@article{a734da520cf64528b6b74a5d4149b431,
title = "Core Imaging Library - Part II: multichannel reconstruction for dynamic and spectral tomography",
abstract = "The newly developed core imaging library (CIL) is a flexible plug and play library for tomographic imaging with a specific focus on iterative reconstruction. CIL provides building blocks for tailored regularized reconstruction algorithms and explicitly supports multichannel tomographic data. In the first part of this two-part publication, we introduced the fundamentals of CIL. This paper focuses on applications of CIL for multichannel data, e.g. dynamic and spectral. We formalize different optimization problems for colour processing, dynamic and hyperspectral tomography and demonstrate CIL's capabilities for designing state-of-the-art reconstruction methods through case studies and code snapshots. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.",
keywords = "X-ray CT, computed tomography, inverse problems, iterative reconstruction, magnetic resonance imaging (MRI), materials science, positron emission tomography (PET), sparse CT",
author = "Evangelos Papoutsellis and Evelina Ametova and Claire Delplancke and Gemma Fardell and J{\o}rgensen, {Jakob S} and Edoardo Pasca and Martin Turner and Ryan Warr and William Lionheart and Philip Withers",
note = "Funding Information: Data accessibility. Python scripts to reproduce the results for all the case studies are provided at [59] with CIL version 21.0 that is available through Anaconda; installation instructions are at https://www.ccpi.ac.uk/cil. In addition, CIL v21.0 and subsequent releases are archived at [5]. The gel phantom used in §4 can be found in [46]. The rock phantom used in §5 can be found in [58]. Authors{\textquoteright} contributions. E.P.(ap) carried out all the experiments, wrote the manuscript and developed the CIL software. J.J. and E.P.(as) conceived the CIL software, assisted with the experiments and developed the CIL software. E.A. and G.F. assisted with the experiments and developed the CIL software. C.D. co-developed the SPDHG algorithm. R.W. assisted with hyperspectral case study and contributed to the CIL software. M.T., W.L. and P.W. helped conceptualize and roll out the CIL software. All authors critically revised the manuscript, gave final approval for publication and agree to be held accountable for the work performed therein. Competing interests. We declare we have no competing interests. Funding. This work was funded by EPSRC grants {\textquoteleft}A Reconstruction Toolkit for Multichannel CT{\textquoteright} (EP/P02226X/1), {\textquoteleft}CCPi: Collaborative Computational Project in Tomographic Imaging{\textquoteright} (EP/M022498/1 and EP/T026677/1). We acknowledge the EPSRC for funding the Henry Moseley X-ray Imaging Facility through grant nos. (EP/F007906/1, EP/F001452/1, EP/I02249X/1, EP/M010619/1, EP/F028431/1 and EP/M022498/1) which is part of the Henry Royce Institute for Advanced Materials funded by EP/R00661X/1. J.S.J. was partially supported by The Villum Foundation (grant no. 25893). E.A. was partially funded by the Federal Ministry of Education and Research (BMBF) and the Baden-W{\"u}rttemberg Ministry of Science as part of the Excellence Strategy of the German Federal and State Governments. W.R.B.L. acknowledges support from a Royal Society Wolfson Research Merit Award. P.J.W and R.W acknowledge support from the European Research Council grant no. 695638 CORREL-CT. C.D. acknowledges support from the EPSRC grant no. EP/S026045/1 {\textquoteleft}PET++: Improving Localization, Diagnosis and Quantification in Clinical and Medical PET Imaging with Randomized Optimization{\textquoteright}. Acknowledgements. This work made use of computational support by CoSeC, the Computational Science Centre for Research Communities, through CCPi. Moreover, E.P.(ap) thank Tommi Heikkil{\"a} from the University of Helsinki for the discussions on the gel phantom. We are grateful to input from Dr. Daniil Kazantsev from the Diamond Light Source, UK, for early stage contributions to this work. The authors thank the reviewers for their comments and efforts towards improving this manuscript. Publisher Copyright: {\textcopyright} 2021 The Authors.",
year = "2021",
month = aug,
day = "23",
doi = "10.1098/rsta.2020.0193",
language = "English",
volume = "379",
journal = "Royal Society of London. Proceedings A. Mathematical, Physical and Engineering Sciences",
issn = "1471-2946",
publisher = "Royal Society",
number = "2204",
}