Improving reproducibility in synchrotron tomography using implementation-adapted filters
Abstract
For reconstructing large tomographic datasets fast, filtered backprojection-type or Fourier-based algorithms are still the method of choice, as they have been for decades. These robust and computationally efficient algorithms have been integrated in a broad range of software packages. The continuous mathematical formulas used for image reconstruction in such algorithms are unambiguous. However, variations in discretization and interpolation result in quantitative differences between reconstructed images, and corresponding segmentations, obtained from different software. This hinders reproducibility of experimental results, making it difficult to ensure that results and conclusions from experiments can be reproduced at different facilities or using different software. In this paper, a way to reduce such differences by optimizing the filter used in analytical algorithms is proposed. These filters can be computed using a wrapper routine around a black-box implementation of a reconstruction algorithm, and lead to quantitatively similar reconstructions. Use cases for this approach are demonstrated by computing implementation-adapted filters for several open-source implementations and applying them to simulated phantoms and real-world data acquired at the synchrotron. Our contribution to a reproducible reconstruction step forms a building block towards a fully reproducible synchrotron tomography data processing pipeline.
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); Netherlands Organisation for Scientific Research (NWO); Marie Sklodowska-Curie Actions
- OSTI Identifier:
- 1812972
- Alternate Identifier(s):
- OSTI ID: 1840685
- Grant/Contract Number:
- AC02-06CH11357; 765604
- Resource Type:
- Published Article
- Journal Name:
- Journal of Synchrotron Radiation (Online)
- Additional Journal Information:
- Journal Name: Journal of Synchrotron Radiation (Online) Journal Volume: 28 Journal Issue: 5; Journal ID: ISSN 1600-5775
- Publisher:
- International Union of Crystallography (IUCr)
- Country of Publication:
- Denmark
- Language:
- English
- Subject:
- 73 NUCLEAR PHYSICS AND RADIATION PHYSICS; filtered backprojection; gridrec; synchrotron tomography; filter optimization; tomographic reconstruction
Citation Formats
Ganguly, Poulami Somanya, Pelt, Daniël M., Gürsoy, Doga, de Carlo, Francesco, and Batenburg, K. Joost. Improving reproducibility in synchrotron tomography using implementation-adapted filters. Denmark: N. p., 2021.
Web. doi:10.1107/S1600577521007153.
Ganguly, Poulami Somanya, Pelt, Daniël M., Gürsoy, Doga, de Carlo, Francesco, & Batenburg, K. Joost. Improving reproducibility in synchrotron tomography using implementation-adapted filters. Denmark. https://doi.org/10.1107/S1600577521007153
Ganguly, Poulami Somanya, Pelt, Daniël M., Gürsoy, Doga, de Carlo, Francesco, and Batenburg, K. Joost. Thu .
"Improving reproducibility in synchrotron tomography using implementation-adapted filters". Denmark. https://doi.org/10.1107/S1600577521007153.
@article{osti_1812972,
title = {Improving reproducibility in synchrotron tomography using implementation-adapted filters},
author = {Ganguly, Poulami Somanya and Pelt, Daniël M. and Gürsoy, Doga and de Carlo, Francesco and Batenburg, K. Joost},
abstractNote = {For reconstructing large tomographic datasets fast, filtered backprojection-type or Fourier-based algorithms are still the method of choice, as they have been for decades. These robust and computationally efficient algorithms have been integrated in a broad range of software packages. The continuous mathematical formulas used for image reconstruction in such algorithms are unambiguous. However, variations in discretization and interpolation result in quantitative differences between reconstructed images, and corresponding segmentations, obtained from different software. This hinders reproducibility of experimental results, making it difficult to ensure that results and conclusions from experiments can be reproduced at different facilities or using different software. In this paper, a way to reduce such differences by optimizing the filter used in analytical algorithms is proposed. These filters can be computed using a wrapper routine around a black-box implementation of a reconstruction algorithm, and lead to quantitatively similar reconstructions. Use cases for this approach are demonstrated by computing implementation-adapted filters for several open-source implementations and applying them to simulated phantoms and real-world data acquired at the synchrotron. Our contribution to a reproducible reconstruction step forms a building block towards a fully reproducible synchrotron tomography data processing pipeline.},
doi = {10.1107/S1600577521007153},
journal = {Journal of Synchrotron Radiation (Online)},
number = 5,
volume = 28,
place = {Denmark},
year = {Thu Aug 12 00:00:00 EDT 2021},
month = {Thu Aug 12 00:00:00 EDT 2021}
}
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