@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}

@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}}

@inproceedings{GeilerEtAl2024,
	author = {Kai Geißler and Daniel Mensing and Markus Wenzel and Jochen G. Hirsch and Stefan Heldmann},
	booktitle = {Medical Imaging 2024: Image Processing},
	editor = {Olivier Colliot and Jhimli Mitra},
	organization = {International Society for Optics and Photonics},
	pages = {1292604},
	publisher = {SPIE},
	title = {Towards TotalSegmentator for MRI data leveraging GIN data augmentation}},
	volume = {12926},
	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}}

@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}
}

@article{hering2021cnn,
  title={CNN-based lung CT registration with multiple anatomical constraints},
  author={Hering, Alessa and H{\"a}ger, Stephanie and Moltz, Jan and Lessmann, Nikolas and Heldmann, Stefan and van Ginneken, Bram},
  journal={Medical Image Analysis},
  volume={72},
  pages={102139},
  year={2021},
  publisher={Elsevier}
}

@inproceedings{hering2021fraunhofer,
  title={Fraunhofer MEVIS Image Registration Solutions for the Learn2Reg 2021 Challenge},
  author={Hering, Alessa and Lange, Annkristin and Heldmann, Stefan and H{\"a}ger, Stephanie and Kuckertz, Sven},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={147--152},
  year={2021},
  organization={Springer}
}

@article{jaeckle2021IJMRCAS,
author = {Jäckle, Sonja and Lange, Annkristin and García-Vázquez, Verónica and Eixmann, Tim and Matysiak, Florian and Sieren, Malte Maria and Horn, Marco and Schulz-Hildebrandt, Hinnerk and Hüttmann, Gereon and Ernst, Floris and Heldmann, Stefan and Pätz, Torben and Preusser, Tobias},
title = {Instrument localisation for endovascular aneurysm repair: Comparison of two methods based on tracking systems or using imaging},
journal = {The International Journal of Medical Robotics and Computer Assisted Surgery},
volume = {17},
number = {6},
pages = {e2327},
year = {2021},
keyword = {NavEVAR}
}

@article{hering2021learn2reg,
  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 and Siebert, Hanna and H{\"a}ger, Stephanie and Lange, Annkristin and Kuckertz, Sven and Heldmann, Stefan and Shao, Wei and others},
  journal={arXiv preprint arXiv:2112.04489},
  year={2021}
}

@inproceedings{kuckertz2020WBIR,
  title={Learning Deformable Image Registration with Structure Guidance Constraints for Adaptive Radiotherapy},
  author={Kuckertz, Sven and Papenberg, Nils and Honegger, Jonas and Morgas, Tomasz and Haas, Benjamin and Heldmann, Stefan},
  booktitle={International Workshop on Biomedical Image Registration},
  pages={44--53},
  year={2020},
  organization={Springer},
  url={http://dx.doi.org/10.1007%2F978-3-030-50120-4_5}
}

@inproceedings{hager2020variable,
  title={Variable fraunhofer MEVIS RegLib comprehensively applied to Learn2Reg challenge},
  author={H{\"a}ger, Stephanie and Heldmann, Stefan and Hering, Alessa and Kuckertz, Sven and Lange, Annkristin},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={74--79},
  year={2020},
  organization={Springer}
}

@inproceedings{lange2020multilevel,
  title={Multilevel 2D-3D Intensity-Based Image Registration},
  author={Lange, Annkristin and Heldmann, Stefan},
  booktitle={International Workshop on Biomedical Image Registration},
  pages={57--66},
  year={2020},
  organization={Springer},
  keywords={NavEVAR},
  url={https://doi.org/10.1007/978-3-030-50120-4_6}
}

@article{sieren2020rapid,
  title={Rapid study assessment in follow-up whole-body computed tomography in patients with multiple myeloma using a dedicated bone subtraction software},
  author={Sieren, MM and Brenne, F and Hering, A and Kienapfel, H and Gebauer, N and Oechtering, TH and F{\"u}rschke, A and Wegner, F and Stahlberg, E and Heldmann, S and others},
  journal={European Radiology},
  volume={30},
  number={6},
  pages={3198--3209},
  year={2020},
  publisher={Springer}
}

@incollection{lange2020intensity,
  title={Intensity-Based 2D-3D Registration Using Normalized Gradient Fields},
  author={Lange, Annkristin and Heldmann, Stefan},
  booktitle={Bildverarbeitung f{\"u}r die Medizin 2020},
  pages={163--168},
  year={2020},
  keywords={NavEVAR},
  url={https://doi.org/10.1007/978-3-658-29267-6_33},
  publisher={Springer}
}

@InProceedings{kuckertz2020BVM,
author={Kuckertz, Sven and Papenberg, Nils and Honegger, Jonas and Morgas, Tomasz and Haas, Benjamin and Heldmann, Stefan},
editor={Tolxdorff, Thomas and Deserno, Thomas M. and Handels, Heinz and Maier, Andreas and Maier-Hein, Klaus H. and Palm, Christoph},
title={Abstract: Deep Learning Based CT-CBCT Image Registration for Adaptive Radio Therapy},
booktitle={Bildverarbeitung f{\"u}r die Medizin 2020},
year={2020},
publisher={Springer},
pages={229--229},
isbn={978-3-658-29267-6},
url={https://doi.org/10.1007/978-3-658-29267-6_51}
}

@inproceedings{kuckertz2020SPIE,
  title={Deep learning based CT-CBCT image registration for adaptive radio therapy},
  author={Kuckertz, Sven and Papenberg, Nils and Honegger, Jonas and Morgas, Tomasz and Haas, Benjamin and Heldmann, Stefan},
  booktitle={Medical Imaging 2020: Image Processing},
  volume={11313},
  pages={113130Q},
  year={2020},
  organization={International Society for Optics and Photonics},
  url={http://dx.doi.org/10.1117%2F12.2549531}
}

@incollection{jaeckle2019shape,
  title={Shape Sensing with Fiber Bragg Grating Sensors},
  author={J{\"a}ckle, Sonja and Strehlow, Jan and Heldmann, Stefan},
  booktitle={Bildverarbeitung f{\"u}r die Medizin 2019},
  pages={258--263},
  year={2019},
  publisher={Springer},
  keywords = {NavEVAR},
  url={https://link.springer.com/chapter/10.1007%2F978-3-658-25326-4_58},
}

@inproceedings{Brehmer2019,
author={Brehmer, Kai and Aggrawal, Hari Om and Heldmann, Stefan and Modersitzki, Jan},
title={Variational registration of multiple images with the SVD based SqN distance measure},
booktitle={Scale Space and Variational Methods in Computer Vision: 7th International Conference, SSVM 2019, Hofgeismar, Germany, June 30-July 4, 2019, Proceedings},
year={2019},
editor={Burger, Martin and Lellmann, Jan and Modersitzki, Jan},
publisher={Springer International Publishing},
pages={251--262},
url={{{https://arxiv.org/abs/1907.09732}}},
doi={{{10.1007/978-3-030-22368-7_20}}}
}

@inproceedings{hering2019SPIE,
author = {Hering, Alessa and Heldmann, Stefan},
title = {{Unsupervised learning for large motion thoracic CT follow-up registration}},
volume = {10949},
booktitle = {Medical Imaging 2019: Image Processing},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {1-7},
year = {2019},
doi = {10.1117/12.2506962},
URL = {https://doi.org/10.1117/12.2506962}
}

@inproceedings{hering2019unsupervised,
  title={Unsupervised learning for large motion thoracic CT follow-up registration},
  author={Hering, Alessa and Heldmann, Stefan},
  booktitle={Medical Imaging 2019: Image Processing},
  volume={10949},
  pages={331--337},
  year={2019},
  organization={SPIE}
}

@inproceedings{hering2019mlvirnet,
  title={mlvirnet: Multilevel variational image registration network},
  author={Hering, Alessa and Ginneken, Bram van and Heldmann, Stefan},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={257--265},
  year={2019},
  organization={Springer}
}

@inproceedings{hering2019MICCAI,
author = {Hering, Alessa and van Ginneken, Bram and Heldmann, Stefan},
title = {{mlVIRNET: Multilevel Variational Image Registration Network}},
volume = {11769},
booktitle = {Proceeding of Medical Image Computing and Computer Assisted Intervention (MICCAI 2019)},
publisher = {Springer},
pages = {257-265},
year = {2019},
doi = {10.1007/978-3-030-32226-7_29},
URL = {https://doi.org/10.1007/978-3-030-32226-7_29}
}

@article{hering2019memory,
  title={Memory-efficient 2.5 D convolutional transformer networks for multi-modal deformable registration with weak label supervision applied to whole-heart CT and MRI scans},
  author={Hering, Alessa and Kuckertz, Sven and Heldmann, Stefan and Heinrich, Mattias P},
  journal={International journal of computer assisted radiology and surgery},
  volume={14},
  number={11},
  pages={1901--1912},
  year={2019},
  publisher={Springer}
}

@incollection{hering2019BVM,
  title={Enhancing label-driven deep deformable image registration with local distance metrics for state-of-the-art cardiac motion tracking},
  author={Hering, Alessa and Kuckertz, Sven and Heldmann, Stefan and Heinrich, Mattias P},
  booktitle={Bildverarbeitung f{\"u}r die Medizin 2019},
  pages={309--314},
  year={2019},
  publisher={Springer},
  url={http://dx.doi.org/10.1007%2F978-3-658-25326-4_69},
}

@incollection{jaeckle2018rigid,
  title={Rigid Lens--Locally Rigid Approximations of Deformable Registration for Change Assessment in Thorax-Abdomen CT Follow-Up Scans},
  author={J{\"a}ckle, Sonja and Heldmann, Stefan},
  booktitle={Image Analysis for Moving Organ, Breast, and Thoracic Images},
  pages={272--283},
  year={2018},
  publisher={Springer},
  url={https://link.springer.com/chapter/10.1007/978-3-030-00946-5_27},
}

@article{ruhaak2017estimation,
  title={Estimation of Large Motion in Lung CT by Integrating Regularized Keypoint Correspondences into Dense Deformable Registration},
  author={R{\"u}haak, Jan and Polzin, Thomas and Heldmann, Stefan and Simpson, Ivor J. A. and Handels, Heinz and Modersitzki, Jan and Heinrich, Mattias P.},
  journal={IEEE Transactions on Medical Imaging},
  volume = {36},
  number = {8},
  pages = {1746--1757},
  year={2017},
  publisher={IEEE}
}

@article{derksen2016joint,
  title={A Joint Registration and Segmentation Approach for Large Bladder Deformations in Adaptive Radiotherapy},
  author={Derksen, A and König, L and Meine, H and Heldmann, S},
  journal={Medical Physics: Proceedings of the AAPM 58th annual meeting, Washington, DC},
  volume={43},
  number={6},
  pages={3429--3429},
  year={2016},
  doi={10.1118/1.4956005},
  publisher={American Association of Physicists in Medicine}
}

@article{Lotz2016Integration,
abstract = {In the last years, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) became an imaging technique which has the potential to characterize complex tumor tissue. The combination with other modalities and with standard histology techniques was achieved by the use of image registration methods and enhances analysis possibilities. We analyzed an oral squamous cell carcinoma with up to 162 consecutive sections with MALDI MSI, hematoxylin and eosin (H{\&}E) staining and immunohistochemistry (IHC) against CD31. Spatial segmentation maps of the MALDI MSI data were generated by similarity-based clustering of spectra. Next, the maps were overlaid with the H{\&}E microscopy images and the results were interpreted by an experienced pathologist. Image registration was used to fuse both modalities and to build a three-dimensional (3D) model. To visualize structures below resolution of MALDI MSI, IHC was carried out for CD31 and results were embedded additionally. The integration of 3D MALDI MSI data with H{\&}E and IHC images allows a correlation between histological and molecular information leading to a better understanding of the functional heterogeneity of tumors. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.},
author = {Lotz, Judith M. and Hoffmann, Franziska and Lotz, Johannes and Heldmann, Stefan and Trede, Dennis and Oetjen, Janina and Becker, Michael and Ernst, G{\"{u}}nther and Maas, Peter and Alexandrov, Theodore and Guntinas-Lichius, Orlando and Thiele, Herbert and von Eggeling, Ferdinand},
doi = {10.1016/j.bbapap.2016.08.018},
issn = {15709639},
journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},
keywords = {3D,Head and Neck Cancer,MALDI imaging,OSCC,image registration,immunohistochemistry,multimodality},
pmid = {27594533},
publisher = {Elsevier B.V.},
title = {{Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition}},
year = {2016}
}

@incollection{Modersitzki2015307,
title = {Nonlinear Registration Via Displacement Fields},
editor = {Toga, Arthur W.},
booktitle = {Brain Mapping},
publisher = {Academic Press},
edition = {},
address = {Waltham},
year = {2015},
pages = {307 - 314},
isbn = {978-0-12-397316-0},
doi = {http://dx.doi.org/10.1016/B978-0-12-397025-1.00300-6},
url = {http://www.sciencedirect.com/science/article/pii/B9780123970251003006},
author = {J. Modersitzki and S. Heldmann and N. Papenberg},
keywords = {Displacement fields, Image fusion,Image registration, Nonlinear registration, Variational formulation},
abstract = {Abstract This article presents a brief review on nonlinear registration techniques based on a variational formulation. The main advantages of this setting are its great modeling potential and its modular setting. This enables easy changes and adaptations for fine-tuning for particular applications. Furthermore, this setting also enables the integration of additional information. This can be formulated in terms of either soft or hard constraints, such as privileged handling of anatomical landmarks, local rigidity of structures, and emphasis on volume preservation or limitations of volume changes. The latter is of particular interest for one-to-one displacement fields (also known as diffeomorphic registration). The setting is supported by a rigorous mathematical theory and can be translated into fast and stable implementations. Although the focus of this article is not on the practical realization, important concepts such as multiscale and multilevel representations and reduction of ambiguities of results based on proper regularization are also briefly discussed.},
}

@inproceedings{Chen2015Deformable,
title={Deformable Image Registration with Automatic Non-Correspondence Detection},
author={Chen, Kanglin and Derksen, Alexander and Heldmann, Stefan and Hallmann, Marc and Berkels, Benjamin},
editor={Aujol, Jean-Fran{\c{c}}ois and Nikolova, Mila and Papadakis, Nicolas},
booktitle={Scale Space and Variational Methods in Computer Vision: 5th International Conference, SSVM 2015, Lège-Cap Ferret, France, May 31 - June 4, 2015, Proceedings},
year={2015},
publisher={Springer International Publishing},
address={Cham},
pages={360--371},
isbn={978-3-319-18461-6},
doi={10.1007/978-3-319-18461-6_29},
url={http://dx.doi.org/10.1007/978-3-319-18461-6_29}
}

@article{konig2015deformable,
  title={Deformable image registration with guaranteed local rigidity},
  author={K{\"o}nig, L and Derksen, A and Heldmann, S and Papenberg, N and Modersitzki, J and Haas, B},
  journal={Radiotherapy and Oncology: Proceedings of the 3rd ESTRO Forum, Barcelona},
  volume={115},
  pages={S197--S198},
  year={2015},
  publisher={Elsevier},
doi={10.1016/S0167-8140(15)40405-0}
}

@inproceedings{2015-BVM-dhpb-sliding,
  title={Image registration with sliding motion constraints for 4D CT motion correction},
  author={Derksen, Alexander and Heldmann, Stefan and Polzin, Thomas and Berkels, Benjamin},
  pages={335--340},
  year={2015},
  publisher={Springer},
  address = {Berlin, Heidelberg},
  booktitle = {Bildverarbeitung f\"{u}r die Medizin 2015, Algorithmen – Systeme –   Anwendungen, Proceedings des Workshops vom 15. bis 17. M\"{a}rz 2015 in L\"{u}beck},
  editor = {Handels, Heinz and Deserno, Thomas M. and Meinzer, Hans-Peter and Tolxdorff, Thomas},
  isbn = {9783662462232},
  month = March,
  url = {http://dx.doi.org/10.1007/978-3-662-46224-9_58},
  series = {Informatik aktuell},
  abstract = {A common assumption in medical image registration is that the estimation of a globally continuous deformation field is plausible in reality. However, a sliding behavior of adjacent organ boundaries (e.g. lung and ribcage) cannot be described in a plausible way by a continuous deformation field. In this paper, we address this issue with a novel registration framework that explicitly models sliding of interfaces and can preserve discontinuities in the deformation field along predefined organ boundaries. Incorporated methods involve constrained nonlinear registration and a finite element discretization on unstructured tetrahedral meshes. Evaluation is based on the freely available DIR-Lab datasets.}
}

@inproceedings{2015-hpdb-SSVM,
author = {Stefan Heldmann and Thomas Polzin and Alexander Derksen and Benjamin Berkels},
title = {An Image Registration Framework for Sliding Motion with Piecewise Smooth Deformations},
booktitle = {Scale Space and Variational Methods in Computer Vision},
year = {2015},
month = {May/June},
abstract = {We present a novel variational framework for image registration with explicit modeling of sliding motion, as it occurs, e.g., in the medical context at organ boundaries. The key of our method is a piecewise smooth deformation model that allows for discontinuities at the sliding interfaces while keeping the sliding domain in contact with its surrounding. The presented approach is generic and can be used with a large class of both image similarity measures and regularizers for the deformations. A useful byproduct of the proposed method is an automatic propagation of a given segmentation from one image to the other. We proof existence of minimizers under rather mild assumptions and present an efficient scheme for computing a numerical solution. The minimization is based on a splitting approach with alternating derivative based Gauss-Newton and fast first order convex optimization. Finally, we evaluate the proposed method on synthetic and real data.},
series = {Lecture Notes in Computer Science},
pages = {335--347},
address = {Lège-Cap Ferret, France},
publisher = {Springer International},
volume = {9087},
editor = {Jean-François Aujol and Mila Nikolova and Nicolas Papadakis},
}

@article{Lotz2015,
abstract = {Objective: Image Registration of whole slide histology images allows the fusion of fine-grained information - like different immunohistochemical stains - from neighboring tissue slides. Traditionally, pathologists fuse this information by looking subsequently at one slide at a time. If the slides are digitized and accurately aligned at cell-level, automatic analysis can be used to ease the pathologist's work. However, the size of those images exceeds the memory capacity of regular computers. Methods: We address the challenge to combine a global motion model that takes the physical cutting process of the tissue into account with image data that is not simultaneously globally available. Typical approaches either reduce the amount of data to be processed or partition the data into smaller chunks to be processed separately. Our novel method first registers the complete images on a low resolution with a nonlinear deformation model and later refines this result on patches by using a second nonlinear registration on each patch. Finally the deformations computed on all patches are combined by interpolation to form one globally smooth nonlinear deformation. The NGF distance measure is used to handle multi-stain images. Results: The method is applied to ten whole slide image pairs of human lung cancer data. The alignment of 85 corresponding structures is measured by comparing manual segmentations from neighboring slides. Their offset improves significantly, by at least 15 %, compared to the low-resolution nonlinear registration. Conclusion/Significance: The proposed method significantly improves the accuracy of multi-stain registration which allows to compare different anti-bodies at cell-level. available. Typical approaches either reduce the amount of data to be processed or partition the data into smaller chunks to be processed separately. Our novel method first registers the complete images on a low resolution with a nonlinear deformation model and later refines this result on patches by using a second nonlinear registration on each patch. Finally the deformations computed on all patches are combined by interpolation to form one globally smooth nonlinear deformation. The NGF distance measure is used to handle multi-stain images.Results: The method is applied to ten whole slide image pairs of human lung cancer data. The alignment of 85 corresponding structures is measured by comparing manual segmentations from neighboring slides. Their offset improves significantly, by at least 15 %, compared to the low-resolution nonlinear registration. Conclusion/Significance: The proposed method significantly improves the accuracy of multi-stain registration which allows to compare different anti-bodies at cell-level.},
author = {Lotz, J and Olesch, J and M{\"{u}}ller, B and Polzin, T and Galuschka, P and Lotz, J M and Heldmann, S and Laue, H and Warth, A and Lahrmann, B and Grabe, N and Sedlaczek, O and Breuhahn, K and Modersitzki, J},
doi = {10.1109/TBME.2015.2503122},
journal = {IEEE Transactions on Biomedical Engineering},
keywords = {computer-aided diagnosis,digital pathology,high resolution histological scans ,histopathology, image registration},
title = {{Patch-Based Nonlinear Image Registration for Gigapixel Whole Slide Images}},
year = {2015},
volume = {63}, 
number = {9},
pages = {1812--1819}
}

@INPROCEEDINGS{2015-SPIE-RDHHM,
	author = {R\"{u}haak, Jan and Derksen, Alexander and Heldmann, Stefan and Hallmann, Marc and Meine, Hans},
	booktitle = {SPIE Medical Imaging 2015: Image Processing},
	title = {Accurate CT-MR image registration for deep brain stimulation: a multi-observer evaluation study},
	year = {2015},
	address = {Orlando, Florida, USA},
	month = {February}	
}

@INPROCEEDINGS{papenberg2015locally,
	author = {Papenberg, Nils and König, Lars and Heldmann, Stefan and Derksen, Alexander and Modersitzki, Jan and Haas, Benjamin},
	booktitle = {Varian Research Partnership Symposium},
	title = {A Locally Variable Transformation Model for Deformable Image Registration Using Tissue Properties},
	year = {2015},
	address = {Atlanta, Georgia, USA},
	month = {March}	
}

@article{thiele20142d,
  title={2D and 3D MALDI-imaging: conceptual strategies for visualization and data mining},
  author={Thiele, Herbert and Heldmann, Stefan and Trede, Dennis and Strehlow, Jan and Wirtz, Stefan and Dreher, Wolfgang and Berger, Judith and Oetjen, Janina and Kobarg, Jan Hendrik and Fischer, Bernd and others},
  journal={Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics},
  volume={1844},
  number={1},
  pages={117--137},
  year={2014},
  publisher={Elsevier}
}

@Misc{trede2014DGMS,
  author = 	 {Dennis Trede and Andreas Bartels and Stefan Schiffler and Janina Oetjen and Michael Becker and Michaela Aichler and Florian Lieb and Klaus Steinhorst and Judith Berger and Stefan Heldmann and Herbert Thiele and Axel Walch and Peter Maass and Theodore Alexandrov},
  title = 	 {A spatially-aware highly-sensitive peak picking method for MALDI-imaging},
  note = {Poster Submission at 47. Jahrestagung der Deutschen Gesellschaft für Massenspektrometrie, Frankfurt am Main},
  year = 	 {2014},
  url = 	 {http://www.pharmazie.uni-frankfurt.de/PharmChem/DGMS2014/Programm/Abstracts/Abstracts-Poster.pdf}
}

@INPROCEEDINGS{2014-DBS-CHRH,
	author = {Chen, Kanglin and Heldmann, Stefan and R\"{u}haak, Jan and Hallmann, Marc},
	booktitle = {Proc. MICCAI 2014 Workshop on Deep Brain Stimulation Methodological Challenges - 2nd Edition},
	title = {Construction of Average STN Atlas using Image Registration and Reconstruction},
	year = {2014},
	address = {Boston, USA},
	month = {September}	
}

@inproceedings{lotz2014elastic,
  title={Elastic image registration on whole slide images for digital double staining and 3D reconstruction},
  author={Johannes Lotz and Judith Berger and Herbert Thiele and Janine Olesch and Benedikt Müller and Kai Breuhahn and Arne Warth  and Niels Grabe and Bernd Lahrmann and Oliver Sedlaczek and Stefan Heldmann
},
  booktitle={Poster Submission at the European Molecular Imaging Meeting - EMIM},
  year={2014},
  url = {http://s.fhg.de/wwu},
  organization={European Society for Molecular Imaging}
}

@inproceedings{lotz2014zooming,
  title={Zooming in: High Resolution 3D Reconstruction of Differently Stained Histological Whole Slide Images},
  author={Johannes Lotz and Judith Berger and Benedikt M\"uller and Kai Breuhahn and Niels Grabe and Stefan Heldmann and Andr\'{e} Homeyer and Bernd Lahrmann and Hendrik Laue and Janine Olesch and Michael Schwier and Oliver Sedlaczek and Arne Warth
},
  booktitle={SPIE Medical Imaging},
  year={2014},
  organization={International Society for Optics and Photonics},
pages = {904104-1--7}
} 

@INPROCEEDINGS{2013-PIA-PRWSHHM,
	author = {Polzin, Thomas and R\"{u}haak, Jan and Werner, Ren\'{e} and Strehlow, Jan and Heldmann, Stefan and Handels, Heinz and Modersitzki, Jan},
	booktitle = {Proc. Fifth International MICCAI Workshop on Pulmonary Image Analysis (PIA 2013)},
	title = {Combining Automatic Landmark Detection and
Variational Methods for Lung CT Registration},
	year = {2013},
	address = {Nagoya, Japan},
	month = {September},
       pages = {85--96}
}

@INPROCEEDINGS{2013-SPIE-RHKF,
	author = {R\"{u}haak, Jan and Heldmann, Stefan and Kipshagen, Till and Fischer, Bernd},
	booktitle = {SPIE Medical Imaging 2013: Image Processing},
	title = {Highly Accurate Fast Lung CT Registration},
	year = {2013},
	address = {Lake Buena Vista, Florida, USA},
	month = {February}	
}

@article{2013-JP-OATSBHBGKWSTWMA,
	Author = {Oetjen, Janina and Aichler, Michaela and Trede, Dennis and Strehlow, Jan and Berger, Judith and Heldmann, Stefan and Becker, Michael and Gottschalk, Michael and Kobarg, Jan Hendrik and Wirtz, Stefan and Schiffler, Stefan and Thiele, Herbert and Walch, Axel and Maass, Peter and Alexandrov, Theodore},
	Journal = {Journal of Proteomics},
	Pages = {52--60},
	Title = {MRI-compatible pipeline for three-dimensional MALDI imaging mass spectrometry using PAXgene fixation},
	Volume = {90},
	Year = {2013}}

@inproceedings{2012-INF-THF,
	Address = {Bonn},
	Author = {Thiele, H. and Heldmann, S. and Fischer, B.},
	Booktitle = {Proceedings der INFORMATIK 2012},
	Editor = {Goltz, U. and Magnor, M. and Appelrath, H-J and Matthies, HK and Balke, W-T and Wolf, L.},
	Pages = {1535--1545},
	Publisher = {Gesellschaft f{\"u}r Informatik},
	Series = {GI-Editon Lecture Notes in Informatics},
	Title = {3D Visualisierung von Organismen},
	Volume = {208},
	Year = {2012}}

@article{2012-AC-TSBWSSAKOHWTMA,
	Author = {Trede, Dennis and Schiffler, Stefan and Becker, Michael and Wirtz, Stefan and Steinhorst, Klaus and Strehlow, Jan and Aichler, Michaela and Kobarg, Jan Hendrik and Oetjen, Janina and Heldmann, Stefan and Walch, Axel and Thiele, Herbert and Maass, Peter and Alexandrov, Theodore},
	Journal = {Analytical Chemistry},
	Pages = {6079-87},
	Title = {Exploring 3D MALDI imaging mass spectrometry data: 3D spatial segmentation of mouse kidney},
	Volume = {84(14)},
	Year = {2012}}

@misc{2012-RH-EMPIRE10,
  title={Variational Lung Registration with Explicit Boundary Alignment},
  author={Rühaak, Jan and Heldmann, Stefan},
  institution={The EMPIRE10 challenge},
  month = {February},
  year={2012}
}

@INPROCEEDINGS{2011-SPIE-OBHPF,
	author = {Olesch, Janine and Beuthien, Björn and Heldmann, Stefan and Papenberg, Nils and Fischer, Bernd},
	booktitle = {SPIE Medical Imaging 2011: Visualization, Image-Guided Procedures, and Modeling},
	title = {Fast intra-operative nonlinear registration of 3D-CT to tracked, selected 2D-ultrasound slices},
	year = {2011},
	address = {Lake Buena Vista, Florida, USA},
	month = {February}	
}

@INPROCEEDINGS{2011-MICCAI-PULMO-RHF,
	author = {R\"{u}haak, Jan and Heldmann, Stefan and Fischer, Bernd},
	booktitle = {Proc. Fourth International MICCAI Workshop on Pulmonary Image Analysis (PULMO 2011)},
	title = {Improving Lung Registration by Incorporating Anatomical Knowledge: A Variational Approach},
	year = {2011},
	address = {Toronto, Canada},
	month = {September},
}

@inproceedings{2010-BVM-PSHBSW,
	Author = {Papenberg, N. and Schumacher, H. and Heldmann, S. and B{\"o}hler, T. and van Straaten, D. and Wirtz, S.},
	Booktitle = {Bildverarbeitung f{\"u}r die Medizin},
	Pages = {335--339},
	Title = {Multimodale Registrierung von Knochen-Szintigraphien und R{\"o}ntgenbildern},
	Year = {2010}}

@INPROCEEDINGS{2010-SPIE-BPHF,
  author    = {Beuthien, B. and Papenberg, B. and Heldmann, S. and Fischer, B.},
  title     = {Volume-constrained image registration for pre- and post-operative {CT} liver data},
  booktitle = {SPIE Medical Imaging},
  year      = {2010},
  address   = {San Diego, California, USA},
  month     = {February}}

@conference{2010-SPIE-H,
  author = {Heldmann, Stefan},
  title = {Multimodal Registration of {MR} Images with a Novel Least-squares Distance Measure},
  journal = {Medical Imaging 2010: Image Processing },
  Xvolume = {7623},
  year = {2010},
  publisher={SPIE},
  month={February},
  DOI={10.1117/12.844466},
  adress={San Diego},
}

@inproceedings{2010-BMT-HBOPF,
	Address = {Rostock, Germany},
	Author = {Heldmann, Stefan and Beuthien, Bj{\"o}rn  and Olesch, Janine and Papenberg, Nils and Fischer, Bernd},
	Booktitle = {BMT 2010 - FAL-Sessions, Hot-Topic Sessions, Projektsessions (BMT 2010 - FAL-Sessions - Hot-Topic Sessions - Projektsessions)},
	Title = {Improved Minimal-Invasive Laparoscopic Liver Surgery by Registration of 3D CT and 2D Ultrasound Slices},
	Year = {2010},
}

@article{LangeEtAl2009,
	Author = {Lange, Thomas and Papenberg, Nils and Heldmann, Stefan and Modersitzki, Jan and Fischer, Bernd and Schlag, Peter M.},
	Journal = {International Journal of Computer Assisted Radiology and Surgery},
	Number = {1},
	Pages = {79--88},
	Title = {3D Ultrasound--{CT} Alignment of the Liver using Combined Landmark--Intensity Registration},
	Volume = {4},
	Year = {2009}}

@ARTICLE{2009-LAA-HHM,
  author = {Haber, Eldad and Heldmann, Stefan and Modersitzki, Jan},
  title = {A Framework for Image-Based Constrained Registration with an Application to Local Rigidity},
  journal = {Linear Algebra and its Applications},
  volume = {431},
  year = {2009},
  pages = {459-470},
 }

@conference{2009-BVM-HP,
  author = {Heldmann, Stefan and Papenberg, Nils},
  title = {A Scale-Space Approach for Image Registration of Vessel Structures},
  journal = {Bildverarbeitung f\"{u}r die Medizin},
  Series = {Informatik aktuell},
  Xvolume = {7},
  year = {2009},
  publisher={Springer},
  pages = {137-141},
  DOI={10.1007/978-3-540-93860-6_28},
}

@INPROCEEDINGS{2009-SSVM-HHM,
  author = {Haber, Eldad and Heldmann, Stefan and Modersitzki, Jan},
  title = {A Scale-Space Approach to Landmark Constrained Image Registration},
  booktitle = {Proceedings of the Second International Conference on Scale Space Methods and  
               Variational Methods in Computer Vision (SSVM)},
  year = {2009},
  pages = {1-12},
  alteditor = {B de Moor and B Motmans},
  publisher = {Springer LNCS},
}

@ARTICLE{2009-SSVM-HP,
  author = {Heldmann, Stefan and Papenberg, Nils},
  title = {A Variational Approach for Volume-to-Slice Registration},
  booktitle= {SSVM '09: Proceedings of the Second International Conference on Scale Space and Variational Methods in Computer Vision},
  Series = {LNCS}
  volume = {5567},
  year = {2009},
  location={Voss, Norway},
  publisher={Springer Berlin/ Heidelberg},
  pages = {624-635},
  DOI={10.1007/978-3-642-02256-2_52},
  ISBN={978-3-642-02255-5},
}

@conference{2009-SPIE-HZ,
  author = {Heldmann, Stefan and Zidowitz, Stephan},
  title = {Elastic Registration of Multiphase {CT} Images of Liver},
  booktitle={SPIE Medical Imaging 2009: Image Processing},
  volume = {7259},
  year = {2009},
  month={March},
  publisher={SPIE},
  location={Lake Buena Vista, FL, USA },
  DOI={10.1117/12.811415},
}

@INPROCEEDINGS{2009-SPIE-EHMF,
  	author = {Ens, Konstantin and Heldmann, Stefan and Modersitzki, Jan and Fischer, Bernd},
 	 title = {Improving a Registration and/or Segmentation Task by Incorporating Characteristics of the Displacement Field},
  	booktitle = {Proceedings of the SPIE 2009, Medical Imaging},
  	year = {2009},
  	editor = {JM Fitzpatrick and M Sonka},
  	volume = {5370},
  	pages = {304--313},
  	publisher = {SPIE},
}

@inproceedings{2008-BVM-SHHF,
	Author = {Schumacher, Hanno and Heldmann, Stefan and Haber, Eldad and Fischer, Bernd},
	Booktitle = {Bildverarbeitung f{\"u}r die Medizin 2008},
	Title = {Iterative Reconstruction of SPECT Images using Adaptive Multil-Level Refinement},
	Year = {2008}}
	Editor = {T. Tolxdoff and J. Braun and T.M. Deserno and H. Handels and A. Horsch and {H.-P. Meinzer}},
	Pages = {318 -- 323},
	Publisher = {Springer},
	Series = {Informatik aktuell},
	Year = {2008}
	ISBN={ 978-3-540-78639-9},
}

@ARTICLE{2008-SIAM-HHM,
  author = {Haber, Eldad and Heldmann, Stefan and Modersitzki, Jan},
  title = {Adaptive Mesh Refinement for Nonparametric Image Registration},
  journal = {SIAM Journal on Scientific Computing},
  volume = {30},
  number={6},
  year = {2008},
  publisher={SIAM},
  pages = {3012-3027},
  DOI={10.1137/070687724},
  url = {http://link.aip.org/link/?SCE/30/3012},
}

@inproceedings{2008-CARS-LPHMFLS,
	Author = {Lange, Thomas and Papenberg, Nils and Heldmann, Stefan and Modersitzki, Jan and Fischer, Bernd and Schlag, Peter M.},
	Booktitle = {Internationnal Conference on Computer Assisted Radiology and Surgery 2008 (CARS '08)},
	Title = {{3D Ultrasound--CT Alignment of the Liver using Combined Landmark--Intensity Registration}},
	Year = {2008}}

@conference{2007-BVM-FLIRT,
  author = {Papenberg, Nils and Schumacher, Hanno and Heldmann, Stefan and Wirtz, Stefan and Bommersheim, Silke and Ens, Konstantin and Modersitzki, Jan and Fischer, Bernd},
  title = {A Fast and Flexible Image Registration Toolbox: Design and Implementation of the General Approach},
  book= {Bildverarbeitung f\"{u}r die Medizin 2007},
  Series = {Informatik aktuell},
  Editor = {A. Horsch and T.M. Deserno and H. Handels and {H.-P. Meinzer} and T. Tolxdoff},
  volume = {5},
  year = {2007},
  publisher={Springer Berlin/ Heidelberg},
  pages = {106-110},
  DOI={10.1007/978-3-540-71091-2},
  ISSN={1431-472X},
  ISBN={978-3-540-71090-5 (Print), 978-3-540-71091-2 (Online)},
}

@ARTICLE{2007-IP-HHA,
  author = {Haber, Eldad and Heldmann, Stefan and Ascher, Uri},
  title = {Adaptive Finite Volume Method for Distributed Non-smooth Parameter Identification},
  journal = {Inverse Problems},
  Xvolume = {23},
  Xnumber = {4},
  year = {2007},
  pages = {1659-1676},
  DOI={10.1088/0266-5611/23/4/017},
}

@ARTICLE{2007-SIAM-HHM,
  author = {Haber, Eldad and Heldmann, Stefen and Modersitzki, Jan },
  title = {An OcTree Method for Parametric Image Registration },
  journal = {SIAM Journal on Scientific Computing},
  volume = {29},
  number={5},
  year = {2007},
  publisher={SIAM},
  pages = {2008-2023},
  DOI={10.1137/060662605},
  url = {http://link.aip.org/link/?SCE/29/2008/1},
}

@ARTICLE{2007-JCP-HH,
  author = {Haber, Eldad and Heldmann, Stefan},
  title = {An OcTree Multigrid Method for Quasi-Static Maxwell’s Equations with Highly
  Discontinuous Coefficients },
  journal = {Journal of Computational Physics},
  Xvolume = {223},
  Xnumber = {2},
  year = {2007},
  publisher={Elsevier Inc},
  pages = {783-796},
  DOI={10.1016/j.jcp.2006.10.012 },
 }

@ARTICLE{2007-IJCV-SMHWF,
  author = {Schmitt, Oliver and Modersitzki, Jan and Heldmann, Stefan and Wirtz, Stefen and Fischer, Bernd},
  title = {Image Registration of Sectioned Brains },
  journal = {International Journal of Computer Vision },
  volume = {73},
  number={1},
  year = {2007},
  publisher={Springer Netherlands},
  pages = {5-39},
  DOI={10.1007/s11263-006-9780-x},
  ISSN={0920-5691 (Print), 1573-1405 (Online)},
}

@phdthesis{2006-PhD-Heldmann,
	Author = {Heldmann, Stefan},
	School = {Institute of Mathematics, University of L\"ubeck},
	Title = {Non-Linear Registration based on Mutual Information},
	ISBN= {978-3-8325-1481-5},
	Year = {2006},
}

@ARTICLE{2005-AE-SMHWHHKW,
  author = {Schmitt, Oliver and Modersitzki, Jan and Heldmann, Stefan and Wirtz, Stefen and H\"{o}mke, L and Heide, W and K\"{o}mpf, D and Wree, A },
  title = {Three-dimensional Cytoarchitectonic Analysis of the Posterior Bank of the Human Precentral sulcus},
  journal = {Anatomy and Embryology},
  volume = {Volume 210, Numbers 5-6},
  year = {2005},
  publisher={Springer Berlin / Heidelberg},
  pages = {387-400},
  DOI={10.1007/s00429-005-0030-8},
  ISSN={0340-2061 (Print), 1432-0568 (Online)},
}

@conference{2004-BVM-HMPMF,
  author = {Heldmann,Stefan and Mahnke, Oliver and Potts, Daniel and Modersitzki, Jan and Fischer, Bernd },
  title ={ Fast Computation of Mutual Information in a Variational Image Registration Approach },
  journal = {Bildverarbeitung f\"{u}r die Medizin},
  year = {2004},
   pages = {448--452},
  publisher={Springer},
  Series = {Informatik aktuell},
}

@misc{2004-SWMFHW,
	Author = {Schmitt, Oliver and Wirtz, Stefan and Modersitzki, Jan and Fischer, Bernd and Heldmann, Stefan and Wree, A.},
	Howpublished = {Poster, TH 330, NeuroImage 22},
	Title = {Microregistration and microreconstruction of a whole mouse brain},
	Year = {2004}}

@TECHREPORT{2004-TR-HHM,
  author = {Haber, Eldad and Modersitzki, Jan and Heldmann, Stefan},
  title = {Multilevel Optimization Methods for Mutual Information Registration},
  institution = {Department of Mathematics and Computer Science},
  year = {2004},
  type = {Technical Report},
  number = {TR-2004-015-A},
  address = {Emory University, Atlanta GA 30322},
  note = {Submitted to Inverse Problems},
}

@ARTICLE{2003-AA-SWDMHHBHK,
author = {Schmitt, Oliver and Wree, A and D\"umbgen, L and Modersitzki, Jan and H\"omke, L. and Heldmann, Stefan and Bock, S and Heide, J. and  K\"ompf, D.},
  title = {Spatial location of the human frontal eye field},
  journal = {Ann. Anal.},
  year = {2003},
  volume = {185},
  pages = {320--321},
}