CCP SyneRBI

Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging

Publications

Journal Articles

  • Jakob S. Jørgensen, Evelina Ametova, Genoveva Burca, Gemma Fardell, Evangelos Papoutsellis, Edoardo Pasca, Kris Thielemans, Martin Turner, Ryan Warr, William R. B. Lionheart, Philip J. Withers,
    Core Imaging Library -- Part I: a versatile Python framework for tomographic imaging, Special issue on Synergistic Image Reconstruction, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 379, no. 2204 (23 August 2021): 20200192. https://doi.org/10.1098/rsta.2020.0192.
  • Richard Brown, Christoph Kolbitsch, Claire Delplancke, Evangelos Papoutsellis, Johannes Mayer, Evgueni Ovtchinnikov, Edoardo Pasca, Radhouene Neji, Casper da Costa-Luis, Ashley G. Gillman, Matthias J. Ehrhardt, Jamie McClelland, Bjoern Eiben, and Kris Thielemans
    “Motion estimation and correction for simultaneous PET/MR using SIRF”, Special issue on Synergistic Image Reconstruction, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 379, no. 2204 (23 August 2021): 20200208. https://doi.org/10.1098/rsta.2020.0208.
  • Mayer, Johannes, Richard Brown, Kris Thielemans, Evgueni Ovtchinnikov, Edoardo Pasca, David Atkinson, Ashley Gillman, et al. ‘
    Flexible Numerical Simulation Framework for Dynamic PET-MR Data’. Physics in Medicine & Biology 65, no. 14 (July 2020): 145003. https://doi.org/10.1088/1361-6560/ab7eee
  • Wadhwa, Palak, Kris Thielemans, Nikos Efthimiou, Kristen Wangerin, Nicholas Keat, Elise Emond, Timothy Deller, Ottavia Bertolli, Daniel Deidda; Gaspar Delso, Michel Tohme, Floris Jansen; Roger Gunn; William Hallett; Charalampos Tsoumpas (2020)
    PET Image reconstruction using physical and mathematical modelling for time of flight PET-MR scanners in the STIR library. Methods, Special Issue on Methods in Simulation of Biomedicine. 185 (1 January 2021): 110–19. doi: https://doi.org/10.1016/j.ymeth.2020.01.005
  • Nikos Efthimiou, Elise Emond, Palak Wadhwa, Christopher Cawthorne, Charalampos Tsoumpas, Kris Thielemans,
    " Implementation and validation of time-of-flight PET image reconstruction module for listmode and sinogram projection data in the STIR library", Phys. Med. Biol., 2019 64 035004, doi: https://doi.org/10.1088/1361-6560/aaf9b9
  • D Deidda, N Karakatsanis, P Robson, YJ Tsai, N Efthimiou, K Thielemans, Z Fayad, R Aykroyd, C Tsoumpas,
    “Hybrid PET-MR List-Mode Kernelized Expectation Maximization Reconstruction”, Inverse Problems, 2019/1/21, https://doi.org/10.1088/1361-6420/ab013f
  • Evgueni Ovtchinnikov, Richard Brown, Christoph Kolbitsch, Edoardo Pasca, Casper da Costa-Luis, Ashley G. Gillman, Benjamin A. Thomas, Nikos Efthymiou, Johannes Mayer, Palak Wadhwa, Matthias J. Ehrhardt, Sam Ellis, Jakob S. Jørgensen, Julian Matthews, Claudia Prieto, Andrew J. Reader, Charalampos Tsoumpas, Martin Turner, David Atkinson, Kris Thielemans,
    SIRF: Synergistic Image Reconstruction Framework, Computer Physics Communications Volume 249, April 2020, 107087, doi: https://doi.org/10.1016/j.cpc.2019.107087

Conference Contributions

  • Evgueni Ovtchinnikov, David Atkinson, Ronald Fowler, Christoph Kolbitsch, Julian Matthews, Claudia Prieto, Andrew Reader, Charalampos Tsoumpas, Martin Turner, Kris Thielemans,
    A Proposal for an Open Source Framework for Synergistic Image Reconstruction of PET-MR Data, PSMR 2016, 5th Conference on PET/MR and SPECT/MR, Koeln, Germany.
  • Ovtchinnikov E, Atkinson D, Bertolli O, da Costa-Luis C, Efthimiou N, Fowler R, Kolbitsch C, Matthews J, Prieto C, Reader A, Thomas BA, Tsoumpas C, Turner M, Thielemans K,
    SIRF: Synergistic Image Reconstruction Framework, PSMR 2017, 6th Conference on PET/MR and SPECT/MR, Lisbon, Portugal
  • Wadhwa P; Thielemans K; Tsoumpas C (2017)
    Validation of recent developments in STIR library for GE SIGNA PET/MR scanner using real data. Conference on Bio-Medical Instrumentation & related Engineering & Physical Sciences. Athens, Greece
  • Richard Brown, Benjamin A. Thomas, Alaleh Rashidnasab, Yu-Jung Tsai, Daniel Deidda, Evgueni Ovtchinnikov, Edoardo Pasca, Casper da Costa-Luis, Brian F. Hutton, Charalampos Tsoumpas, Kris Thielemans,
    “Motion-Corrected PET Reconstruction with SIRF”, PSMR 2018, 7th Conference on PET/MR and SPECT/MR, 21-23 May, Isle of Elba, Italy.
  • Deidda D; Karakatsanis N; Robson PM; Tsai Y-J; Efthimiou N; Thielemans K; Fayad ZA; Aykroyd RG; Tsoumpas C (2018)
    A comparison on two ways of including MR information into the PET reconstruction algorithm: the hybrid kernel and the parallel level sets. PSMR 2018, 7th Conference on PET/MR and SPECT/MR, 21-23 May, Isle of Elba, Italy.
  • Thielemans K; Tsoumpas C; Efthimiou N (2018)
    STIR: an open source library for PET and SPECT image reconstruction. SIAM Conference on Imaging Science, 5-8 June, Bologna, Italy.
  • Mayer J, Thielemans K, Brown R, Ovtchinnikov E, Atkinson D, Marsden P, Schaffter T, Kolbitsch C,
    Flexible numerical simulation framework for dynamic PET-MRI, International Society for Magnetic Resonance in Medicine, Montreal, Canada, 11 May 2019 - 16 May 2019. 6235. 28 Apr 2019.
  • Wadhwa P; Efthimiou N; Thielemans K; Emond E; Wangerin K; Jansen F; Delso G; Hallett W; Gunn R; Buckley D; Tsoumpas C (2019)
    Integrating ToF PET image reconstruction for the GE SIGNA PET/MR scanner in STIR. 8th Conference on PET/MR and SPECT/MR, 15-17 April, Munich, Germany.

Conference Proceedings

  • Deidda D; Efthimiou N; Manber R; Markiewicz P; Thielemans K; Aykroyd R; Tsoumpas C (2016)
    Comparative evaluation of image reconstruction methods for the Siemens PET-MR scanner using STIR library. IEEE Nucl Sci Symp Med Imaging Conf, Strasbourg, France
  • Ovtchinnikov E, Atkinson D, Kolbitsch C, Thomas BA, Bertolli O, da Costa-Luis C, Efthimiou N, Fowler R, Pasca E, Wadhwa P, Emond E, Matthews J, Reader A, Tsoumpas C, Prieto C, Turner M, Thielemans K,
    SIRF: Synergistic Image Reconstruction Framework, IEEE MIC 2017, Atlanta, George, USA
  • P. Wadhwa, K. Thielemans, O. Bertolli, N. Efthimiou, E. Emond, B. A. Thomas, M. Tohme, G. Delso, W. Hallett, R. Gunn, D. Buckley, C. Tsoumpas,
    “Implementation and Validation of Image Reconstruction for PET Data From GE SIGNA PET/MR Scanners In the STIR Library”, IEEE NSS/MIC, 2018.
  • Richard Brown, Benjamin A. Thomas, Alaleh Rashidnasab, Kjell Erlandsson, Evgueni Ovtchinnikov, Edoardo Pasca, Andrew Reader, Julian Matthews, Charalampos Tsoumpas, Kris Thielemans,
    “Motion-Corrected Reconstruction of Parametric Images from Dynamic PET Data with the Synergistic Image Reconstruction Framework (SIRF)”, IEEE NSS/MIC, 2018.
  • Daniil Kazantsev , Edoardo Pasca, Mark Basham, Martin Turner, Matthias J. Ehrhardt, Kris Thielemans, Benjamin A. Thomas, Evgueni Ovtchinnikov, Philip J. Withers, Alun W. Ashton,
    “Versatile regularisation toolkit for iterative image reconstruction with proximal splitting algorithms”, Fully3D 2019, Philadelphia, USA. DOI: https://dx.doi.org/10.1117/12.2534289