Journal of Applied Crystallography最新文献

QuickProcess2: an integrated package for crystallography data visualization, processing and management at the GM/CA Structural Biology Facility. QuickProcess2: GM/CA结构生物学设施晶体学数据可视化、处理和管理的集成包。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2026-09-30 eCollection Date: 2026-10-01 DOI: 10.1107/S1600576726008289

Qingping Xu, Mark C Hilgart, Nagarajan Venugopalan, David Kissick, Michael Becker, Shenglan Xu, Oleg Makarov, Sergey Stepanov, Janet L Smith, Robert F Fischetti

{"title":"QuickProcess2: an integrated package for crystallography data visualization, processing and management at the GM/CA Structural Biology Facility.","authors":"Qingping Xu, Mark C Hilgart, Nagarajan Venugopalan, David Kissick, Michael Becker, Shenglan Xu, Oleg Makarov, Sergey Stepanov, Janet L Smith, Robert F Fischetti","doi":"10.1107/S1600576726008289","DOIUrl":"10.1107/S1600576726008289","url":null,"abstract":"The rapid evolution of macromolecular crystallography towards high-frame-rate detectors and complex serial data collection strategies requires better integration of traditional software tools and the development of new solutions. Managing data flow, assessing quality in real time and merging results from thousands of crystals - as required by synchrotron serial crystallography - present significant challenges for beamline operations. Existing solutions often fragment the workflow into disconnected steps: visualization, processing and experiment data management. We present QuickProcess2 (QP2), an open-source package designed to unify these tasks into a cohesive system. Built on a client-server architecture using Python, Redis and HDF5, and developed using AI-assisted coding, QP2 integrates a low-latency 'Live' image viewer with an automated, context-aware data processing engine. Key features include native support for multiple datasets that facilitates the handling of both standard rotation and serial crystallography experiments; a flexible plugin-based architecture for integrating processing suites, such as XDS and CrystFEL; and persistent database tracking of all experiment parameters and results. The package offers user-friendly visualization and processing features, while also providing dedicated tools for beamline staff. By bridging the gap between data collection and reduction, QP2 aims to streamline beamline operations and support efficient handling of high-throughput data.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1746-1756"},"PeriodicalIF":2.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Jungfraujoch: 38 GB s^-1 real-time serial crystallography - data acquisition and live indexing feedback. Jungfraujoch: 38gb s-1实时串行晶体学-数据采集和实时索引反馈。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2026-09-30 eCollection Date: 2026-10-01 DOI: 10.1107/S1600576726008083

J Duan, H-C Stadler, J Nan, Z Matěj, G Gotthard, F Dworkowski, M Bjelcic, O Aurelius, A Mozzanica, S Grimm, M Burian, T Ursby, M Wang, F Leonarski

引用次数: 0

Stroboscopic neutron scattering measurements using Raspberry Pi-based sample environment event mode. 基于树莓派样本环境事件模式的频闪中子散射测量。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2026-09-28 eCollection Date: 2026-10-01 DOI: 10.1107/S1600576726008332

Andrew R J Nelson, Elliot P Gilbert, Joshua P King

引用次数: 0

Development of a neutron texture analysis reduction pipeline in Mantid. Mantid中子织构分析还原管道的研制。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2026-09-28 eCollection Date: 2026-10-01 DOI: 10.1107/S1600576726007661

Andy Bridger, Winfried Kockelmann, Joe Kelleher, Manuel Morgano, Richard Waite, Sarah Foxley, Florencia Malamud

引用次数: 0

The effect of Nb and O on the martensitic transformation in Ti-Nb-O alloys. Nb和O对Ti-Nb-O合金马氏体相变的影响。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2026-09-25 eCollection Date: 2026-10-01 DOI: 10.1107/S1600576726007739

Kristián Šalata, Dalibor Preisler, Josef Stráský, Jiří Kozlík, Lukáš Horák, Václav Holý

{"title":"The effect of Nb and O on the martensitic transformation in Ti-Nb-O alloys.","authors":"Kristián Šalata, Dalibor Preisler, Josef Stráský, Jiří Kozlík, Lukáš Horák, Václav Holý","doi":"10.1107/S1600576726007739","DOIUrl":"https://doi.org/10.1107/S1600576726007739","url":null,"abstract":"This study examines the influence of niobium and oxygen on phase stability, crystal structure and martensitic transformation pathways in Ti-Nb-O alloys. A series of Ti-(8-28)Nb-(0-3)O (at.%) alloys were prepared and solution-treated in the β-phase field. The microstructure and crystallography were characterized by X-ray diffraction (XRD), electron microscopy and reciprocal-space mapping. A 2D-XRD orientation simulation approach was applied to distinguish all 12 crystallographically equivalent α″-martensitic variants originating from a single prior β grain, enabling detailed diffraction analysis. This method further allowed quantitative evaluation of the atomic shuffle parameter y, describing the β→α″ transformation. The results demonstrate that Nb primarily governs α″-martensite evolution. Increasing Nb stabilizes the β phase and shifts the α″ structure toward higher symmetry, as reflected by systematic changes in lattice parameters and increasing shuffle parameter y, indicating suppression of the transformation to the hexagonal α' phase. Oxygen, in contrast, modifies the transformation pathways. At lower Nb contents, it suppresses ω-phase formation and promotes β→α″ transformation, while at higher Nb levels it inhibits long-range martensitic transformation, resulting in retained β or competing ω phase. These effects are attributed to local lattice distortions induced by interstitial oxygen.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1570-1583"},"PeriodicalIF":2.8,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PolarEyes with enhanced digital imaging, a high-throughput solution for locating and grading crystals. PolarEyes具有增强的数字成像，用于定位和分级晶体的高通量解决方案。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2026-09-25 eCollection Date: 2026-10-01 DOI: 10.1107/S1600576726007727

Thomas D Smith, Alexandra Longcake, Michael J Hall, Michael R Probert

{"title":"PolarEyes with enhanced digital imaging, a high-throughput solution for locating and grading crystals.","authors":"Thomas D Smith, Alexandra Longcake, Michael J Hall, Michael R Probert","doi":"10.1107/S1600576726007727","DOIUrl":"https://doi.org/10.1107/S1600576726007727","url":null,"abstract":"The long-range internal order of crystals enables them to exhibit a well known and long-exploited phenomenon: birefringence. Simple assessment of the interaction of crystals with a polarized light source has guided the hand of many crystallographers through history in matters of crystal selection. Historically the interaction of plane-polarized light has been analysed manually by the user. However, adapting the use of a motorized polarized light microscope to a modern small-molecule-optimized high-throughput workflow can allow for more efficient screening of crystals, in turn alleviating the analysis bottleneck previously encountered in parallel crystallization techniques, such as encapsulated nanodroplet crystallization. Presented herein are developments to an existing open-source imaging robot, including the novel integration of a commercial imaging device and a new software suite for analysis. The open-source program PolarEyes is presented for the extraction of polarization quantities from optical light micrographs. Included in PolarEyes are facilities to perform normalization against a background image and false-colour visualization using the hue, saturation, luminance colour model, and capabilities to perform analysis of multiple different incident polarization states.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1557-1569"},"PeriodicalIF":2.8,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Determination of water permeability in stress-free lipid membranes through time-resolved small-angle neutron scattering. 用时间分辨小角中子散射法测定无应力脂质膜的透水性。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2026-09-25 eCollection Date: 2026-10-01 DOI: 10.1107/S1600576726007788

Moritz P K Frewein, Ursula Perez-Salas, O H Samuli Ollila, Georg Pabst, Lionel Porcar

引用次数: 0

Deterministic segmentation of grains in dense Laue microdiffraction datasets. 密集Laue微衍射数据集中颗粒的确定性分割。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2026-09-25 eCollection Date: 2026-10-01 DOI: 10.1107/S1600576726007995

Sergio Bongiorno, Jean-Sébastien Micha, Samuel Tardif, Joël Eymery

{"title":"Deterministic segmentation of grains in dense Laue microdiffraction datasets.","authors":"Sergio Bongiorno, Jean-Sébastien Micha, Samuel Tardif, Joël Eymery","doi":"10.1107/S1600576726007995","DOIUrl":"https://doi.org/10.1107/S1600576726007995","url":null,"abstract":"Although Laue microdiffraction is an essential non-destructive technique for probing crystallographic orientation and strain at submicrometre resolution, the extreme density of overlapping Bragg reflections often hinders its application to polycrystalline materials. We present a novel analysis pipeline, implemented in the open-source Python package graintools, designed to segment these complex datasets without prior knowledge of the microstructure. The workflow uses a multi-round peak search to handle diverse spot morphologies and constructs a look-up table to identify recurring reflections across raster-scan positions. These reflections are organized into spot families and represented as 2D binary appearance maps, which indicate the spatial occurrence of specific grains. To enhance data fidelity, connected component analysis is applied to clean these maps before they are grouped into clusters using cosine similarity. The method was successfully validated on a 3C-SiC polycrystalline sample, demonstrating its ability to isolate grain footprints, extract accurate orientations and reconstruct intra-grain deviatoric strain maps. This deterministic approach effectively circumvents the combinatorial and memory bottlenecks of traditional indexing and dictionary-based methods, providing a robust solution for analyzing highly populated diffraction patterns.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1584-1594"},"PeriodicalIF":2.8,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Elliptical neutron-focusing supermirrors with Ni-P-plated Al-Si alloy substrates for multi-incident-angle neutron reflectometry. 用于多入射角中子反射的镀ni -p Al-Si合金基底椭圆中子聚焦超反射镜。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2026-09-15 eCollection Date: 2026-10-01 DOI: 10.1107/S1600576726009088

Yan Wei, Takuya Hosobata, Norifumi L Yamada, Masahiro Hino, Masako Yamada, Yutaka Yamagata, Shinya Morita

{"title":"Elliptical neutron-focusing supermirrors with Ni-P-plated Al-Si alloy substrates for multi-incident-angle neutron reflectometry.","authors":"Yan Wei, Takuya Hosobata, Norifumi L Yamada, Masahiro Hino, Masako Yamada, Yutaka Yamagata, Shinya Morita","doi":"10.1107/S1600576726009088","DOIUrl":"https://doi.org/10.1107/S1600576726009088","url":null,"abstract":"This study introduces a novel approach for multi-incident-angle neutron reflectometry utilizing metallic elliptical supermirrors to enable the simultaneous focusing of two distinct neutron beams. The supermirror is composed of depth-graded NiC/Ti multilayers and functions as a reflector for grazing-incidence neutrons. Two mirror pairs consisting of precise elliptical supermirrors with diamond-machined and polished Ni-P-plated Al-Si alloy substrates were fabricated. Thermal deformation is minimized by this Al-Si alloy, which has a thermal expansion coefficient similar to that of Ni-P. The focusing performance was evaluated using the SOFIA neutron reflectometer located at BL16, Materials and Life Science Experimental Facility, Japan Proton Accelerator Research Complex. The experimental results confirmed that the two neutron beams converged to a single spot with a full width at half-maximum of 0.26 mm. Optimizing the simultaneous focusing of dual beams presents technical challenges that warrant further investigation in the future.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1509-1516"},"PeriodicalIF":2.8,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Faster and targeted raster imaging through non-rectangular scanning. 通过非矩形扫描实现更快、更有针对性的光栅成像。

IF 2.8 3区材料科学

Journal of Applied Crystallography Pub Date : 2026-09-15 eCollection Date: 2026-10-01 DOI: 10.1107/S1600576726008277

Frederik H Gjørup, Thorbjørn E K Christensen, Yimeng Li, Marcelo J P Alcocer, Henrik Birkedal, Innokenty Kantor, Mads R V Jørgensen

{"title":"Faster and targeted raster imaging through non-rectangular scanning.","authors":"Frederik H Gjørup, Thorbjørn E K Christensen, Yimeng Li, Marcelo J P Alcocer, Henrik Birkedal, Innokenty Kantor, Mads R V Jørgensen","doi":"10.1107/S1600576726008277","DOIUrl":"https://doi.org/10.1107/S1600576726008277","url":null,"abstract":"Many materials are spatially heterogenous and it is important to characterize this heterogeneity, which can be done by scanning microbeam X-ray diffraction (µXRD) or X-ray fluorescence (µXRF) microscopy. A modified approach to raster scanning is presented, where each line in a raster scan is of varying length, allowing for efficient scanning of non-rectangular areas. This shortens the measurement time significantly and similarly reduces the large amount of data generated from the area outside the sample that is normally produced for non-rectangular samples. The scanning procedure has been implemented for µ-X-ray diffraction and fluorescence mapping at the DanMAX diffraction beamline at MAX IV, Sweden. It was found that the reduction in required measurement time was nearly proportional to the reduction in scanned area, a significant reduction for non-rectangular samples. As an example, a section of the dactyl club of a stomatopod specimen (Odontodactylus scyllarus) was scanned.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"59 Pt 5","pages":"1544-1549"},"PeriodicalIF":2.8,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13636037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149109750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0