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Title: TomoBank: a tomographic data repository for computational x-ray science

Abstract

There is a widening gap between the fast advancement of computational methods for tomographic reconstruction and their successful implementation in production software at various synchrotron facilities. This is due in part to the lack of readily available instrument datasets and phantoms representative of real materials for validation and comparison of new numerical methods. Recent advancements in detector technology made sub-second and multi-energy tomographic data collection possible [1], but also increased the demand to develop new reconstruction methods able to handle in-situ [2] and dynamic systems [3] that can be quickly incorporated in beamline production software [4]. The X-ray Tomography Data Bank, tomoBank, provides a repository of experimental and simulated datasets with the aim to foster collaboration among computational scientists, beamline scientists, and experimentalists and to accelerate the development and implementation of tomographic reconstruction methods for synchrotron facility production software by providing easy access to challenging dataset and their descriptors.

Authors:
ORCiD logo [1];  [1]; ORCiD logo [2];  [3];  [4]; ORCiD logo [5];  [6];  [7]; ORCiD logo [8];  [9];  [10]
+ Show Author Affiliations
  1. Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
  2. Oregon State Univ., Corvallis, OR (United States)
  3. Centrum Wiskunde & Informatica, Amsterdam, (Netherlands)
  4. European Synchrotron Radiation Facility (ESRF), Grenoble (France)
  5. Elettra-Sincrotrone Trieste, Basovizza (Italy)
  6. Paul Scherrer Inst. (PSI), Villigen (Switzerland). Swiss Light Source
  7. MAX IV Laboratory, Lund (Sweden)
  8. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  9. Univ. of Antwerp, Antwerp (Belgium). imec-Vision Lab.
  10. Univ. of Chicago, IL (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF)
OSTI Identifier:
1427546
Grant/Contract Number:  
AC02-06CH11357; FG02-94ER14466
Resource Type:
Accepted Manuscript
Journal Name:
Measurement Science and Technology
Additional Journal Information:
Journal Volume: 29; Journal Issue: 3; Journal ID: ISSN 0957-0233
Publisher:
IOP Publishing
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; tomography; tomographic data archive; tomographic data analysis; x-ray tomography

Citation Formats

De Carlo, Francesco, Gürsoy, Doğa, Ching, Daniel J., Batenburg, K. Joost, Ludwig, Wolfgang, Mancini, Lucia, Marone, Federica, Mokso, Rajmund, Pelt, Daniël M., Sijbers, Jan, and Rivers, Mark. TomoBank: a tomographic data repository for computational x-ray science. United States: N. p., 2018. Web. doi:10.1088/1361-6501/aa9c19.
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De Carlo, Francesco, Gürsoy, Doğa, Ching, Daniel J., Batenburg, K. Joost, Ludwig, Wolfgang, Mancini, Lucia, Marone, Federica, Mokso, Rajmund, Pelt, Daniël M., Sijbers, Jan, & Rivers, Mark. TomoBank: a tomographic data repository for computational x-ray science. United States. https://doi.org/10.1088/1361-6501/aa9c19
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De Carlo, Francesco, Gürsoy, Doğa, Ching, Daniel J., Batenburg, K. Joost, Ludwig, Wolfgang, Mancini, Lucia, Marone, Federica, Mokso, Rajmund, Pelt, Daniël M., Sijbers, Jan, and Rivers, Mark. Thu . "TomoBank: a tomographic data repository for computational x-ray science". United States. https://doi.org/10.1088/1361-6501/aa9c19. https://www.osti.gov/servlets/purl/1427546.
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@article{osti_1427546,
title = {TomoBank: a tomographic data repository for computational x-ray science},
author = {De Carlo, Francesco and Gürsoy, Doğa and Ching, Daniel J. and Batenburg, K. Joost and Ludwig, Wolfgang and Mancini, Lucia and Marone, Federica and Mokso, Rajmund and Pelt, Daniël M. and Sijbers, Jan and Rivers, Mark},
abstractNote = {There is a widening gap between the fast advancement of computational methods for tomographic reconstruction and their successful implementation in production software at various synchrotron facilities. This is due in part to the lack of readily available instrument datasets and phantoms representative of real materials for validation and comparison of new numerical methods. Recent advancements in detector technology made sub-second and multi-energy tomographic data collection possible [1], but also increased the demand to develop new reconstruction methods able to handle in-situ [2] and dynamic systems [3] that can be quickly incorporated in beamline production software [4]. The X-ray Tomography Data Bank, tomoBank, provides a repository of experimental and simulated datasets with the aim to foster collaboration among computational scientists, beamline scientists, and experimentalists and to accelerate the development and implementation of tomographic reconstruction methods for synchrotron facility production software by providing easy access to challenging dataset and their descriptors.},
doi = {10.1088/1361-6501/aa9c19},
journal = {Measurement Science and Technology},
number = 3,
volume = 29,
place = {United States},
year = {2018},
month = {2}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1088/1361-6501/aa9c19
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Cited by: 45 works
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Figures / Tables:

Table A1 Table A1: Datasets currently available in tomoBank
All figures and tables (14 total)
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Works referenced in this record:

The Three-Dimensional Morphology of Growing Dendrites
journal, July 2015

  • Gibbs, J. W.; Mohan, K. A.; Gulsoy, E. B.
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep11824

Fast Tomographic Reconstruction From Limited Data Using Artificial Neural Networks
journal, December 2013

  • Pelt, Daniel Maria; Batenburg, Kees Joost
  • IEEE Transactions on Image Processing, Vol. 22, Issue 12
  • DOI: 10.1109/TIP.2013.2283142

TIMBIR: A Method for Time-Space Reconstruction From Interlaced Views
journal, June 2015

  • Aditya Mohan, K.; Venkatakrishnan, S. V.; Gibbs, John W.
  • IEEE Transactions on Computational Imaging, Vol. 1, Issue 2
  • DOI: 10.1109/TCI.2015.2431913

TomoPy: a framework for the analysis of synchrotron tomographic data
journal, August 2014

  • Gürsoy, Dogˇa; De Carlo, Francesco; Xiao, Xianghui
  • Journal of Synchrotron Radiation, Vol. 21, Issue 5
  • DOI: 10.1107/S1600577514013939

Developments in synchrotron x-ray computed microtomography at the National Synchrotron Light Source
conference, September 1999

  • Dowd, Betsy A.; Campbell, Graham H.; Marr, Robert B.
  • SPIE's International Symposium on Optical Science, Engineering, and Instrumentation, SPIE Proceedings
  • DOI: 10.1117/12.363725

ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics
journal, October 2012

  • Howe, Douglas G.; Bradford, Yvonne M.; Conlin, Tom
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks938

The Open Quantum Materials Database (OQMD): assessing the accuracy of DFT formation energies
journal, December 2015

The Coherent X-ray Imaging Data Bank
journal, August 2012

The Protein Data Bank
journal, January 2000

EMDataBank.org: unified data resource for CryoEM
journal, October 2010

  • Lawson, C. L.; Baker, M. L.; Best, C.
  • Nucleic Acids Research, Vol. 39, Issue Database
  • DOI: 10.1093/nar/gkq880

Scientific data exchange: a schema for HDF5-based storage of raw and analyzed data
journal, October 2014

  • De Carlo, Francesco; Gürsoy, Dogˇa; Marone, Federica
  • Journal of Synchrotron Radiation, Vol. 21, Issue 6
  • DOI: 10.1107/S160057751401604X

TXM-Wizard : a program for advanced data collection and evaluation in full-field transmission X-ray microscopy
journal, January 2012

  • Liu, Yijin; Meirer, Florian; Williams, Phillip A.
  • Journal of Synchrotron Radiation, Vol. 19, Issue 2
  • DOI: 10.1107/S0909049511049144

XDesign : an open-source software package for designing X-ray imaging phantoms and experiments
journal, February 2017

A comparative study of X-ray tomographic microscopy on shales at different synchrotron facilities: ALS, APS and SLS
journal, November 2012

  • Kanitpanyacharoen, Waruntorn; Parkinson, Dilworth Y.; De Carlo, Francesco
  • Journal of Synchrotron Radiation, Vol. 20, Issue 1
  • DOI: 10.1107/S0909049512044354

Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object
journal, April 2002

Holotomography: Quantitative phase tomography with micrometer resolution using hard synchrotron radiation x rays
journal, November 1999

  • Cloetens, P.; Ludwig, W.; Baruchel, J.
  • Applied Physics Letters, Vol. 75, Issue 19
  • DOI: 10.1063/1.125225

Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data
journal, April 2016

  • Pelt, Daniël M.; Gürsoy, Dogˇa; Palenstijn, Willem Jan
  • Journal of Synchrotron Radiation, Vol. 23, Issue 3
  • DOI: 10.1107/S1600577516005658

Fast and flexible X-ray tomography using the ASTRA toolbox
journal, January 2016

  • van Aarle, Wim; Palenstijn, Willem Jan; Cant, Jeroen
  • Optics Express, Vol. 24, Issue 22
  • DOI: 10.1364/OE.24.025129
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    Works referencing / citing this record:

    Investigating Osteocytic Perilacunar/Canalicular Remodeling
    journal, June 2019

    • Yee, Cristal S.; Schurman, Charles A.; White, Carter R.
    • Current Osteoporosis Reports, Vol. 17, Issue 4
    • DOI: 10.1007/s11914-019-00514-0

    Advanced x-ray tomography: experiment, modeling, and algorithms
    journal, July 2018

    • Batenburg, K. Joost; De Carlo, Francesco; Mancini, Lucia
    • Measurement Science and Technology, Vol. 29, Issue 8
    • DOI: 10.1088/1361-6501/aacd25

    3D reconstruction of magnetization from dichroic soft X-ray transmission tomography
    journal, May 2018

    • Hierro-Rodriguez, Aurelio; Gürsoy, Doga; Phatak, Charudatta
    • Journal of Synchrotron Radiation, Vol. 25, Issue 4
    • DOI: 10.1107/s1600577518005829

    Tomosaic : efficient acquisition and reconstruction of teravoxel tomography data using limited-size synchrotron X-ray beams
    journal, August 2018

    • Vescovi, Rafael; Du, Ming; de Andrade, Vincent
    • Journal of Synchrotron Radiation, Vol. 25, Issue 5
    • DOI: 10.1107/s1600577518010093

    Nanoporous gold: a hierarchical and multiscale 3D test pattern for characterizing X-ray nano-tomography systems
    journal, January 2019

    • Larsson, Emanuel; Gürsoy, Doğa; De Carlo, Francesco
    • Journal of Synchrotron Radiation, Vol. 26, Issue 1
    • DOI: 10.1107/s1600577518015242

    Nanoporous gold: a hierarchical and multiscale 3D test pattern for characterizing X-ray nano-tomography systems
    text, January 2019

    • Larsson, Emanuel; Gürsoy, Doğa; De Carlo, Francesco
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2018-05482

    Tomographic reconstruction with a generative adversarial network
    text, January 2020

    • Yang, Xiaogang; Kahnt, Maik; Brückner, Dennis
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2020-01013

    Tomographic reconstruction with a generative adversarial network
    text, January 2020

    Nanoporous gold : a hierarchical and multiscale 3D test pattern for characterizing X-ray nano-tomography systems
    text, January 2019

    Tomographic reconstruction with a generative adversarial network
    text, January 2020

    Micro-computed tomography for natural history specimens: a handbook of best practice protocols
    journal, April 2019

    • Keklikoglou, Kleoniki; Faulwetter, Sarah; Chatzinikolaou, Eva
    • European Journal of Taxonomy, Issue 522
    • DOI: 10.5852/ejt.2019.522

    A cone-beam X-ray computed tomography data collection designed for machine learning
    journal, October 2019

    • Der Sarkissian, Henri; Lucka, Felix; van Eijnatten, Maureen
    • Scientific Data, Vol. 6, Issue 1
    • DOI: 10.1038/s41597-019-0235-y
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      Figures / Tables found in this record:

      Table A1 (p. 11)table
      Table A2 (p. 12)table
      Table A3 (p. 12)table
      Table A4 (p. 12)table
      Table A5 (p. 13)table
      Table A6 (p. 13)table
      Figure A1 (p. 14)figure
      Figure A2 (p. 15)figure
      Figure A3 (p. 15)figure
      Figure A4 (p. 16)figure
      Figure A5 (p. 16)figure
      Figure A6 (p. 16)figure
      Figure A7 (p. 17)figure
      Figure A8 (p. 18)figure
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