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CIL software papers and research using CIL

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Citing CIL

If you use CIL in your research, please cite the appropriate CIL paper(s) based on your work. Additionally, to support software citation best practices, please also cite the software itself via Zenodo.

CIL Software

E. Pasca, J. S. Jørgensen, E. Papoutsellis, E. Ametova, G. Fardell, K. Thielemans, L. Murgatroyd, M. Duff and H. Robarts (2023)
Core Imaging Library (CIL)
Zenodo [software archive]
DOI: 10.5281/zenodo.4746198

Published CIL Papers

In most cases, the first CIL paper will be the appropriate choice:

J. S. Jørgensen, E. Ametova, G. Burca, G. Fardell, E. Papoutsellis, E. Pasca, K. Thielemans, M. Turner, R. Warr, W. R. B. Lionheart and P. J. Withers (2021)
Core Imaging Library - Part I: a versatile Python framework for tomographic imaging.
Phil. Trans. R. Soc. A. 379: 20200192.
DOI | arXiv | Code | Citations
Export citation (BibTeX, RIS)

BibTeX:

@article{Jorgensen2021CIL1,
  title={Core Imaging Library-Part I: a versatile Python framework for tomographic imaging},
  author={J{\o}rgensen, Jakob Sauer and Ametova, Evelina and Burca, Genoveva and Fardell, Gemma and Papoutsellis, Evangelos and Pasca, Edoardo and Thielemans, Kris and Turner, Martin and Warr, Ryan and Lionheart, William RB and Withers, Philip J},
  journal={Philosophical Transactions of the Royal Society A},
  volume={379},
  number={2204},
  pages={20200192},
  year={2021},
  publisher={The Royal Society Publishing},
  doi={10.1098/rsta.2020.0192}
}

RIS:

TY  - JOUR
T1  - Core Imaging Library-Part I: a versatile Python framework for tomographic imaging
AU  - Jørgensen, Jakob Sauer
AU  - Ametova, Evelina
AU  - Burca, Genoveva
AU  - Fardell, Gemma
AU  - Papoutsellis, Evangelos
AU  - Pasca, Edoardo
AU  - Thielemans, Kris
AU  - Turner, Martin
AU  - Warr, Ryan
AU  - Lionheart, William RB
AU  - Withers, Philip J
JO  - Philosophical Transactions of the Royal Society A
VL  - 379
IS  - 2204
SP  - 20200192
PY  - 2021
PB  - The Royal Society Publishing
DO  - 10.1098/rsta.2020.0192
ER  -

However, if your work is more closely related to topics covered in our second CIL paper then please additionally or alternatively reference the second paper:

E. Papoutsellis, E. Ametova, C. Delplancke, G. Fardell, J. S. Jørgensen, E. Pasca, M. Turner, R. Warr, W. R. B. Lionheart and P. J. Withers (2021)
Core Imaging Library - Part II: multichannel reconstruction for dynamic and spectral tomography.
Phil. Trans. R. Soc. A. 379: 20200193.
DOI | arXiv | Code | Citations
Export citation (BibTeX, RIS)

BibTeX:

@article{Papoutsellis2021CIL2,
  title={Core Imaging Library-Part II: multichannel reconstruction for dynamic and spectral tomography},
  author={Papoutsellis, Evangelos and Ametova, Evelina and Delplancke, Claire and Fardell, Gemma and J{\o}rgensen, Jakob Sauer and Pasca, Edoardo and Turner, Martin and Warr, Ryan and Lionheart, William RB and Withers, Philip J},
  journal={Philosophical Transactions of the Royal Society A},
  volume={379},
  number={2204},
  pages={20200193},
  year={2021},
  publisher={The Royal Society Publishing},
  doi={10.1098/rsta.2020.0193}
}

RIS:

TY  - JOUR
T1  - Core Imaging Library-Part II: multichannel reconstruction for dynamic and spectral tomography
AU  - Papoutsellis, Evangelos
AU  - Ametova, Evelina
AU  - Delplancke, Claire
AU  - Fardell, Gemma
AU  - Jørgensen, Jakob Sauer
AU  - Pasca, Edoardo
AU  - Turner, Martin
AU  - Warr, Ryan
AU  - Lionheart, William RB
AU  - Withers, Philip J
JO  - Philosophical Transactions of the Royal Society A
VL  - 379
IS  - 2204
SP  - 20200193
PY  - 2021
PB  - The Royal Society Publishing
DO  - 10.1098/rsta.2020.0193
ER  -

Conference Papers and Forthcoming Publications

If your work uses stochastic methods in CIL, please additionally reference:

E. Papoutsellis, C. da Costa-Luis, D. Deidda, C. Delplancke, M. Duff, G. Fardell, A. Gillman, J. S. Jørgensen, K. Thielemans, E. Pasca and L. Murgatroyd (2024)
Stochastic Optimisation Framework using the Core Imaging Library and Synergistic Image Reconstruction Framework for PET Reconstruction. [conference paper]
arXiv:2406.15159
arXiv | Citations
Note: This reference is for a conference submission and we are currently working on a more substantial paper for early 2026.
Export citation (BibTeX)

BibTeX:

@article{Papoutsellis2024CIL3,
  title={Stochastic Optimisation Framework using the Core Imaging Library and Synergistic Image Reconstruction Framework for PET Reconstruction},
  author={Papoutsellis, Evangelos and da Costa-Luis, Casper and Deidda, Daniel and Delplancke, Claire and Duff, Margaret and Fardell, Gemma and Gillman, Ashley and J{\o}rgensen, Jakob Sauer and Thielemans, Kris and Pasca, Edoardo and Murgatroyd, Laura},
  journal={arXiv preprint arXiv:2406.15159},
  year={2024}
}

Additional Citation Guidelines

Backend libraries: If you use projection operators or reconstruction algorithms from backend libraries (e.g., TIGRE, ASTRA toolbox) accessed through CIL, please also cite the appropriate papers for those tools.

Acknowledgements and collaboration: If members of the CIL development team have provided substantial personal support or contributions to your research, please consider acknowledging them appropriately or offering co-authorship where warranted. We welcome opportunities to advise, support, and collaborate on research projects. Please contact us to discuss.

Research Using CIL

The following publications (journal papers, conference proceedings, and PhD theses) have used CIL in their research:

If you have used CIL in your work and would like to add your publication to this list, please contact us.

Journal Papers

2026

Mitchell IT, Martini F, Stephens GF, Middleburgh SC, Vidal FP.
Assessing manufacturing defects in ceramic composites with both simulated and experimental synchrotron computed tomography
Progress in Nuclear Energy 190: 106002
DOI

2025

Warnett JM, Harris SJP, Zwanenburg EA, Williams MA.
"Don't stop me now!": Stopping rules for iterative reconstruction with dimensional X-ray Computed Tomography
Precision Engineering 93: 406-416
DOI
Protopapa L, Duff M, Mayer J, Schulz-Menger J, Thielemans K, Kolbitsch C, Pasca E.
Efficient motion-corrected image reconstruction for 3D cardiac MRI through stochastic optimisation
Physics in Medicine & Biology 70(18): 185012
DOI
Ehrhardt MJ, Kereta Ž, Liang J, Tang J.
A guide to stochastic optimisation for large-scale inverse problems
Inverse Problems 41(5): 53001
DOI
Watson FM, Hellier J, Lionheart WRB.
On regularisation of coherent imagery with proximal methods
Inverse Problems 41(6): 65005
DOI
Allan H, Partridge T, Jacob J, Endrizzi M.
Dynamic laboratory x-ray phase-contrast microtomography with structure-based prior regularisation
Measurement Science and Technology 36(9): 95405
DOI
Mitchell IT, Létang JM, Evans LM, Vidal FP.
WebCT – OpenSource web-based GUI for real-time X-ray simulation
Tomography of Materials and Structures 8: 100057
DOI
Vidal FP, Afshari S, Ahmed S, Albiol A, Albiol F, Béchet É, Bellot AC, Bosse S, Burkhard S, Chahid Y, Chou C-Y, Culver R, Desbarats P, Dixon L, Friemann J, Garbout A, García-Lorenzo M, Giovannelli J-F, Hanna R, Hatton C, Henry A, Kelly G, Leblanc C, Leonardi A, Létang JM, Lipscomb H, Manchester T, Meere B, Michelet C, Middleburgh S, Mihail RP, Mitchell I, Perera L, Puig M, Racy M, Rouwane A, Seznec H, Sújar A, Tugwell-Allsup J, Villard P-F.
X-ray simulations with gVXR in education, digital twining, experiment planning, and data analysis
Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 568: 165804
DOI

2024

Simmendefeldt Schmidt B, Sauer J, Jørgensen JSR, Galdon-Quíroga J, García-Muñoz M, Salewski M.
Anisotropic regularization for inversion of fast-ion loss detector measurements
Nuclear Fusion 64(10): 106053
DOI
Kumrular RK, Blumensath T.
Unsupervised Denoising in Spectral CT: Multi-Dimensional U-Net for Energy Channel Regularisation
Sensors 24(20): 6654
DOI
Christensen SL, Riis NAB, Pereyra M, Jørgensen JS.
A Bayesian approach for CT reconstruction with defect detection for subsea pipelines
Inverse Problems 40(2): 25003
DOI
Watson FM, Andre D, Lionheart WRB.
Resolving full-wave through-wall transmission effects in multi-static synthetic aperture radar
Inverse Problems 40(8): 85009
DOI
Riis NAB, Alghamdi AMA, Uribe F, Christensen SL, Afkham BM, Hansen PC, Jørgensen JS.
CUQIpy: I. Computational uncertainty quantification for inverse problems in Python
Inverse Problems 40(4): 45009
DOI
Zillhardt TAC, van Westrenen W, Nuij M, Langenhorst F, Poupon G, Burca G, Grazzi F, Klein V, Eppink JJGM, Melai J, Bauch KE.
The Dutch Apollo 11 Goodwill display contains genuine Moon rocks
Communications Earth & Environment 5: 765
DOI

2023

Jørgensen JS, Papoutsellis E, Murgatroyd L, Fardell G, Pasca E.
A directional regularization method for the limited-angle Helsinki Tomography Challenge using the Core Imaging Library (CIL)
Applied Mathematics for Modern Challenges 1(2): 143-169
DOI
Zharov Y, Ametova E, Spiecker R, Baumbach T, Burca G, Heuveline V.
Shot noise reduction in radiographic and tomographic multi-channel imaging with self-supervised deep learning
Optics Express 31(16): 26226
DOI
Pointon JL, Wen T, Tugwell-Allsup J, Létang JM, Vidal FP.
gVirtualXray (gVXR): Simulating X-ray radiographs and CT volumes of anthropomorphic phantoms
Software Impacts 16: 100513
DOI
Pointon JL, Wen T, Tugwell-Allsup J, Sújar A, Létang JM, Vidal FP.
Simulation of X-ray projections on GPU: Benchmarking gVirtualXray with clinically realistic phantoms
Computer Methods and Programs in Biomedicine 234: 107500
DOI
Daugherty MC, DiStefano VH, LaManna JM, Jacobson DL, Kienzle PA, Kim Y, Hussey DS, Bajcsy P.
Assessment of Dose-Reduction Strategies in Wavelength-Selective Neutron Tomography
SN Computer Science 4(5)
DOI

2022

Warr R, Handschuh S, Glösmann M, Cernik RJ, Withers PJ.
Quantifying multiple stain distributions in bioimaging by hyperspectral X-ray tomography
Scientific Reports 12(1)
DOI
Davis GR.
Development of two-dimensional beam hardening correction for X-ray micro-CT
Journal of X-Ray Science and Technology 30(5): 863
DOI
Piccolomini EL.
A comparison of regularization models for few-view CT image reconstruction
Annali dell'Università di Ferrara 68(2): 385
DOI
Watson FM.
Focusing dynamic single‐channel synthetic aperture radar video with optical flow‐informed reconstruction
Electronics Letters 58(25): 991
DOI

2021

Ametova E, Burca G, Chilingaryan S, Fardell G, Jørgensen JS, Papoutsellis E, Pasca E, Warr R, Turner M, Lionheart WRB, Withers PJ.
Crystalline phase discriminating neutron tomography using advanced reconstruction methods
Journal of Physics D: Applied Physics 54(32): 325502
DOI
Warr R, Ametova E, Cernik RJ, Fardell G, Handschuh S, Jørgensen JS, Papoutsellis E, Pasca E, Withers PJ.
Enhanced hyperspectral tomography for bioimaging by spatiospectral reconstruction
Scientific Reports 11(1): 20818
DOI
Brown R, Kolbitsch C, Delplancke C, Papoutsellis E, Mayer J, Ovtchinnikov E, Pasca E, Neji R, da Costa-Luis C, Gillman AG, Ehrhardt MJ, McClelland JR, Eiben B, Thielemans K.
Motion estimation and correction for simultaneous PET/MR using SIRF and CIL
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 379(2204): 20200208
DOI

Conference Proceedings

2025

Kumrular RK, Blumensath T.
Balance between the number of projections and exposure time in photon counting CT with a data-driven approach
Proceedings of SPIE 13405, Medical Imaging 2025: Physics of Medical Imaging: 134053P
DOI

2024

Roche i Morgo O, Jia Y, Allan H, Batey DJ, Birkbak ME, Boardman R, Brown E, Buckman J, Cacho-Nerin F, Calder S, Caunt S, Christou K, Clifford CJ, Endrizzi M, Evans JPM, Fell B, Ferreira SA, Fish KN, Friis ET, Gibbard J, Gogotsi Y, Hall CJ, Lee PD, Martinez PA, Michell C, Mitchell TM, Mosselmans JFW, Nowell MM, Nowicki T, Olbinado M, Pedersen GK, Preston A, Punshon CS, Rau C, Sawhney K, Schlepütz CM, Scott TB, Senesi AJ, Thibault P, Wadeson N, Walton RI, Withers PJ, Zdora M-C.
A new user facility with flexible multi-scale, multi-contrast micro-CT capabilities
Proceedings of SPIE 13152, X-Ray Nanoimaging: Instruments and Methods VII: 1315209
DOI
Kumrular RK, Blumensath T.
Unsupervised denoising for spectral CT images using a U-Net with block-based training
Proceedings of SPIE 13043, Anomaly Detection and Imaging with X-Rays (ADIX) IX: 1304307
DOI

PhD Theses

2024

Christensen SW.
Prior modelling and uncertainty quantification in X-ray computed tomography with application to defect detection in subsea pipes
PhD Thesis, Technical University of Denmark
DOI | PDF