Open Source Software for Medical Imaging

Medical imaging requires an enormous amount of expert knowledge in signal processing, image reconstruction and image processing. At our institute we develop imaging algorithms using the open source scientific programming language Julia and make them available via the collaborative version control platform GitHub under the MIT license. This enables the documentation of scientific methodology and ensures the reproducibility of our own research contributions. Furthermore, even scientists with only rudimentary knowledge of medical imaging are enabled to use state-of-the-art image reconstruction methods. We are happy about any feedback / suggestions that can be send by email to us. Improvements and amendments can be also directly made on GitHub.

All MPI related projects are collected in the MagneticParticleImaging organization, while the institute's contributions to MRI are collected in the MagneticResonanceImaging organization. Projects, which cannot be assigned clearly to an imaging method, are maintained JuliaImageRecon organization, where are our main contributions are:

Furthermore, some individual packages are mainteined under the account of Tobias Knopp and the IBIResearch organization, where our main contributions are:

Magnetic Particle Imaging
Magnetic Resonance Imaging
Further Projects

Publications

  • P. Jürß, C. Droigk, M. Boberg, and T. Knopp (2025). TrainingPhantoms.jl: Simple and Versatile Image Phantom Generation. International Journal on Magnetic Particle Imaging. 11. (1 Suppl 1), 1-2 [Abstract] [doi] [www]

  • N. Hackelberg, M. Grosser, A. Tsanda, F. Mohn, K. Scheffler, M. Möddel, and T. Knopp (2024). RegularizedLeastSquares.jl: Modality Agnostic Julia Package for Solving Regularized Least Squares Problems. International Journal on Magnetic Particle Imaging. 10. (1 Suppl 1), 1-4 [Abstract] [doi]

  • N. Hackelberg, J. Schumacher, J. Ackers, M. Möddel, F. Foerger, M. Graeser, and T. Knopp (2023). MPIMeasurements.jl: An Extensible Julia Framework for Composable Magnetic Particle Imaging Devices. International Journal on Magnetic Particle Imaging. 9. (1), 1-4 [Abstract] [doi] [www]

  • T. Knopp, M. Boberg, and M. Grosser (2023). NFFT.jl: Generic and Fast Julia Implementation of the Nonequidistant Fast Fourier Transform. SIAM Journal on Scientific Computing. 45. (3), C179-C205 [Abstract] [doi] [www]

  • T. Knopp and M. Grosser (2021). MRIReco.jl: An MRI Reconstruction Framework written in Julia. Magn. Reson. Med.. 86. (3), 1633-1646 [doi] [www]

  • T. Knopp and M. Grosser (2019). MRIReco.jl: An Extensible Open-Source Image Reconstruction Framework written in Julia. Proc. ISMRM 2019.

  • T. Knopp, M. Möddel, F. Griese, F. Werner, P. Szwargulski, N. Gdaniec, and M. Boberg (2019). MPIFiles.jl: A Julia Package for Magnetic Particle Imaging Files. Journal of Open Source Software. 4. (38), 1331 [doi] [www]

  • T. Knopp, P. Szwargulski, F. Griese, M. Grosser, M. Boberg, and M. Möddel (2019). MPIReco.jl: Julia Package for Image Reconstruction in MPI. International Journal on Magnetic Particle Imaging. 5. (1), 9 pp [doi]