@article{oettinger2026diffeomorphism,
  title={Diffeomorphism-Equivariant Neural Networks},
  author={Oettinger, Josephine Elisabeth and Shumaylov, Zakhar and Bostelmann, Johannes and Lellmann, Jan and Sch{\"o}nlieb, Carola-Bibiane},
  journal={arXiv preprint arXiv:2602.06695},
  year={2026}
}

Analysis of 3D/2D Image Registration and a New
Registration Approach Based on Residual Neural Networks

@article{heldmann2026practical,
  title={A practical probabilistic framework for deformable image registration uncertainty in radiotherapy dose propagation},
  author={Heldmann, Stefan and Kuckertz, Sven and Givehchi, Nasim and Coradi, Thomas and Byrne, Mikel and Archibald-Heeren, Ben and Papenberg, Nils},
  journal={arXiv preprint arXiv:2606.09253},
  year={2026}
}

@inbook {
author={Kohlbrandt, Temke and Geissler, Kai and Heldmann, Stefan},
year={2026},
month={03},
pages={26-32},
title={How Predictable is the Human Body?: Predicting Organ Bounding Boxes With a Statistical Atlas Based on Four Keypoints},
isbn={978-3-658-51099-2},
doi={10.1007/978-3-658-51100-5_5}
}

@inbook{inbook,
author = {Walluscheck, Sina and Cangalovic, Vanja and Lossau, Tanja and Heldmann, Stefan and Moltz, Jan},
year = {2026},
month = {03},
pages = {468-474},
title = {Neural Instance Optimization for Lesion Segmentation in Follow-up CT},
isbn = {978-3-658-51099-2},
doi = {10.1007/978-3-658-51100-5_95}
}

@inproceedings{bostelmann2026liemorph,
  title={Liemorph-Transformer-based Image Registration using Flows on Lie Groups.},
  author={Bostelmann, Johannes and Lellmann, Jan},
  booktitle={Bildverarbeitung f{\"u}r die Medizin},
  pages={106--107},
  year={2026}
}

@article{bostelmann2026stationary,
  title={Stationary velocity fields on matrix groups for deformable image registration},
  author={Bostelmann, Johannes and Gildemeister, Ole and Lellmann, Jan},
  journal={Journal of Mathematical Imaging and Vision},
  volume={68},
  number={2},
  pages={9},
  year={2026},
  publisher={Springer}
}

@article{gatidis2026longitudinal,
  title={A longitudinal whole-body CT dataset with manually annotated tumor lesions},
  author={Gatidis, Sergios and Peisen, Felix and Wagner, Andreas and Choudja, Pauline Ornela Megne and Othman, Ahmed and Sanner, Antoine and Grauhan, Nils and Kim, Suam and Graafen, Dirk and M{\"u}ller, Lukas and others},
  journal={Scientific Data},
  year={2026},
  publisher={Nature Publishing Group UK London}
}

@article{de2026multicenter,
  title={Multicenter AI-versus Expert-Assisted RECIST Target Lesion Measurements in Follow-Up Body CT of Cancer Patients},
  author={de Grauw, Max JJ and Westphal, Max and Smit, Ewoud J and Scholten, Ernst Th and Lo{\ss}au, Tanja and Moltz, Jan and Bottazzi, Silvia and Cuocolo, Renato and D’Angelo, Anna and George, Ajo B and others},
  journal={Radiology Advances},
  pages={umag028},
  year={2026},
  publisher={Oxford University Press}
}

@article{laue2026joint,
  title={Joint zonated quantification of multiple parameters in hepatic lobules},
  author={Laue, Hendrik and Budelmann, Daniel and Albadry, Mohamed and Engel, Christiane and Weiss, Nick and Dahmen, Uta and Schwen, Lars Ole},
  journal={Scientific Reports},
  year={2026},
  publisher={Nature Publishing Group UK London}
}

@inproceedings{schulz2025appropriate,
  title={Appropriate Order of Regularization in 3D/2D Image Registration},
  author={Schulz, Pia F and Mannel, Florian and Modersitzki, Jan},
  booktitle={International Conference on Scale Space and Variational Methods in Computer Vision},
  pages={377--390},
  year={2025},
  organization={Springer}
}

@inproceedings{neuber2025multigrid,
  title={A Multigrid Approach for Fourth-Order Equations in Image Registration},
  author={Neuber, Saskia and Modersitzki, Jan},
  booktitle={International Conference on Scale Space and Variational Methods in Computer Vision},
  pages={391--403},
  year={2025},
  organization={Springer}
}

@inproceedings{gildemeister2025time,
  title={Time-Continuous Sliding Motion Image Registration Using Stationary Velocity Fields for Respiratory Motion Interpolation},
  author={Gildemeister, Ole and Bostelmann, Johannes and Schulz, Pia F and Oltmann, Andra and Rostalski, Phillip and Modersitzki, Jan and Lellmann, Jan},
  booktitle={International Conference on Scale Space and Variational Methods in Computer Vision},
  pages={404--416},
  year={2025},
  organization={Springer}
}

@inproceedings{schulz2025image,
  title={Image registration for a dynamic breathing model},
  author={Schulz, Pia F and Oltmann, Andra and Bostelmann, Johannes and Gildemeister, Ole and Wegner, Franz and Lellmann, Jan and Rostalski, Philipp and Modersitzki, Jan},
  booktitle={BVM Workshop},
  pages={5--11},
  year={2025},
  organization={Springer}
}

@inproceedings{oltmann2025simulation,
  title={Simulation of Diaphragmatic Motor Unit Action Potentials Throughout the Respiratory Cycle Using a Dynamic Breathing Model.},
  author={Oltmann, Andra and Gildemeister, Ole and Bostelmann, Johannes and Schulz, Pia F and Grashoff, Jan and Wegner, Franz and Frydrychowicz, Alex and Lellmann, Jan and Modersitzki, Jan and Knopp, Tobias and others},
  booktitle={Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference},
  volume={2025},
  pages={1--7},
  year={2025}
}

@article{nicke2025tissue,
  title={Tissue concepts: Supervised foundation models in computational pathology},
  author={Nicke, Till and Sch{\"a}fer, Jan Raphael and H{\"o}fener, Henning and Feuerhake, Friedrich and Merhof, Dorit and Kie{\ss}ling, Fabian and Lotz, Johannes},
  journal={Computers in Biology and Medicine},
  volume={186},
  pages={109621},
  year={2025},
  publisher={Elsevier}
}

@inproceedings{huang2025preservation,
  title={Preservation of Image Content in Stain-to-stain Translation for Digital Pathology},
  author={Huang, Boqiang and Benjeddou, Wissem and Schaadt, Nadine S and Lotz, Johannes and Feuerhake, Friedrich and Merhof, Dorit},
  booktitle={BVM Workshop},
  pages={119--128},
  year={2025},
  organization={Springer}
}

@article{nicke2025tissue,
  title={Tissue Concepts v2: A Supervised Foundation Model For Whole Slide Images},
  author={Nicke, Till and Schacherer, Daniela and Sch{\"a}fer, Jan Raphael and Artysh, Natalia and Prasse, Antje and Homeyer, Andr{\'e} and Schenk, Andrea and H{\"o}fener, Henning and Lotz, Johannes},
  journal={arXiv preprint arXiv:2507.05742},
  year={2025}
}

@article{grzeski2025integrating,
  title={Integrating MALDI-MSI-Based Spatial Proteomics and Machine Learning to Predict Chemoradiotherapy Outcomes in Head and Neck Cancer},
  author={Grzeski, Marta and Jensen, Patrick Moeller and Hempel, Benjamin-Florian and Thiele, Herbert and Lellmann, Jan and Schallenberg, Simon and Budach, Volker and Keilholz, Ulrich and Tinhofer, Ingeborg and Klein, Oliver},
  journal={International journal of molecular sciences},
  volume={26},
  number={18},
  pages={9084},
  year={2025},
  publisher={MDPI}
}

@article{mannel2025structured,
  title={A structured L-BFGS method with diagonal scaling and its application to image registration},
  author={Mannel, Florian and Aggrawal, Hari Om},
  journal={Journal of Mathematical Imaging and Vision},
  volume={67},
  number={1},
  pages={7},
  year={2025},
  publisher={Springer}
}

@article{neuber2025second,
  title={A Second-Order Divergence-Curl Regularization in Variational Image Registration},
  author={Neuber, Saskia},
  year={2025}
}

@article{bostelmann2025liemorph,
  title={LieMorph: Transformer-based Image Registration Using Flows on Lie Groups},
  author={Bostelmann, Johannes and Lellmann, Jan},
  year={2025}
}

@article{article,
author = {Kipritidis, John and Quinn, Alexandra and Morgas, Tomasz and Kuckertz, Sven and Papenberg, Nils and Heldmann, Stefan and Givehchi, Nasim and Coradi, Thomas and Booth, Jeremy},
year = {2025},
month = {09},
pages = {},
title = {Method for end‐user validation of deformable dose accumulation uncertainty modelling tools},
volume = {52},
journal = {Medical Physics},
doi = {10.1002/mp.18094}
}

@article{article,
author = {Bendak, Sebastian and Georgii, Joachim and Taghizadeh, Elham and Heldmann, Stefan and Meine, Hans and Lange, Thomas and Buchholtz, Jonas and Fuchs, Andreas and Mayr, Moritz and Schmal, Hagen and Izadpanah, Kaywan},
year = {2025},
month = {08},
pages = {},
title = {In vivo dynamic intrusion and extrusion of the menisci in varus and valgus load within a healthy population},
volume = {12},
journal = {Journal of Experimental Orthopaedics},
doi = {10.1002/jeo2.70325}
}

@inproceedings{inproceedings,
author = {Geißler, Kai and Mensing, Daniel and Kohlbrandt, Temke and Hirsch, Jochen and Heldmann, Stefan},
year = {2025},
month = {04},
pages = {58},
title = {Predicting anatomical structures from 2D depth images of patients},
doi = {10.1117/12.3046770}
}

@inproceedings{inproceedings,
author = {Mensing, Daniel and Geißler, Kai and Hirsch, Jochen and Heldmann, Stefan and Günther, Matthias},
year = {2025},
month = {04},
pages = {65},
title = {MR-to-CT synthesis for cross-modality model adaptation},
doi = {10.1117/12.3046926}
}

@inproceedings{inproceedings,
author = {Weiler, Florian and Koller, Tom and Krismer, Laura and Roelz, Roland and Heldmann, Stefan and Klein, Jan},
year = {2025},
month = {04},
pages = {49},
title = {Landmark-based 2D/3D registration of preoperative planning data to intraoperative photographs for mapping of functional areas in awake brain surgery},
doi = {10.1117/12.3048787}
}

@inproceedings{jordan2025integrating,
  title={Integrating heart-on-chip technology and 3D porcine living myocardial slices for cardiotoxicity screening},
  author={Jordan, Maria and Schmieder, Florian and Stucki-Koch, Angelika and Polk, Christoph and Hansen, Christina and Philipp, J{\"u}rgen and Behrens, Stephan and Ramm, Robert and Nicke, Till and Budelmann, Daniel and others},
  booktitle={Current Directions in Biomedical Engineering},
  volume={11},
  number={1},
  pages={270--273},
  year={2025},
  organization={De Gruyter}
}

@article{nicke2025whole,
  title={Whole Slide Concepts: A Supervised Foundation Model For Pathological Images},
  author={Nicke, Till and Schacherer, Daniela and Sch{\"a}fer, Jan Raphael and Artysh, Natalia and Prasse, Antje and Homeyer, Andr{\'e} and Schenk, Andrea and H{\"o}fener, Henning and Lotz, Johannes},
  journal={arXiv preprint arXiv:2507.05742},
  year={2025}
}

@article{eichelberg2025prosurvival,
  title={PROSurvival-{\"U}berlebensvorhersage f{\"u}r Prostatakrebspatienten mithilfe von f{\"o}deriertem maschinellem Lernen und pr{\"a}diktiven morphologischen Mustern},
  author={Eichelberg, Marco and Wolters, Timo and Xu, Tingyan and Lotz, Johannes and Nicke, Till and Sch{\"a}fer, Jan Raphael and Schwen, Ole and Thielke, Felix and Bein, Julia and Chun, Felix and others},
  year={2025},
  publisher={Hannover: Technische Informationsbibliothek}
}

@article{schafer2025labeling,
  title={Labeling system for labeling a medical image},
  author={Sch{\"a}fer, Jan Raphael and Nicke, Till and Lotz, Johannes and H{\"o}fener, Henning and Kie{\ss}ling, Fabian},
  year={2025}
}

@article{van2025tumor,
  title={Tumor-infiltrating lymphocytes in breast cancer through artificial intelligence: biomarker analysis from the results of the TIGER challenge},
  author={van Rijthoven, Mart and Aswolinskiy, Witali and Tessier, Leslie and Balkenhol, Maschenka and Bogaerts, Joep MA and Drubay, Damien and Blesa, Laura Comerma and Peeters, Dieter and Stovgaard, Elisabeth Specht and L{\ae}nkholm, Anne-Vibeke and others},
  journal={medRxiv},
  pages={2025--02},
  year={2025},
  publisher={Cold Spring Harbor Laboratory Press}
}

@misc{nicke2024tissueconceptssupervisedfoundation,
      title={Tissue Concepts: supervised foundation models in computational pathology}, 
      author={Till Nicke and Jan Raphael Schaefer and Henning Hoefener and Friedrich Feuerhake and Dorit Merhof and Fabian Kiessling and Johannes Lotz},
      year={2024},
      eprint={2409.03519},
      archivePrefix={arXiv},
      primaryClass={eess.IV},
      url={https://arxiv.org/abs/2409.03519}, 
}

@article{schafer2024overcoming,
  title={Overcoming data scarcity in biomedical imaging with a foundational multi-task model},
  author={Schäfer, Raphael and Nicke, Till and Höfener, Henning and Lange, Annkristin and Merhof, Dorit and Feuerhake, Friedrich and Schulz, Volkmar and Lotz, Johannes and Kiessling, Fabian},
  journal={Nature Computational Science},
  volume={4},
  number={7},
  pages={495--509},
  year={2024},
  publisher={Nature Publishing Group US New York}
}

@phdthesis{bednarski2024functional,
  title={Functional Lifting: Nonlinear Inverse Scale Space Iterations and Neural Fields},
  author={Bednarski, Danielle},
  year={2024},
  school={Universit{\"a}t zu L{\"u}beck}
}

@inproceedings{neuber2024segmentation,
title={Segmentation-inspired Image Registration},
author={Neuber, Saskia and Schulz, Pia F and Kuckertz, Sven and Modersitzki, Jan},
booktitle={Bildverarbeitung für die Medizin 2024: Proceedings, German Conference on Medical Image Computing, Erlangen, March 10-12, 2024},
pages={205},
year={2024},
organization={Springer-Verlag}
}

@article{schumacher2024covid,
  title={COVID-19 isolation and quarantine orders in Berlin-Reinickendorf (Germany): How many, how long and to whom?},
  author={Schumacher, Jakob and Kühne, Lisa and Brüssermann, Sophia and Geisler, Benjamin and Jäckle, Sonja},
  journal={Plos one},
  volume={19},
  number={3},
  pages={e0271848},
  year={2024},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{WalluscheckEtAl2024,
	author = {Sina Walluscheck and Annika Gerken and Ivana Galinovic and Kersten Villringer and Jochen B. Fiebach and Jan Klein and Stefan Heldmann},
	journal = {Journal of Medical Imaging},
	number = {4},
	pages = {044508},
	title = {Generative adversarial network--based reconstruction of healthy anatomy for anomaly detection in brain CT scans}},
	volume = {11},
	year = {2024}

@article{RoerichEtAl2024,
	author = {Anna Rörich and Annkristin Lange and Stefan Heldmann and Jan Hendrik Moltz and Lars Walczak and Sinef Yarar-Schlickewei and Felix Güttler and Joachim Georgii},
	journal = {Computer Methods in Biomechanics and Biomedical Engineering: Imaging \& Visualization},
	number = {1},
	pages = {2359397},
	title = {Inferring 3D finger bone shapes from 2D images -- a detailed analysis of shape accuracy},
	volume = {12},
	year = {2024}}

@inproceedings{KohlbrandtEtAl2024,
	address = {Wiesbaden},
	author = {Kohlbrandt, Temke and Moltz, Jan and Heldmann, Stefan and Hering, Alessa and Lellmann, Jan},
	booktitle = {Bildverarbeitung für die Medizin 2024},
	editor = {Maier, Andreas and Deserno, Thomas M. and Handels, Heinz and Maier-Hein, Klaus and Palm, Christoph and Tolxdorff, Thomas},
	pages = {46--51},
	publisher = {Springer Fachmedien Wiesbaden},
	title = {Joint Learning of Image Registration and Change Detection for Lung CT Images},
	year = {2024}}

@inproceedings{BrosigEtAl2024,
	author = {Johanna Brosig and Nina Krüger and Isaac Wamala and Matthias Ivantsits and Simon Sündermann and Jörg Kempfert and Stefan Heldmann and Anja Hennemuth},
	booktitle = {Medical Imaging 2024: Computer-Aided Diagnosis},
	editor = {Weijie Chen and Susan M. Astley},
	organization = {International Society for Optics and Photonics},
	pages = {129271S},
	publisher = {SPIE},
	title = {Learning 3D aortic root assessment based on sparse annotations}},
	volume = {12927},
	year = {2024}

@article{BrosigEtAl2024b,
	author = {Johanna Brosig and Nina Krüger and Inna Khasyanova and Isaac Wamala and Matthias Ivantsits and Simon Sündermann and Jörg Kempfert and Stefan Heldmann and Anja Hennemuth},
	journal = {Journal of Medical Imaging},
	number = {4},
	pages = {044504},
	title = {Learning three-dimensional aortic root assessment based on sparse annotations},
	volume = {11},
	year = {2024}}

@inproceedings{GeißlerEtl2024,
	author = {Kai Geißler and Jochen G. Hirsch and Stefan Heldmann and Hans Meine},
	booktitle = {Medical Imaging with Deep Learning},
	title = {Structure Size as Confounder in Uncertainty Based Segmentation Quality Prediction},
	year = {2024}}

@article{WeitzEtAl2024,
	author = {Philippe Weitz and Masi Valkonen and Leslie Solorzano and Circe Carr and Kimmo Kartasalo and Constance Boissin and Sonja Koivukoski and Aino Kuusela and Dusan Rasic and Yanbo Feng and Sandra Sinius Pouplier and Abhinav Sharma and Kajsa Ledesma Eriksson and Stephanie Robertson and Christian Marzahl and Chandler D. Gatenbee and Alexander R.A. Anderson and Marek Wodzinski and Artur Jurgas and Niccolò Marini and Manfredo Atzori and Henning Müller and Daniel Budelmann and Nick Weiss and Stefan Heldmann and Johannes Lotz and Jelmer M. Wolterink and Bruno {De Santi} and Abhijeet Patil and Amit Sethi and Satoshi Kondo and Satoshi Kasai and Kousuke Hirasawa and Mahtab Farrokh and Neeraj Kumar and Russell Greiner and Leena Latonen and Anne-Vibeke Laenkholm and Johan Hartman and Pekka Ruusuvuori and Mattias Rantalainen},
	journal = {Medical Image Analysis},
	pages = {103257},
	title = {The ACROBAT 2022 challenge: Automatic registration of breast cancer tissue},
	volume = {97},
	year = {2024}}

@article{modersitzki2024spectral,
  title={The Spectral Decomposition of the Continuous and Discrete Linear Elasticity Operators with Sliding Boundary Conditions},
  author={Modersitzki, Jan},
  journal={SIAM Journal on Matrix Analysis and Applications},
  volume={45},
  number={1},
  pages={134--147},
  year={2024},
  publisher={SIAM}
}

@article{bostelmann2024stationary,
  title={Stationary Velocity Fields on Matrix Groups for Deformable Image Registration},
  author={Bostelmann, Johannes and Gildemeister, Ole and Lellmann, Jan},
  journal={arXiv preprint arXiv:2410.10997},
  year={2024}
}

@article{diepeveen2024riemannian,
  title={Riemannian geometry for efficient analysis of protein dynamics data},
  author={Diepeveen, Willem and Esteve-Yagüe, Carlos and Lellmann, Jan and Öktem, Ozan and Schönlieb, Carola-Bibiane},
  journal={Proceedings of the National Academy of Sciences},
  volume={121},
  number={33},
  pages={e2318951121},
  year={2024},
  publisher={National Academy of Sciences}
}

@INPROCEEDINGS{10635778,
  author={Huang, Boqiang and Ying, Jiayu and Lyu, Ruizhi and Schaadt, Nadine S. and Klinkhammer, Barbara M. and Boor, Peter and Lotz, Johannes and Feuerhake, Friedrich and Merhof, Dorit},
  booktitle={2024 IEEE International Symposium on Biomedical Imaging (ISBI)}, 
  title={Utnetpara: A Hybrid CNN-Transformer Architecture with Multi-Scale Fusion for Whole-Slide Image Segmentation}, 
  year={2024},
  volume={},
  number={},
  pages={1-5},
  keywords={Training;Image segmentation;Veins;Neural networks;Computer architecture;Transformers;Convolutional neural networks;CNN;Transformer;Multi-scale Fusion;Whole-Slide Image;Instance Segmentation},
  doi={10.1109/ISBI56570.2024.10635778}}

@misc{schaefer2024multi,
  title={A multi-task learning strategy to pretrain models for medical image analysis},
  author={Schaefer, Raphael and Lotz, Johannes and Kiessling, Fabian},
  journal={NATURE COMPUTATIONAL SCIENCE},
  volume={4},
  number={7},
  pages={479--480},
  year={2024},
  publisher={SPRINGERNATURE CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND}
}

@incollection{xu2024prosurvival,
  title={PROSurvival: A Technical Case Report on Creating and Publishing a Dataset for Federated Learning on Survival Prediction of Prostate Cancer Patients},
  author={Xu, Tingyan and Wolters, Timo and Lotz, Johannes and Bisson, Tom and Kiehl, Tim-Rasmus and Flinner, Nadine and Zerbe, Norman and Eichelberg, Marco},
  booktitle={Collaboration across Disciplines for the Health of People, Animals and Ecosystems},
  pages={220--224},
  year={2024},
  publisher={IOS Press}
}

@article{modersitzki2024spectral,
  title={The Spectral Decomposition of the Continuous and Discrete Linear Elasticity Operators with Sliding Boundary Conditions},
  author={Modersitzki, Jan},
  journal={SIAM Journal on Matrix Analysis and Applications},
  volume={45},
  number={1},
  pages={134--147},
  year={2024},
  publisher={SIAM}
}

@inproceedings{kock2024automatic,
  title={Automatic precision cut lung slice analysis with few annotations using a two-stage deep learning approach},
  author={Kock, F and Nicke, T and Artysh, N and Prasse, A and Hoefener, H and Schenk, A},
  booktitle={VIRCHOWS ARCHIV},
  volume={485},
  pages={S387--S387},
  year={2024},
  organization={SPRINGER ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES}
}

@article{meli2024quantum,
  title={Quantum Algorithms for Binary Problems with Applications to Image Processing},
  author={Meli, Natacha Kuete},
  year={2024}
}

@InProceedings{bednarski2023emnef,
  author    = {Bednarski, Danielle and Lellmann, Jan},
  title     = {EmNeF: Neural Fields for Embedded Variational Problems in Imaging},
  booktitle = {Scale Space and Variational Methods in Computer Vision},
  year      = {2023},
  editor    = {Calatroni, Luca and Donatelli, Marco and Morigi, Serena and Prato, Marco and Santacesaria, Matteo},
  pages     = {137--148},
  address   = {Cham},
  publisher = {Springer International Publishing},
  doi       = {https://doi.org/10.1007/978-3-031-31975-4_11},
  isbn      = {978-3-031-31975-4},
 url = {https://link.springer.com/chapter/10.1007/978-3-031-31975-4_11},
}

@article{kanter2023classification,
  title={Classification of Pancreatic Ductal Adenocarcinoma Using MALDI Mass Spectrometry Imaging Combined with Neural Networks},
  author={Kanter, Frederic and Lellmann, Jan and Thiele, Herbert and Kalloger, Steve and Schaeffer, David F and Wellmann, Axel and Klein, Oliver},
  journal={Cancers},
  volume={15},
  number={3},
  pages={686},
  year={2023},
  publisher={MDPI}
}

@phdthesis{2023-PhD-Kanter,
  Author = {{Frederic Georg Kanter}},
  Title = {Deep Learning for Mass Spectrometry Imaging and Image Registration},
  School = {Institute of Mathematics and Image Computing, University of L\"ubeck},
  Year = {2023},
}

@article{alpers2023evaluation,
  title={Evaluation of the EsteR Toolkit for COVID-19 Decision Support: Sensitivity Analysis and Usability Study},
  author={Alpers, Rieke and K{\"u}hne, Lisa and Truong, Hong-Phuc and Zeeb, Hajo and Westphal, Max and J{\"a}ckle, Sonja},
  journal={JMIR Formative Research},
  volume={7},
  pages={e44549},
  year={2023},
  publisher={JMIR Publications Toronto, Canada}
}

@article{kuete2023universal,
  title={A universal quantum algorithm for weighted maximum cut and Ising problems},
  author={Kuete Meli, Natacha and Mannel, Florian and Lellmann, Jan},
  journal={Quantum Information Processing},
  volume={22},
  number={7},
  pages={279},
  year={2023},
  publisher={Springer}
}

@article{mannel2024structured,
  title={A structured L-BFGS method and its application to inverse problems},
  author={Mannel, Florian and Om Aggrawal, Hari and Modersitzki, Jan},
  journal={Inverse Problems},
  volume={40},
  number={4},
  pages={045022},
  year={2024},
  publisher={IOP Publishing}
}

@article{diepeveen2023regularizing,
  title={Regularizing orientation estimation in cryogenic electron microscopy three-dimensional map refinement through measure-based lifting over riemannian manifolds},
  author={Diepeveen, Willem and Lellmann, Jan and {\"O}ktem, Ozan and Sch{\"o}nlieb, Carola-Bibiane},
  journal={SIAM Journal on Imaging Sciences},
  volume={16},
  number={3},
  pages={1440--1490},
  year={2023},
  publisher={SIAM}
}

@inproceedings{walluscheck2023unsupervised,
  title={Unsupervised learning of healthy anatomy for anomaly detection in brain CT scans},
  author={Walluscheck, Sina and Canalini, Luca and Klein, Jan and Heldmann, Stefan},
  booktitle={Medical Imaging 2023: Computer-Aided Diagnosis},
  volume={12465},
  pages={11--14},
  year={2023},
  organization={SPIE}
}

@article{walluscheck2023mr,
  title={MR-CT multi-atlas registration guided by fully automated brain structure segmentation with CNNs},
  author={Walluscheck, Sina and Canalini, Luca and Strohm, Hannah and Diekmann, Susanne and Klein, Jan and Heldmann, Stefan},
  journal={International journal of computer assisted radiology and surgery},
  volume={18},
  number={3},
  pages={483--491},
  year={2023},
  publisher={Springer}
}

@inproceedings{kuckertz2023efficient,
  title={Efficient Registration of Longitudinal Studies for Follow-Up Lesion Assessment by Exploiting Redundancy and Composition of Deformations},
  author={Kuckertz, Sven and Heldmann, Stefan and Moltz, Jan Hendrik},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={91--99},
  year={2023},
  organization={Springer}
}

@article{golla2023cervical,
  title={Cervical spine fracture detection in computed tomography using convolutional neural networks},
  author={Golla, Alena-Kathrin and Lorenz, Cristian and Buerger, Christian and Lossau, Tanja and Klinder, Tobias and Mutze, Sven and Arndt, Holger and Spohn, Frederik and Mittmann, Marlene and Goelz, Leonie},
  journal={Physics in Medicine \& Biology},
  volume={68},
  number={11},
  pages={115010},
  year={2023},
  publisher={IOP Publishing}
}

@article{lotz2023comparison,
  title={Comparison of consecutive and restained sections for image registration in histopathology},
  author={Lotz, Johannes and Weiss, Nick and van der Laak, Jeroen and Heldmann, Stefan},
  journal={Journal of Medical Imaging},
  volume={10},
  number={6},
  pages={067501--067501},
  year={2023},
  publisher={Society of Photo-Optical Instrumentation Engineers}
}

@article{sieren2022radiation,
  title={Radiation-free thoracic endovascular aneurysm repair with fiberoptic and electromagnetic guidance: a phantom study},
  author={Sieren, Malte Maria and J{\"a}ckle, Sonja and Eixmann, Tim and Schulz-Hildebrandt, Hinnerk and Matysiak, Florian and Preuss, Mark and Garc{\'\i}a-V{\'a}zquez, Ver{\'o}nica and Stahlberg, Erik and Kleemann, Markus and Barkhausen, J{\"o}rg and others},
  journal={Journal of Vascular and Interventional Radiology},
  volume={33},
  number={4},
  pages={384--391},
  year={2022},
  publisher={Elsevier}
}

@article{haase2022deformable,
  title={Deformable groupwise image registration using low-rank and sparse decomposition},
  author={Haase, Roland and Heldmann, Stefan and Lellmann, Jan},
  journal={Journal of Mathematical Imaging and Vision},
  volume={64},
  number={2},
  pages={194--211},
  year={2022},
  publisher={Springer}
}

@incollection{jackle20223d,
  title={3D Stent Graft Guidance Based on Tracking Systems},
  author={J{\"a}ckle, Sonja and Eixmann, Tim and Matysiak, Florian and Sieren, Malte M and Horn, Marco and Schulz-Hildebrandt, Hinnerk and H{\"u}ttmann, Gereon and P{\"a}tz, Torben},
  booktitle={Bildverarbeitung f{\"u}r die Medizin 2022},
  pages={253--253},
  year={2022},
  publisher={Springer}
}

@inproceedings{Meli2022,
  title={An Iterative Quantum Approach for Transformation Estimation From Point Sets},
  author={Kuete Meli, N. and Mannel, F. and Lellmann, J.},
  booktitle={Computer Vision and Pattern Recognition},
  pages={529--537},
  year={2022}
}

@article{Miesen_2022, 
doi={10.1242/dmm.046342}, 
url={https://doi.org/10.1242%2Fdmm.046342}, 
year={2022}, 
month={mar}, 
publisher={The Company of Biologists}, 
volume={15}, 
number={3}, 
author={Miesen, Laura and Bándi, Péter and Willemsen, Brigith and Mooren, Fieke and Strieder, Thiago and Boldrini, Eva  and Drenic, Vedran and Eymael, Jennifer and Wetzels, Roy and Lotz, Johannes and Weiss, Nick and  Steenbergen, Eric and van Kuppevelt, Toin H. and van Erp, Merijn and van der Laak, Jeroen and Endlich, Nicole and Moeller, Marcus J. and Wetzels, Jack F. M. and Jansen, Jitske and Smeets, Bart}, 
title={Parietal epithelial cells maintain the epithelial cell continuum forming Bowman's space in focal segmental glomerulosclerosis}, 
journal={Disease Models & Mechanisms}
}

@article{Budelmann2022100001,
title={Automated Detection of Portal Fields and Central Veins in
Whole-Slide Images of Liver Tissue},
journal={Journal of Pathology Informatics},
volume={13},
pages={100001},
year={2022},
issn={2153-3539},
doi={https://doi.org/10.1016/j.jpi.2022.100001},
url={https://www.sciencedirect.com/science/article/pii/S2153353922000013},
author={Budelmann, Daniel and Laue, Hendrick and Weiss, Nick and Dahmen, Uta and D’Alessandro, Lorenza A. and Biermayer , Ina and Klingmüller, Ursula and Ghallab, Ahmed and Hassan, Reham and Begher-Tibbe, Brigitte and Hengstler, Jan G. and Schwen, Lars Ole},
keywords={liver, portal field, central vein, object detection,
convolutional neural network, zonated quantification}
}

@inproceedings{hering2022towards,
  title={Towards more efficient tumor follow-up assessment using AI assistance},
  author={Hering, Alessa and Peisen, Felix and Moltz, Jan Hendrik},
  booktitle={Medical Imaging with Deep Learning},
  year={2022}
}

@article{hansen2022continuous,
  title={Continuous benchmarking in medical image registration-review of the current state of the Learn2Reg challenge},
  author={Hansen, Lasse and Hering, Alessa and Großbröhmer, Christoph and Heinrich, Mattias P},
  journal={Medical Imaging with Deep Learning},
  year={2022}
}

@article{peisen2022combination,
  title={Combination of Whole-Body Baseline CT Radiomics and Clinical Parameters to Predict Response and Survival in a Stage-IV Melanoma Cohort Undergoing Immunotherapy},
  author={Peisen, Felix and H{\"a}nsch, Annika and Hering, Alessa and Brendlin, Andreas S and Afat, Saif and Nikolaou, Konstantin and Gatidis, Sergios and Eigentler, Thomas and Amaral, Teresa and Moltz, Jan H and others},
  journal={Cancers},
  volume={14},
  number={12},
  pages={2992},
  year={2022},
  publisher={Multidisciplinary Digital Publishing Institute}
}

@incollection{hager2022robin,
  title={Robust Intensity-based Initialization for 2D-3D Pelvis Registration
(RobIn)},
  author={Häger, Stephanie and Lange, Annkristin and Heldmann, Stefan {and} Modersitzki, Jan and Petersik, Andreas and Schröder, Manuel and Gottschling, Heiko and Lieth, Thomas and Zähringer, Erich and Moltz, Jan H},
  booktitle={Bildverarbeitung für die Medizin 2022},
  pages={69--74},
  year={2022},
  publisher={Springer}
}

@Article{Mannel1,
Author={Hafemeyer, Dominik and Mannel, Florian},
Title={A path-following inexact Newton method for {PDE}-constrained optimal control in {BV}},
FJournal={{Computational Optimization and Applications}},
Journal={{COAP}},
Volume={82},
Number={3},
Pages={753--794},
Year={2022},
Language={English},
doi = {10.1007/s10589-022-00370-2},
}

@Article{Mannel2,
Author={{Mannel, Florian}},
Title={{On the convergence of Broyden’s method and some accelerated schemes for singular problems}},
FJournal={{IMA Journal of Numerical Analysis}},
Volume={},
Number={},
Pages={1--29},
Year={2022},
Language={English},
DOI= 10.1093/imanum/drab096},
eprint={https://academic.oup.com/imajna/advance-article-pdf/doi/10.1093/imanum/drab096/42198372/drab096.pdf},
}

@Article{Mannel3,
Author={{Mannel, Florian and Rund, Armin}},
Title={{A hybrid semismooth quasi-Newton method for structured nonsmooth operator equations in Banach spaces}},
FJournal={{Journal of Convex Analysis}},
Journal={{JoCA}},
Volume={29},
Number={1},
Pages={183--204},
Year={2022},
Language={English},
url={https://www.heldermann.de/JCA/JCA29/JCA291/jca29011.htm},
}

@Article{Mannel5,
title={{SHINE}: {SH}aring the {IN}verse Estimate from the forward pass for bi-level optimization and implicit models},
author={Ramzi, Zaccharie and Mannel, Florian and Bai, Shaojie and Starck, Jean-Luc and Ciuciu, Philippe and Moreau, Thomas},
FJournal={The Tenth International Conference on Learning Representations (ICLR)},
year={2022},
Language={English},
url={https://openreview.net/forum?id=-ApAkox5mp}
}

@incollection{jackle2022ester,
  title={EsteR--A Digital Toolkit for COVID-19 Decision Support in Local Health Authorities},
  author={J{\"a}ckle, Sonja and Alpers, Rieke and K{\"u}hne, Lisa and Schumacher, Jakob and Geisler, Benjamin and Westphal, Max},
  booktitle={German Medical Data Sciences 2022--Future Medicine: More Precise, More Integrative, More Sustainable!},
  pages={17--24},
  year={2022},
  publisher={IOS Press}
}

@Article{bednarski2022inverse,
  author  = {Danielle Bednarski and Jan Lellmann},
  title   = {Inverse Scale Space Iterations for Non-Convex Variational Problems: The Continuous and Discrete Case},
  journal = {J Math Imaging Vis},
  year    = {2022},
  doi     = {10.1007/s10851-022-01125-8},
  url = {https://link.springer.com/article/10.1007/s10851-022-01125-8},
}

@InProceedings{pmlr-v172-kanter22a,
title = {A Flexible Meta Learning Model for Image Registration},
author = {Kanter, Frederic and Lellmann, Jan},
booktitle = {Proceedings of The 5th International Conference on Medical Imaging with Deep Learning},
pages = {638-652},
year = {2022},
editor = {Konukoglu, Ender and Menze, Bjoern and Venkataraman, Archana and Baumgartner, Christian and Dou, Qi and Albarqouni, Shadi},  
volume =  {172},  
series =  {Proceedings of Machine Learning Research},  
month =  {06--08 Jul},  
publisher = {PMLR}
}

@phdthesis{hering2022deep,
  title={Deep-Learning-based Image Registration and Tumor Follow-Up Analysis},
  author={Hering, AD},
  year={2022},
  school={[Sl]:[Sn]}
}

@inproceedings{nicke2022realtime,
  title={Realtime optical flow estimation on vein and artery ultrasound sequences based on knowledge-distillation},
  author={Nicke, Till and Graf, Laura and Lauri, Mikko and Mischkewitz, Sven and Frintrop, Simone and Heinrich, Mattias P},
  booktitle={International Workshop on Biomedical Image Registration},
  pages={134--143},
  year={2022},
  organization={Springer}
}

@article{hering2022learn2reg,
  title={Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning},
  author={Hering, Alessa and Hansen, Lasse and Mok, Tony CW and Chung, Albert CS and Siebert, Hanna and H{\"a}ger, Stephanie and Lange, Annkristin and Kuckertz, Sven and Heldmann, Stefan and Shao, Wei and others},
  journal={IEEE Transactions on Medical Imaging},
  volume={42},
  number={3},
  pages={697--712},
  year={2022},
  publisher={IEEE}
}

@inproceedings{barann2022python,
  title={A Python SDK for Authoring and using Computer-interpretable Guidelines.},
  author={Barann, Marcus and Heldmann, Stefan and Klein, Jan and Kra{\ss}, Stefan},
  booktitle={BIOINFORMATICS},
  pages={99--106},
  year={2022}
}

@article{fuchs2022vivo,
  title={In-vivo assessment of meniscal movement in the knee joint during internal and external rotation under load},
  author={Fuchs, Andreas and Georgii, Joachim and Taghizadeh, Elham and Heldmann, Stefan and Lange, Thomas and Bendak, Sebastian F and Siegel, Markus and Yilmaz, Tayfun and Schmal, Hagen and Izadpanah, Kaywan},
  journal={Journal of experimental orthopaedics},
  volume={9},
  number={1},
  pages={102},
  year={2022},
  publisher={Springer}
}

@inproceedings{kuckertz2022fully,
  title={Fully automated longitudinal tracking and in-depth analysis of the entire tumor burden: unlocking the complexity},
  author={Kuckertz, Sven and Klein, Jan and Engel, Christiane and Geisler, Benjamin and Kra{\ss}, Stefan and Heldmann, Stefan},
  booktitle={Medical Imaging 2022: Computer-Aided Diagnosis},
  volume={12033},
  pages={469--473},
  year={2022},
  organization={SPIE}
}

@article{weber2022association,
  title={Association of iron rim lesions with brain and cervical cord volume in relapsing multiple sclerosis},
  author={Weber, Claudia E and Kr{\"a}mer, Julia and Wittayer, Matthias and Gregori, Johannes and Randoll, Sigurd and Weiler, Florian and Heldmann, Stefan and Ro{\ss}manith, Christina and Platten, Michael and Gass, Achim and others},
  journal={European radiology},
  volume={32},
  number={3},
  pages={2012--2022},
  year={2022},
  publisher={Springer}
}

@article{sieren2022automated,
  title={Automated segmentation and quantification of the healthy and diseased aorta in CT angiographies using a dedicated deep learning approach},
  author={Sieren, Malte Maria and Widmann, Cornelia and Weiss, Nick and Moltz, Jan Hendrik and Link, Florian and Wegner, Franz and Stahlberg, Erik and Horn, Marco and Oecherting, Thekla Helene and Goltz, Jan Peter and others},
  journal={European radiology},
  volume={32},
  number={1},
  pages={690--701},
  year={2022},
  publisher={Springer}
}

@article{romberg2022empaia,
  title={EMPAIA app interface: an open and vendor-neutral interface for AI applications in pathology},
  author={Romberg, Daniel and Strohmenger, Klaus and Jansen, Christoph and K{\"u}ster, Tobias and Weiss, Nick and Gei{\ss}ler, Christian and So{\l}tysi{\'n}ski, Tomasz and Takla, Michael and Hufnagl, Peter and Zerbe, Norman and others},
  journal={Computer methods and programs in biomedicine},
  volume={215},
  pages={106596},
  year={2022},
  publisher={Elsevier}
}

@phdthesis{2021-PhD-Brehmer,
  Author = {{Kai Brehmer}},
  Title = {SqN: A Novel Distance Measure for Multiple Images and Applications},
  School = {Institute of Mathematics and Image Computing, University of L\"ubeck},
  Year = {2021},
}

@incollection{jaeckle20213BVM_3DCatheter,
  title={Abstract: 3D Guidance Including Shape Sensing of a Stentgraft System},
  author={J{\"a}ckle, Sonja and Garc\'ia-V{\'a}zquez, Ver{\'o}nica and Eixmann, Tim and Matysiak, Florian and von Haxthausen, Felix and Sieren, Malte and Schulz-Hildebrandt, Hinnerk and H{\"u}ttmann, Gereon and Ernst, Floris and Kleemann, Markus and P{\"a}tz, Torben},
  booktitle={Bildverarbeitung f{\"u}r die Medizin 2021},
  pages={34--34},
  year={2021},
  doi={10.1007/978-3-658-33198-6_9},
  url={https://link.springer.com/chapter/10.1007%2F978-3-658-33198-6_9},
  keywords={NavEVAR},
  publisher={Springer}
}

@Article{jaeckle2021IJERPH,
AUTHOR = {Jäckle, Sonja and Röger, Elias and Dicken, Volker and Geisler, Benjamin and Schumacher, Jakob and Westphal, Max},
TITLE = {A Statistical Model to Assess Risk for Supporting COVID-19 Quarantine Decisions},
JOURNAL = {International Journal of Environmental Research and Public Health},
VOLUME = {18},
YEAR = {2021},
NUMBER = {17},
ARTICLE-NUMBER = {9166},
URL = {https://www.mdpi.com/1660-4601/18/17/9166},
ISSN = {1660-4601},
ABSTRACT = {In Germany, local health departments are responsible for surveillance of the current pandemic situation. One of their major tasks is to monitor infected persons. For instance, the direct contacts of infectious persons at group meetings have to be traced and potentially quarantined. Such quarantine requirements may be revoked, when all contact persons obtain a negative polymerase chain reaction (PCR) test result. However, contact tracing and testing is time-consuming, costly and not always feasible. In this work, we present a statistical model for the probability that no transmission of COVID-19 occurred given an arbitrary number of negative test results among contact persons. Hereby, the time-dependent sensitivity and specificity of the PCR test are taken into account. We employ a parametric Bayesian model which combines an adaptable Beta-Binomial prior and two likelihood components in a novel fashion. This is illustrated for group events in German school classes. The first evaluation on a real-world dataset showed that our approach can support important quarantine decisions with the goal to achieve a better balance between necessary containment of the pandemic and preservation of social and economic life. Future work will focus on further refinement and evaluation of quarantine decisions based on our statistical model.},
DOI = {10.3390/ijerph18179166}
}