The NeXus data format

Könnecke, Mark; Akeroyd, Frederick A.; Bernstein, Herbert J.; Brewster, Aaron S.; Campbell, Stuart I.; Clausen, Björn; Cottrell, Stephen; Hoffmann, Jens Uwe; Jemian, Pete R.; Männicke, David; Osborn, Raymond; Peterson, Peter F.; Richter, Tobias; Suzuki, Jiro; Watts, Benjamin; Wintersberger, Eugen; Wuttke, Joachim

doi:10.1107/S1600576714027575

The NeXus data format

Journal Article · Fri Jan 30 04:00:00 EST 2015 · Journal of Applied Crystallography (Online)

DOI:https://doi.org/10.1107/S1600576714027575· OSTI ID:1391966

Könnecke, Mark; Akeroyd, Frederick A.; Bernstein, Herbert J.; Brewster, Aaron S.; Campbell, Stuart I.; Clausen, Björn; Cottrell, Stephen; Hoffmann, Jens Uwe; Jemian, Pete R.; Männicke, David; Osborn, Raymond; Peterson, Peter F.; Richter, Tobias; Suzuki, Jiro; Watts, Benjamin; Wintersberger, Eugen; Wuttke, Joachim

NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitions for the exchange of data between applications. NeXus provides structures for raw experimental data as well as for processed data.

Research Organization:: Argonne National Laboratory (ANL)

Sponsoring Organization:: USDOE Office of Science - Office of Basic Energy Sciences - Materials Sciences and Engineering Division

DOE Contract Number:: AC02-06CH11357

OSTI ID:: 1391966

Journal Information:: Journal of Applied Crystallography (Online), Journal Name: Journal of Applied Crystallography (Online) Journal Issue: 1 Vol. 48; ISSN JACGAR; ISSN 1600-5767

Publisher:: International Union of Crystallography

Country of Publication:: United States

Language:: English

References (3)

The application of the NeXus data format to ISIS muon data Flannery, D.; Cottrell, S. P.; King, P. J. C. Physica B: Condensed Matter, Vol. 326, Issue 1-4 https://doi.org/10.1016/S0921-4526(02)01613-7	journal	February 2003
Data Formats and Analysis Codes–New Software for μSR Cottrell, Stephen; Pratt, Francis; Hillier, Adrian Physics Procedia, Vol. 30 https://doi.org/10.1016/j.phpro.2012.04.031	journal	January 2012
McStas 1.7 - a new version of the flexible Monte Carlo neutron scattering package Willendrup, Peter; Farhi, Emmanuel; Lefmann, Kim Physica B: Condensed Matter, Vol. 350, Issue 1-3 https://doi.org/10.1016/j.physb.2004.03.193	journal	July 2004

Cited By (47)

Automatic processing of multimodal tomography datasets Parsons, Aaron D.; Price, Stephen W. T.; Wadeson, Nicola Journal of Synchrotron Radiation, Vol. 24, Issue 1 https://doi.org/10.1107/s1600577516017756	journal	January 2017
Event-based processing of neutron scattering data at the Spallation Neutron Source Granroth, Garrett E.; An, Ke; Smith, Hillary L. Journal of Applied Crystallography, Vol. 51, Issue 3 https://doi.org/10.1107/s1600576718004727	journal	May 2018
LiberTEM/LiberTEM: 0.2.0 Clausen, Alexander; Weber, Dieter; Caron, Jan Zenodo https://doi.org/10.5281/zenodo.3474941	software	October 2019
LiberTEM/LiberTEM: 0.5.0 Clausen, Alexander; Weber, Dieter; Ruzaeva, Karina Zenodo https://doi.org/10.5281/zenodo.3763313	software	April 2020
Super-resolution energy spectra from neutron direct-geometry spectrometers Islam, Fahima; Lin, Jiao Y. Y.; Archibald, Richard Review of Scientific Instruments, Vol. 90, Issue 10 https://doi.org/10.1063/1.5116147	journal	October 2019
LiberTEM/LiberTEM: 0.4.0 Clausen, Alexander; Weber, Dieter; Ruzaeva, Karina Zenodo https://doi.org/10.5281/zenodo.3666686	software	February 2020
Serial protein crystallography in an electron microscope Bücker, Robert; Hogan-Lamarre, Pascal; Mehrabi, Pedram Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-14793-0	journal	February 2020
Processing serial crystallography data with CrystFEL : a step-by-step guide White, Thomas A. International Union of Crystallography (IUCr) https://doi.org/10.1107/s205979831801238x/ba5291sup2.txt	text	January 2019
The challenge of constructing an international XAFS database Asakura, Kiyotaka; Abe, Hitoshi; Kimura, Masao Journal of Synchrotron Radiation, Vol. 25, Issue 4 https://doi.org/10.1107/s1600577518006963	journal	May 2018
DA+ data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines Wojdyla, Justyna Aleksandra; Kaminski, Jakub W.; Panepucci, Ezequiel Journal of Synchrotron Radiation, Vol. 25, Issue 1 https://doi.org/10.1107/s1600577517014503	journal	January 2018
Processing two-dimensional X-ray diffraction and small-angle scattering data in DAWN 2 Filik, J.; Ashton, A. W.; Chang, P. C. Y. Journal of Applied Crystallography, Vol. 50, Issue 3 https://doi.org/10.1107/s1600576717004708	journal	May 2017
LiberTEM/LiberTEM-blobfinder: 0.4.0 Clausen, Alexander; Weber, Dieter; Ruzaeva, Karina Zenodo https://doi.org/10.5281/zenodo.3663437	software	February 2020
Recent developments of MCViNE and its applications at SNS Lin, Jiao Y. Y.; Islam, Fahima; Sala, Gabriele Journal of Physics Communications, Vol. 3, Issue 8 https://doi.org/10.1088/2399-6528/ab3622	journal	August 2019
Performance and characteristics of the BILBY time-of-flight small-angle neutron scattering instrument Sokolova, Anna; Whitten, Andrew E.; de Campo, Liliana Journal of Applied Crystallography, Vol. 52, Issue 1 https://doi.org/10.1107/s1600576718018009	journal	February 2019
Climbing the Data Mountain: Processing of SFX Data Yoon, Chun Hong; White, Thomas A. Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2019-00970	text	January 2018
ECHIDNA: a decade of high-resolution neutron powder diffraction at OPAL Avdeev, Maxim; Hester, James R. Journal of Applied Crystallography, Vol. 51, Issue 6 https://doi.org/10.1107/s1600576718014048	journal	November 2018
LiberTEM/LiberTEM: 0.4.1 Clausen, Alexander; Weber, Dieter; Ruzaeva, Karina Zenodo https://doi.org/10.5281/zenodo.3674003	software	February 2020
A convolutional neural network for fast upsampling of undersampled tomograms in X-ray CT time-series using a representative highly sampled tomogram Bellos, Dimitrios; Basham, Mark; Pridmore, Tony Journal of Synchrotron Radiation, Vol. 26, Issue 3 https://doi.org/10.1107/s1600577519003448	journal	April 2019
Serial protein crystallography in an electron microscope Bücker, Robert; Hogan-Lamarre, Pascal; Mehrabi, Pedram Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2020-00822	text	January 2020
Serial protein crystallography in an electron microscope Bücker, Robert; Hogan-Lamarre, Pascal; Mehrabi, Pedram Nature Publishing Group UK https://doi.org/10.15480/882.2722	text	January 2020
Sharing powder diffraction raw data: challenges and benefits Aranda, Miguel A. G. Journal of Applied Crystallography, Vol. 51, Issue 6 https://doi.org/10.1107/s160057671801556x	journal	November 2018
Experimental Directory Structure (Exdir): An alternative to HDF5 without introducing a new file format Dragly, Svenn-Arne; Mobarhan, Milad Hobbi; Lepperod, Mikkel Frontiers in Neuroinformatics https://doi.org/10.1101/249979	journal	January 2018
LiberTEM/LiberTEM: 0.2.2 Clausen, Alexander; Weber, Dieter; Caron, Jan Zenodo https://doi.org/10.5281/zenodo.3489385	software	October 2019
Time-of-Flight Neutron Imaging on IMAT@ISIS: A New User Facility for Materials Science Kockelmann, Winfried; Minniti, Triestino; Pooley, Daniel Journal of Imaging, Vol. 4, Issue 3 https://doi.org/10.3390/jimaging4030047	journal	February 2018
LiberTEM/LiberTEM: 0.2.1 Clausen, Alexander; Weber, Dieter; Caron, Jan Zenodo https://doi.org/10.5281/zenodo.3474968	software	October 2019
Xi-cam : a versatile interface for data visualization and analysis Pandolfi, Ronald J.; Allan, Daniel B.; Arenholz, Elke Journal of Synchrotron Radiation, Vol. 25, Issue 4 https://doi.org/10.1107/s1600577518005787	journal	May 2018
LiberTEM/LiberTEM-blobfinder: 0.4.0 Clausen, Alexander; Weber, Dieter; Ruzaeva, Karina Zenodo https://doi.org/10.5281/zenodo.3663436	software	February 2020
Automated data collection and real-time data analysis suite for serial synchrotron crystallography Basu, Shibom; Kaminski, Jakub W.; Panepucci, Ezequiel Journal of Synchrotron Radiation, Vol. 26, Issue 1 https://doi.org/10.1107/s1600577518016570	journal	January 2019
Processing serial crystallography data with CrystFEL : a step-by-step guide White, Thomas Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2019-00931	text	January 2019
JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography Leonarski, Filip; Mozzanica, Aldo; Brückner, Martin ETH Zurich https://doi.org/10.3929/ethz-b-000405482	text	January 2020
The MAX IV imaging concept Matěj, Zdeněk; Mokso, Rajmund; Larsson, Krister Advanced Structural and Chemical Imaging, Vol. 2, Issue 1 https://doi.org/10.1186/s40679-016-0029-7	journal	December 2016
Reciprocal space imaging of ionic correlations in intercalation compounds Krogstad, Matthew J.; Rosenkranz, Stephan; Wozniak, Justin M. Nature Materials, Vol. 19, Issue 1 https://doi.org/10.1038/s41563-019-0500-7	journal	October 2019
Processing serial crystallography data with CrystFEL : a step-by-step guide White, Thomas A. International Union of Crystallography (IUCr) https://doi.org/10.1107/s205979831801238x/ba5291sup1.pdf	text	January 2019
JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography Leonarski, Filip; Mozzanica, Aldo; Brückner, Martin Structural Dynamics, Vol. 7, Issue 1 https://doi.org/10.1063/1.5143480	journal	January 2020
Processing serial crystallography data with CrystFEL : a step-by-step guide White, Thomas A. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 2 https://doi.org/10.1107/s205979831801238x	journal	January 2019
A multipurpose instrument for time-resolved ultra-small-angle and coherent X-ray scattering Narayanan, Theyencheri; Sztucki, Michael; Van Vaerenbergh, Pierre Journal of Applied Crystallography, Vol. 51, Issue 6 https://doi.org/10.1107/s1600576718012748	journal	October 2018
Synchrotron Big Data Science Wang, Chunpeng; Steiner, Ullrich; Sepe, Alessandro Small, Vol. 14, Issue 46 https://doi.org/10.1002/smll.201802291	journal	September 2018
Implementation of cross correlation for energy discrimination on the time-of-flight spectrometer CORELLI Ye, Feng; Liu, Yaohua; Whitfield, Ross Journal of Applied Crystallography, Vol. 51, Issue 2 https://doi.org/10.1107/s160057671800403x	journal	March 2018
Climbing the Data Mountain: Processing of SFX Data Yoon, Chun Hong; White, Thomas A. X-ray Free Electron Lasers https://doi.org/10.1007/978-3-030-00551-1_7	book	January 2018
LiberTEM/LiberTEM: 0.3.0 Clausen, Alexander; Weber, Dieter; Ruzaeva, Karina Zenodo https://doi.org/10.5281/zenodo.3572855	software	December 2019
A NeXus/HDF5 based file format for STXM Watts, Benjamin; Raabe, Jörg XRM 2014: Proceedings of the 12th International Conference on X-Ray Microscopy, AIP Conference Proceedings https://doi.org/10.1063/1.4937536	conference	January 2016
DatView : a graphical user interface for visualizing and querying large data sets in serial femtosecond crystallography Stander, Natasha; Fromme, Petra; Zatsepin, Nadia Journal of Applied Crystallography, Vol. 52, Issue 6 https://doi.org/10.1107/s1600576719012044	journal	October 2019
LiberTEM/LiberTEM: 0.5.1 Clausen, Alexander; Weber, Dieter; Ruzaeva, Karina Zenodo https://doi.org/10.5281/zenodo.1477847	software	August 2020
Reciprocal Space Imaging of Ionic Correlations in Intercalation Compounds Krogstad, Matthew J.; Rosenkranz, Stephan; Wozniak, Justin M. arXiv https://doi.org/10.48550/arxiv.1902.03318	text	January 2019
Bluesky's Ahead: A Multi-Facility Collaboration for an a la Carte Software Project for Data Acquisition and Management Allan, Daniel; Caswell, Thomas; Campbell, Stuart Synchrotron Radiation News, Vol. 32, Issue 3 https://doi.org/10.1080/08940886.2019.1608121	journal	May 2019
Experimental Directory Structure (Exdir): An Alternative to HDF5 Without Introducing a New File Format Dragly, Svenn-Arne; Hobbi Mobarhan, Milad; Lepperød, Mikkel E. Frontiers in Neuroinformatics, Vol. 12 https://doi.org/10.3389/fninf.2018.00016	journal	April 2018
The fast azimuthal integration Python library: pyFAI Ashiotis, Giannis; Deschildre, Aurore; Nawaz, Zubair Journal of Applied Crystallography, Vol. 48, Issue 2 https://doi.org/10.1107/s1600576715004306	journal	March 2015

Similar Records

The NeXus data format

Journal Article · Thu Jan 29 19:00:00 EST 2015 · Journal of Applied Crystallography (Online) · OSTI ID:1212697

Related Subjects

97 MATHEMATICS AND COMPUTING

The NeXus data format

Citation Formats

References (3)

Cited By (47)

Similar Records

Related Subjects