rate, the proposed approach achieved average PSNRs of 37.57 dB and 35.15 dB, respectively. When coupled with the appropriate combination of high-speed cameras, the proposed approach will enhance the performance and therefore the scientific value of UHS X-ray imaging experiments.","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"432-441"},"PeriodicalIF":2.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143400470","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