Improving reproducibility in synchrotron tomography using implementation‐adapted filters

• Published in: Journal of synchrotron radiation 2021-09, Vol.28 (5), p.1583-1597
• Main Authors: Ganguly, Poulami Somanya, Pelt, Daniël M., Gürsoy, Doga, de Carlo, Francesco, Batenburg, K. Joost
• Format: Article
• Language: English
• Subjects: Algorithms; Data acquisition; Data processing; filter optimization; filtered backprojection; gridrec; Image reconstruction; Interpolation; NUCLEAR PHYSICS AND RADIATION PHYSICS; Reproducibility; Research Papers; Robustness (mathematics); Software; Software packages; synchrotron tomography; Synchrotrons; tomographic reconstruction; Tomography
• ISSN: 1600-5775; 0909-0495; 1600-5775
• DOI: 10.1107/S1600577521007153

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. Dissimilar hardware and software conventions at various synchrotrons lead to quantitative differences in experimental results. This paper proposes a method to improve reproducibility of tomographic reconstructions by optimizing the filtering step in commonly used reconstruction algorithms.