Cargando…

Improving reproducibility in synchrotron tomography using implementation-adapted filters

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Ganguly, Poulami Somanya, Pelt, Daniël M., Gürsoy, Doga, de Carlo, Francesco, Batenburg, K. Joost
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8415339/
https://www.ncbi.nlm.nih.gov/pubmed/34475305
http://dx.doi.org/10.1107/S1600577521007153
_version_ 1783747948851494912
author Ganguly, Poulami Somanya
Pelt, Daniël M.
Gürsoy, Doga
de Carlo, Francesco
Batenburg, K. Joost
author_facet Ganguly, Poulami Somanya
Pelt, Daniël M.
Gürsoy, Doga
de Carlo, Francesco
Batenburg, K. Joost
author_sort Ganguly, Poulami Somanya
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8415339
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher International Union of Crystallography
record_format MEDLINE/PubMed
spelling pubmed-84153392021-09-16 Improving reproducibility in synchrotron tomography using implementation-adapted filters Ganguly, Poulami Somanya Pelt, Daniël M. Gürsoy, Doga de Carlo, Francesco Batenburg, K. Joost J Synchrotron Radiat Research Papers 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. International Union of Crystallography 2021-08-12 /pmc/articles/PMC8415339/ /pubmed/34475305 http://dx.doi.org/10.1107/S1600577521007153 Text en © Poulami Somanya Ganguly et al. 2021 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Research Papers
Ganguly, Poulami Somanya
Pelt, Daniël M.
Gürsoy, Doga
de Carlo, Francesco
Batenburg, K. Joost
Improving reproducibility in synchrotron tomography using implementation-adapted filters
title Improving reproducibility in synchrotron tomography using implementation-adapted filters
title_full Improving reproducibility in synchrotron tomography using implementation-adapted filters
title_fullStr Improving reproducibility in synchrotron tomography using implementation-adapted filters
title_full_unstemmed Improving reproducibility in synchrotron tomography using implementation-adapted filters
title_short Improving reproducibility in synchrotron tomography using implementation-adapted filters
title_sort improving reproducibility in synchrotron tomography using implementation-adapted filters
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8415339/
https://www.ncbi.nlm.nih.gov/pubmed/34475305
http://dx.doi.org/10.1107/S1600577521007153
work_keys_str_mv AT gangulypoulamisomanya improvingreproducibilityinsynchrotrontomographyusingimplementationadaptedfilters
AT peltdanielm improvingreproducibilityinsynchrotrontomographyusingimplementationadaptedfilters
AT gursoydoga improvingreproducibilityinsynchrotrontomographyusingimplementationadaptedfilters
AT decarlofrancesco improvingreproducibilityinsynchrotrontomographyusingimplementationadaptedfilters
AT batenburgkjoost improvingreproducibilityinsynchrotrontomographyusingimplementationadaptedfilters