Jupyter Notebooks for Neutron Radiography Data Processing and Analysis

Jupyter Notebooks for Neutron Radiography Data Processing and Analysis

Jean-Christophe Bilheux, Jiao Y. Y. Lin, Hassina Z. Bilheuxc

Abstract. Neutron radiography and computed tomography encompass a vibrant range of scientific applications, requiring advanced technique development and cutting-edge data processing and analysis software. We have developed an extensive portfolio of Python-based Jupyter notebooks that are custom-made for a specific experiment and sample geometry. These notebooks do not require any programming skills, although the code is accessible to programming experts if they wish to modify it. The notebooks are available on our analysis servers where the imaging data is also stored, preventing unnecessary and lengthy data transfer. This manuscript gives an overview of our efforts to empower the research community, that uses both the Spallation Neutron Source and High Flux Isotope Reactor imaging capabilities, to process and analyze their data in collaboration with our imaging team.

Keywords
Notebooks, Jupyter, Python, Neutron, Imaging, Analysis, Normalization

Published online 1/5/2020, 7 pages
Copyright © 2020 by the author(s)
Published under license by Materials Research Forum LLC., Millersville PA, USA

Citation: Jean-Christophe Bilheux, Jiao Y. Y. Lin, Hassina Z. Bilheuxc, Jupyter Notebooks for Neutron Radiography Data Processing and Analysis, Materials Research Proceedings, Vol. 15, pp 198-204, 2020

DOI: https://doi.org/10.21741/9781644900574-31

The article was published as article 31 of the book Neutron Radiography

Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI.

References
[1] R. R. Dehoff, M. Kirka, W. Sames, H. Bilheux, A. Tremsin, L. Lowe, S. Babu. Site specific control of crystallographic grain orientation through electron beam additive manufacturing, Materials Science and Technology 31 (8) (2015) 931-938. https://doi.org/10.1179/1743284714Y.0000000734
[2] Y. Zhang, K. R. Chandran, H. Z. Bilheux, Imaging of the Li spatial distribution within v 2 o 5 cathode in a coin cell by neutron computed tomography, Journal of Power Sources 376 (2018) 125-130. https://doi.org/10.1016/j.jpowsour.2017.11.080
[3] D. J. Duke, C. E. Finney, A. Kastengren, K. Matusik, N. Sovis, L. Santodonato, H. Bilheux, D. Schmidt, C. Powell, T. Toops, High resolution x-ray and neutron computed tomography of an engine combustion network spray g gasoline injector, SAE International Journal of Fuels and Lubricants 10 (2017-01-0824) (2017) 328-343. https://doi.org/10.4271/2017-01-0824
[4] F. Salvemini, S. Olsen, V. Luzin, U. Garbe, J. Davis, T. Knowles, K. Sheedy, Neutron tomographic analysis: Material characterization of silver and electrum coins from the 6th and 5th centuries bce, Materials Characterization 118 (2016) 175-185. https://doi.org/10.1016/j.matchar.2016.05.018
[5] M. Holz, A. Carminati, Y. Kuzyakov, Distribution of root exudates and mucilage in the rhizosphere: combining 14c imaging with neutron radiography, in: EGU General Assembly Conference Abstracts, Vol. 17, 2015.
[6] E. Perfect, C.-L. Cheng, M. Kang, H. Bilheux, J. Lamanna, M. Gragg, D. Wrigth, Neutron imaging of hydrogen-rich fluids in geomaterials and engineered porous media: A review, Earth-Science Reviews 129 (2014) 120-135. https://doi.org/10.1016/j.earscirev.2013.11.012
[7] H. Z. Bilheux, J.-C. Bilheux, W. B. Bailey, W. S. Keener, L. E. Davis, K. W. Herwig, K. Cekanova, Neutron imaging at the Oak Ridge National Laboratory: Application to biological research, in: Biomedical Science and Engineering Center Conference (BSEC), 2014 Annual Oak Ridge National Laboratory, IEEE, 2014, pp. 1-4. https://doi.org/10.1109/BSEC.2014.6867751
[8] H. Z. Bilheux, M. Cekanova, A. A. Vass, T. L. Nichols, J.-C. Bilheux, R. L. Donnell, V. Finochiarro, A novel approach to determine post mortem interval using neutron radiography, Forensic science international 251 (2015) 11-21. https://doi.org/10.1016/j.forsciint.2015.02.017
[9] L. Santodonato, H. Bilheux, B. Bailey, J. Bilheux, P. Nguyen, A. Tremsin, D. Selby, L. Walker, the CG-1D neutron imaging beamline at the Oak Ridge National Laboratory High Flux Isotope reactor, Physics Procedia 69 (2015) 104-108. https://doi.org/10.1016/j.phpro.2015.07.015
[10] Neutron Imaging at ORNL Home Page. https://neutronimaging.pages.ornl.gov.
[11] Jupyter Notebooks. http://jupyter.org.
[12] Python Web Page. https://python.org
[13] Python notebook tutorial. https://neutronimaging.pages.ornl.gov/tutorial/how_to_run_notebooks/
[14] thinlinc – a remote desktop server. https://www.cendio.com/thinlinc/what-is-thinlinc
[15] Conda environment. https://conda.io/docs/index.html.
[16] Garrett E. Granroth, K. An, H. L. Smith, P. Whitfield, J. C. Neuefeind, J. Lee, W. Zhou, V. N. Sedov, P. F. Peterson, A. Parizzi, H. Skorpenske, S. M. Hartman, A. Huq and D. L. Abernathy. Event-based processing of neutron scattering data at the Spallation Neutron Source, J. Appl. Cryst. (2018 51, 616-629. https://doi.org/10.1107/S1600576718004727