Helmholtz Imaging

A citable reference will follow with the first release. Until then, please cite nnInteractive and nnU-Net.

Isensee, Rokuss, Krämer, et al. nnInteractive: Redefining 3D Promptable Segmentation. arXiv:2503.08373, 2025.

@misc{isensee2025nninteractive,
  title={nnInteractive: Redefining 3D Promptable Segmentation},
  author={Isensee, Fabian and Rokuss, Maximilian and Kr{\"a}mer, Lars and Dinkelacker, Stefan and Ravindran, Ashis and Stritzke, Florian and Hamm, Benjamin and Wald, Tassilo and Langenberg, Moritz and Ulrich, Constantin and Deissler, Jonathan and Floca, Ralf and Maier-Hein, Klaus},
  year={2025},
  eprint={2503.08373},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  url={https://arxiv.org/abs/2503.08373}
}

Isensee, Jaeger, Kohl, Petersen, Maier-Hein. nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nature Methods 18(2), 203–211, 2021.

@article{isensee2021nnunet,
  title={nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation},
  author={Isensee, Fabian and Jaeger, Paul F. and Kohl, Simon A. A. and Petersen, Jens and Maier-Hein, Klaus H.},
  journal={Nature Methods},
  volume={18},
  number={2},
  pages={203--211},
  year={2021},
  doi={10.1038/s41592-020-01008-z}
}

Isensee, Wald, Ulrich, et al. nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation. MICCAI 2024. (Residual encoder planners, the nnWorkbench default.)

@inproceedings{isensee2024nnunetrevisited,
  title={nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation},
  author={Isensee, Fabian and Wald, Tassilo and Ulrich, Constantin and Baumgartner, Michael and Roy, Saikat and Maier-Hein, Klaus and Jaeger, Paul F.},
  booktitle={Medical Image Computing and Computer Assisted Intervention (MICCAI)},
  year={2024},
  eprint={2404.09556},
  archivePrefix={arXiv},
  url={https://arxiv.org/abs/2404.09556}
}

van Nistelrooij, Krämer, Kempers, et al. ToothSeg: Robust Tooth Instance Segmentation and Numbering in CBCT Using Deep Learning and Self-Correction. IEEE Journal of Biomedical and Health Informatics 30(8), 6801–6812, 2026.

@article{vannistelrooij2026toothseg,
  title={ToothSeg: Robust Tooth Instance Segmentation and Numbering in CBCT Using Deep Learning and Self-Correction},
  author={van Nistelrooij, Niels and Kr{\"a}mer, Lars and Kempers, Steven and Beyer, Michel and Bolelli, Federico and Xi, Tong and Berg{\'e}, Stefaan and Heiland, Max and Maier-Hein, Klaus H. and Vinayahalingam, Shankeeth and Isensee, Fabian},
  journal={IEEE Journal of Biomedical and Health Informatics},
  volume={30},
  number={8},
  pages={6801--6812},
  year={2026},
  doi={10.1109/JBHI.2025.3650444}
}