@inproceedings{brehmer2018simultaneous,
  title={Simultaneous Registration of Image Sequences – a novel singular value
based images similarity measure},
  author={Brehmer, Kai and Wacker, Benjamin and Modersitzki, Jan},
  booktitle={Proceedings in Applied Mathematics and Mechanics - 89th GAMM Annual Meeting},
  pages={},
  year={2018},
  organization={Wiley}
}

@article{loewenhauser2018functional,
  title={Functional Lifting for Variational Problems with Higher-Order},
  author={Loewenhauser, Benedikt and Lellmann, Jan},
  journal={Imaging, Vision and Learning Based on Optimization and PDEs: IVLOPDE, Bergen, Norway, August 29--September 2, 2016},
  pages={101},
  year={2018},
  publisher={Springer},
  URL={https://link.springer.com/chapter/10.1007%2F978-3-319-91274-5_5}
}

@phdthesis{2017-PhD-Sandmann,
  Author = {Constantin M. Sandmann},
  Title = {Dynamic Models and Coupling in Medical 4D Imaging},
  School = {Institute of Mathematics and Image Computing, University of L\"ubeck},
  Year = {2017},
}

@TechReport{KorolevLellmann2017,
  author =      {Korolev, Y. and Lellmann, J.},
  title =       {Image reconstruction with imperfect forward models and applications in deblurring},
  institution = {University of Luebeck},
  year =        {2017},
  type =        {Preprint},
  number =      {arXiv:1708.01244},
  url =         {https://arxiv.org/abs/1708.01244}
}

@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}
}

@incollection{mader2017detection,
  title={Detection and Localization of Landmarks in the Lower Extremities Using an Automatically Learned Conditional Random Field},
  author={Mader, Alexander Oliver and Lorenz, Cristian and Bergtholdt, Martin and von Berg, Jens and Schramm, Hauke and Modersitzki, Jan and Meyer, Carsten},
  booktitle={Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics},
  pages={64--75},
  year={2017},
  publisher={Springer}
}

@ARTICLE{ruhaak2017matrix,
  author = {R\"{u}haak, Jan and K\"{o}nig, Lars and Tramnitzke, Florian and K\"{o}stler, Harald and Modersitzki, Jan},
  title = {A {M}atrix-{F}ree {A}pproach to {E}fficient {A}ffine-{L}inear {I}mage {R}egistration on {CPU} and {GPU}},
  journal = {{J}ournal of {R}eal-{T}ime {I}mage {P}rocessing},
  year      = {2017},
  volume    = {13},
  number    = {1},
  pages     = {205--225},
  issn      = {1861-8219},
  publisher = {Springer},
  url = {http://dx.doi.org/10.1007/s11554-016-0564-4}
}

@INPROCEEDINGS{vogt2017qball,
author={Vogt, Thomas and Lellmann, Jan},
title={An Optimal Transport-Based Restoration Method for Q-Ball Imaging},
booktitle={Scale Space and Variational Methods in Computer Vision: 6th International Conference, SSVM 2017, Kolding, Denmark, June 4-8, 2017, Proceedings},
pages={271--282},
year={2017},
publisher={Springer International Publishing},
editor={Lauze, Fran{\c{c}}ois and Dong, Yiqiu and Dahl, Anders Bjorholm},
doi={{{10.1007/978-3-319-58771-4_22}}}
}

@article{rust3robust,
  title={A robust algorithm for optic disc segmentation and fovea detection in retinal fundus images},
  author={Rust, Caterina and H{\"a}ger, Stephanie and Traulsen, Nadine and Modersitzki, Jan},
  journal={Current Directions in Biomedical Engineering},
  volume={3},
  number={2},
  year={2017},
  pages={533--537},
  publisher={De Gruyter}
}

@article{ruthotto2017stabilized,
  title={A stabilized multigrid solver for hyperelastic image registration},
  author={Ruthotto, Lars and Greif, Chen and Modersitzki, Jan},
  journal={Numerical Linear Algebra with Applications},
  volume={24},
  number={5},
  pages={e2095},
  year={2017},
  publisher={Wiley Online Library}
}

@article{konig2016deformable,
  title={Deformable image registration for adaptive radiotherapy with guaranteed local rigidity constraints},
  author={K{\"o}nig, Lars and Derksen, Alexander and Papenberg, Nils and Haas, Benjamin},
  journal={Radiation Oncology},
  volume={11},
  number={1},
  pages={122},
  year={2016},
  publisher={BioMed Central},
doi={10.1186/s13014-016-0697-4}
}

@InProceedings{Moellenhoff2016,
  author =    {M{\"o}llenhoff, T. and Laude, E. and M{\"o}ller, M. and Lellmann, J. and Cremers, D.},
  title =     {Sublabel-Accurate Relaxation of Nonconvex Energies},
  booktitle = {Proc. IEEE Conf. Comp. Vis. Patt. Recogn.},
  year =      {2016}
}

@InProceedings{Laude2016,
  author = {Laude, E. and M{\"o}llenhoff, T. and M{\"o}ller, M. and Lellmann, J and Cremers, D.},
  title =  {Sublabel-Accurate Convex Relaxation of Vectorial Multilabel Energies},
  year =   {2016},
  booktitle  = {Proc. Europ. Conf. Comp. Vision}
}

@article{stutzer2016evaluation,
  title={Evaluation of a deformable registration algorithm for subsequent lung computed tomography imaging during radiochemotherapy},
  author={St{\"u}tzer, Kristin and Haase, Robert and Lohaus, Fabian and Barczyk, Steffen and Exner, Florian and L{\"o}ck, Steffen and R{\"u}haak, Jan and Lassen-Schmidt, Bianca and Corr, D{\"o}rte and Richter, Christian},
  journal={Medical Physics},
  volume={43},
  number={9},
  pages={5028--5039},
  year={2016},
  publisher={Wiley Online Library}
}

@article{derksen2016alternating,
  title={An Alternating Image Registration Approach for Large Scale Bladder Deformations in Radiation Therapy},
  author={Derksen, A and König, L and Meine, H},
  journal={18th International Conference on the use of Computers in Radiation Therapy (ICCR), London},
  year={2016},
}

@article{SandmannEtAl2016,
author = {Constantin Sandmann and Erlend Hodneland and Jan Modersitzki},
title = {A practical guideline for T1 reconstruction from various flip angles in MRI},
journal = {Journal of Algorithms \& Computational Technology},
volume = {10},
number = {4},
pages = {213-223},
year = {2016},
URL = {http://dx.doi.org/10.1177/1748301816656288},
abstract = { A fast and robust method for T1 estimation in MRI is the so-called variable flip angle technique. We introduce a novel family of T1 reconstruction methods from data acquired with various flip angles and propose a family member which combines the robustness of a nonlinear- with the computational advantages of a linear reconstruction. The constructed family contains the most common approaches for T1 estimation, namely a linear and a nonlinear approach. A general sensitivity analysis for arbitrary members of the family is established. Advantages of the optimized reconstruction are demonstrated on phantom- as well as real data, showing improvements of up to 24\% as compared with the linear method. As a further means to stabilize T1 estimation, spatial stabilization methods are compared. We demonstrate on phantom and on real data that improved results can be obtained if not only T1 but also a second unknown M0 in the reconstruction is stabilized. }
}

@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}
}

@INPROCEEDINGS{PolzinEtAl2016,
  author = {Polzin, Thomas and Niethammer, Marc and Heinrich, Mattias Paul and
	Handels, Heinz and Modersitzki, Jan},
  title = {{Memory Efficient LDDMM for Lung CT}},
  booktitle = {Medical Image Computing and Computer-Assisted Intervention 2016},
  pages = {28--36},
  year = {2016},
  publisher = {Springer},
 editor = {Sebastién Ourselin and Leo Joskowicz and Mert R. Sabuncu and Gozde Unal and William Wells}
}

@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}
}

@Article{LeeCaiLellmannEtAl2016,
  author =  {Lee, J. and Cai, X. and Lellmann, J. and Dalponte, M. and Malhi, Y. and Butt, N. and Morecroft, M. and Schönlieb, C.-B. and Coomes, D.},
  title =   {Individual Tree Species Classification From Airborne Multisensor Imagery Using Robust {PCA}},
  journal = {Appl. Earth Obs. Remote Sensing},
  year =    {2016},
  note =    {In Press.}
}

@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, L{\`e}ge-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{gunther2015towards,
  title={Towards MR-guided biopsy outside the MR-scanner},
  author={G{\"u}nther, M and Bartscherer, T and Georgii, J and Hewener, H and Kipshagen, T and Ojdanic, D and Kocev, B and Lotz, J and Olesch, J and Rothl{\"u}bbers, S and others},
  year={2015}
}

@article{deluca2015the,
  author={V De Luca and T Benz and S Kondo and L König and D Lübke and S Rothlübbers and O Somphone and S Allaire and M A Lediju Bell and D Y F
Chung and A Cifor and C Grozea and M Günther and J Jenne and T Kipshagen and M Kowarschik and N Navab and J Rühaak and J Schwaab and C
Tanner},
  title={The 2014 liver ultrasound tracking benchmark},
  journal={Physics in Medicine and Biology},
  volume={60},
  number={14},
  pages={5571},
  url={http://dx.doi.org/10.1088/0031-9155/60/14/5571},
  year={2015}
}

@article{pompe2015parametric,
  title={Parametric Response Mapping Adds Value to Current Computed Tomography Biomarkers in Diagnosing Chronic Obstructive Pulmonary Disease},
  author={Pompe, Esther and van Rikxoort, Eva M and Schmidt, Michael and R{\"u}haak, Jan and Estrella, Leticia Gallardo and Vliegenthart, Rozemarijn and Oudkerk, Matthijs and de Koning, Harry J and van Ginneken, Bram and de Jong, Pim A and Lammers, Jan-Willem J and Hoesein, Firdaus A A Mohamed},
  journal={American {J}ournal of {R}espiratory and {C}ritical {C}are {M}edicine},
  volume={191},
  number={9},
  pages={1084--1086},
  year={2015},
  url={http://www.atsjournals.org/doi/abs/10.1164/rccm.201411-2105LE#.VebzExG8PRY},
  publisher={Am Thoracic Soc}
}

@INPROCEEDINGS{konig2015parallel,
	author = {K\"{o}nig, Lars and Derksen, Alexander and Hallmann, Marc and Papenberg, Nils},
	booktitle = {IEEE International Symposium on Biomedical Imaging: From Nano to Macro},
	title = {Parallel and Memory Efficient Multimodal Image Registration for Radiotherapy using Normalized Gradient Fields},
	year = {2015},
	address = {New York City, USA},
	month = {April},
        url = {http://dx.doi.org/10.1109/ISBI.2015.7163977}
}

@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{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.}
}

@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-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{Lellmann2015,
  author =      {Lellmann, J. and Papafitsoros, K. and Sch\"onlieb, C. and Spector, D.},
  title =       {Analysis and Application of a non-local Hessian},
  journal =     {SIAM Journal on Imaging Sciences},
  year =        {2015},
  volume =      {8},
  number =      {4},
  pages =       {2161--2202},
  owner =       {Jan},
  timestamp =   {2014.07.02},
}

@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{2015-BVM-CD,
	author = {Chen, Kanglin and Derksen, Alexander},
	booktitle = {Workshop: Bildverarbeitung für die Medizin},
	title = {A Variational Method for Contructing Unbiased Atlas with Probabilistic Label Maps},
	year = {2015},
	address = {},
	month = {}	
}

@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}	
}

@INPROCEEDINGS{2015-SPIE-WSRDDLH,
	author = {Wang, Lei and Strehlow, Jan and R\"{u}haak, Jan and Diez, Yago and Diekmann, Susanne and Laue, Hendrik and Hahn, Horst K.},
	booktitle = {SPIE Medical Imaging 2015: Image Processing},
	title = {A fast alignment method for breast MRI follow-up studies using automated breast segmentation and current-prior registration},
	year = {2015},
	address = {Orlando, Florida, USA},
	month = {February}	
}

@Article{Kappes2015,
  Title                    = {A Comparative Study of Modern Inference Techniques for Discrete Energy Minimization Problems},
  Author                   = {Kappes, J.~H. and Andres, B. and Hamprecht, F. A. and Schn\"orr, C. and Nowozin, S. and Batra, D. and Kim, S. and Kausler, B. X. and Kröger, T and Lellmann, J. and Komodakis, N. and Savchynskyy, B. and Rother, C.},
  Journal                  = {Int.~J.~Comp.~Vis},
  Year                     = {2015},
  Note                     = {(online first)},
}

@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{Weiss2015,
abstract = {Abstract. 3D reconstruction and digital double staining offer pathologists many new insights into tissue structure and metabolism. Key to these applications is the precise registration of histological slide images, that is challenging in several ways. One major challenge are differently stained slides, that highlight different parts of the tissue. In this paper we introduce a new registration method to face this multimodality. It abstracts the image information to cell nuclei densities. By minimizing the distance of these densities an affine transformation is determined that restores the lost spatial correspondences. The proposed density based registration is evaluated using consecutive histological slides. It is compared to a Mutual Information based registration and shown to be more accurate and robust.},
address = {Berlin, Heidelberg},
author = {Weiss, Nick and Lotz, Johannes and Modersitzki, Jan},
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},
doi = {10.1007/978-3-662-46224-9},
editor = {Handels, Heinz and Deserno, Thomas M. and Meinzer, Hans-Peter and Tolxdorff, Thomas},
file = {:home/jo/Seafile/misc/mendeley/Weiss, Lotz, Modersitzki - 2015 - Multimodal Image Registration in Digital Pathology Using Cell Nuclei Densities.pdf:pdf},
isbn = {9783662462232},
month = mar,
pages = {245},
publisher = {Springer Vieweg},
title = {{Multimodal Image Registration in Digital Pathology Using Cell Nuclei Densities}},
year = {2015}
}

@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{2014-BVM-TBM,
	Author = {Trull, Anna Katharina and Berkels, Benjamin and Modersitzki, Jan },
Booktitle = {BVM 2014, Bildverarbeitung f{\"u}r die Medizin 2014},
	Title = {Glomerular Filtration Rate Estimation from Dynamic Contrast-Enhanced MRI using a Separable Compartment Model and Parameter Elimination}
pages = {30--35}}

@ARTICLE{2014-MIM-PRWHM, 
  author = {Polzin, Thomas and R\"{u}haak, Jan and Werner, Ren\'{e} and Handels, Heinz and Modersitzki, Jan},
  title = {Lung Registration using Automatically Detected Landmarks},
  journal = {Methods of Information in Medicine},
  year = {2014},
  volume={53},
  pages={250--256}
}

@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}
} 

@article{kowallick2014quantification,
  title={Quantification of left ventricular torsion and diastolic recoil using cardiovascular magnetic resonance myocardial feature tracking},
  author={Kowallick, Johannes T and Lamata, Pablo and Hussain, Shazia T and Kutty, Shelby and Steinmetz, Michael and Sohns, Jan M and Fasshauer, Martin and Staab, Wieland and Unterberg-Buchwald, Christina and Bigalke, Boris and others},
  journal={PloS one},
  volume={9},
  number={10},
  pages={e109164},
  year={2014},
  publisher={Public Library of Science San Francisco, USA}
}

@article{QIMS4050,
	author = {Shuo Zhang and Arun A. Joseph and Dirk Voit and Sebastian Schaetz and Klaus-Dietmar Merboldt and Christina Unterberg-Buchwald and Anja Hennemuth and Joachim Lotz and Jens Frahm},
	title = {Real-time magnetic resonance imaging of cardiac function and flow—Recent progress},
	journal = {Quantitative Imaging in Medicine and Surgery},
	volume = {4},
	number = {5},
	year = {2014},
	keywords = {},
	abstract = {Cardiac structure, function and flow are most commonly studied by ultrasound, X-ray and magnetic resonance imaging (MRI) techniques. However, cardiovascular MRI is hitherto limited to electrocardiogram (ECG)-synchronized acquisitions and therefore often results in compromised quality for patients with arrhythmias or inabilities to comply with requested protocols—especially with breath-holding. Recent advances in the development of novel real-time MRI techniques now offer dynamic imaging of the heart and major vessels with high spatial and temporal resolution, so that examinations may be performed without the need for ECG synchronization and during free breathing. This article provides an overview of technical achievements, physiological validations, preliminary patient studies and translational aspects for a future clinical scenario of cardiovascular MRI in real time.},
	issn = {2223-4306},	url = {https://qims.amegroups.org/article/view/4050}
}

@phdthesis{2014-PhD-Beuthien,
  Author = {Bj\"orn Beuthien},
  Title = {Restringierte Medizinische Bildregistrierung},
  School = {Institute of Mathematics and Image Computing, University of L\"ubeck},
  Year = {2014},
}

@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{2014-DEGRO-HLRSZR,
title={Einfluss deformierbarer {B}ildregistrierung von {P}{E}{T}/{C}{T}-{V}erlaufsdaten auf die {S}ignalwerte innerhalb einer {K}ontur: {D}eformation auf {K}onturen oder {B}ilddaten anwenden?},
author={Robert Haase and Fabian Lohaus and Jan R\"uhaak and D\"orte van Straaten and Klaus Z\"ophel and Christian Richter},
booktitle={Proceedings of 20. Jahrestagung der Deutschen Gesellschaft f\"ur Radioonkologie (DEGRO), D\"usseldorf},
year={2014}
}

@Inproceedings{2014-BVM-HRMB,
	Author = {Heck, Constantin and Ruthotto, Lars and Modersitzki, Jan and Berkels, Benjamin},
booktitle = {BVM 2014, Bildverarbeitung f{\"u}r die Medizin 2014},
	Date-Added = {2014-01-22 13:52:07 +0000},
	Date-Modified = {2014-01-22 13:54:28 +0000},
	Title = {Model-based parameter estimation in DCE-MRI without an Arterial Input Function}
pages = {246--251}}

@ARTICLE{2014-JRTIP-BKRLF,
  author = {Berg, Roelof and K\"{o}nig, Lars and R\"{u}haak, Jan and Lausen, Ralph and Fischer, Bernd},
  title = {{H}ighly {E}fficient {I}mage {R}egistration for {E}mbedded {S}ystems
	{U}sing a {D}istributed {M}ulticore {DSP} {A}rchitecture},
  journal = {{J}ournal of {R}eal-{T}ime {I}mage {P}rocessing},
  year = {2014},
  month = {November},
  publisher = {Springer},
  url = {http://dx.doi.org/10.1007/s11554-014-0457-3}
}

@article {PATH:PATH4416,
author = {Bronsert, P and Enderle-Ammour, K and Bader, M and Timme, S and Kuehs, M and Csanadi, A and Kayser, G and Kohler, I and Bausch, D and Hoeppner, J and Hopt, UT and Keck, T and Stickeler, E and Passlick, B and Schilling, O and Reiss, CP and Vashist, Y and Brabletz, T and Berger, J and Lotz, J and Olesch, J and Werner, M and Wellner, UF},
title = {Cancer cell invasion and EMT marker expression - a three-dimensional study of the human cancer-host interface -},
journal = {The Journal of Pathology},
publisher = {John Wiley & Sons, Ltd},
issn = {1096-9896},
url = {http://dx.doi.org/10.1002/path.4416},
pages = {},
keywords = {cancer cell invasion, epithelial-mesenchymal transition, tumor budding, human adenocarcinoma, three dimensional reconstruction},
year = {2014}
}

@inproceedings{georgi2014IGIC,
author = {Georgii, J and Bartscherer, T and Degel, C and Fonfara, H and Hewener, H and Kipshagen, T and Kocev, B and Lotz, J and Ojdanic, D and Olesch, J and Rothlübbers, S and Speicher, D and Tretbar, S and Hahn, H and Günther, M},
title = { Improving Breast Biopsies by Motion Tracking. Proc. of Image-Guided Interventions},
booktitle = {Proc. of Image-Guided Interventions (IGIC)},
pages = {79-80},
year = {2014}
}

@INPROCEEDINGS{sorrentino2014Entwicklung,
  author = {Sorrentino,S and Peperhove,M and Kaireit,T and R{\"u}haak,J and Strehlow,J
	and Wacker,F and Vogel-Claussen,J and Shin,H},
  title = {{E}ntwicklung eines virtuellen 2{D}-{H}erz-{P}hantoms f{\"u}r die
	{B}erechnung regionaler myokardialer {W}andbewegung mittels nicht-rigider
	{B}ildregistrierung},
  year = {2014},
  volume = {186},
  number = {S 01},
  pages = {RK{\_}VO207{\_}4},
  bdsk-url-1 = {http://dx.doi.org/10.1055/s-0034-1372881},
  da = {22.04.2014},
  date = {2014///},
  date-added = {2014-07-10 15:19:06 +0000},
  date-modified = {2014-07-10 15:19:06 +0000},
  doi = {10.1055/s-0034-1372881},
  isbn = {1438-9029},
  journal = {{F}ortschritte auf dem Gebiet der {R}{\"o}ntgenstrahlen und der bildgebenden Verfahren},
  la = {DE},
  m2 = {RK{\_}VO207{\_}4},
  ty = {JOUR}
}

@INPROCEEDINGS{2014-MICCAI-HPC-TRKMK,
  author = {Tramnitzke, Florian and R\"{u}haak, Jan and K\"{o}nig, Lars and Modersitzki, Jan and K\"{o}stler, Harald},
  title = {{GPU} {B}ased {A}ffine {L}inear {I}mage {R}egistration
using {N}ormalized {G}radient {F}ields},
  booktitle = {Proc. Seventh International Workshop on High Performance Computing for Biomedical Image Analysis (HPC-MICCAI)},
  year = {2014},
  address = {Boston, USA},
  month = {September},
pages = {5--14}
}

@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}
}

@INPROCEEDINGS{2014-CLUST-KKR,
	author = {K\"{o}nig, Lars and Kipshagen, Till and R\"{u}haak, Jan},
	booktitle = {Proc. MICCAI Challenge on Liver Ultrasound Tracking (CLUST 2014)},
	title = {A Non-Linear Image Registration Scheme for Real-Time Liver Ultrasound Tracking using Normalized Gradient Fields},
	year = {2014},
	address = {Boston, USA},
	month = {September},
pages = {29--36}
}

@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}
}

@BOOK{Olesch201311,
title={Bildregistrierung für die navigierte Chirurgie},
series = {Aktuelle Forschung Medizintechnik},
author={Janine Olesch},
publisher={Springer Vieweg},
year={2014},
isbn={9783658056544},
price={EUR 59,99},
totalpages={267}
}

@INPROCEEDINGS{2013-Deformable,
	author = {K\"{o}nig, Lars and Papenberg, Nils and Haas, Benjamin and Modersitzki, Jan},
	booktitle = {Varian Research Partnership Symposium},
	title = {Deformable Registration for Adaptive Radiotherapy with Guaranteed Local Rigidity Constraints},
	year = {2013},
	address = {Atlanta, Georgia, USA},
	month = {March}	
}

@Misc{berger2013virtual,
  author = 	 {Judith Berger and Johannes Lotz and Janine Olesch and Mark Schenk
Kai Breuhahn and Benedikt Müller and Arne Warth and Niels Grabe and Bernd Lahrmann and
Oliver Sedlaczek},
  title = 	 {Virtual Double Staining Using Elastic Image Registration},
  note = {Poster Submission at Pathology Visions, San Antonio},
  year = 	 {2013},
  url = 	 {https://digitalpathologyassociation.org/poster-presentations}
}

@inproceedings{lotz2013real,
author = {Lotz, Johannes and Fischer, Bernd and Olesch, Janine and Günther, Matthias},
title = {Real time motion analysis in 4D medical imaging using conditional density propagation},
booktitle ={SPIE Medical Imaging 2015: Image Processing},
volume = {8669},
number = {},
pages = {86690T-86690T-7},
abstract = {Motion, like tumor movement due to respiration, constitutes a major problem in radiotherapy and/or diagnostics.
A common idea to compensate for the motion in 4D imaging, is to invoke a registration strategy, which aligns
the images over time. This approach is especially challenging if real time processing of the data and robustness
with respect to noise and acquisition errors is required.
To this end, we present a novel method which is based only on selected image features and uses a probabilistic
approach to compute the wanted transformations of the 3D images. Moreover, we restrict the search space to
rotation, translation and scaling.
In an initial phase, landmarks in the first image of the series have to be identified, which are in the course
of the scheme automatically transferred to the next image. To find the associated transformation parameters,
a probabilistic approach, based on factored sampling, is invoked. We start from a state set containing a fixed
number of different candidate parameters whose probabilities are approximated based on the image information
at the landmark positions. Subsequent time frames are analyzed by factored sampling from this state set and
by superimposing a stochastic diffusion term on the parameters.
The algorithm is successfully applied to clinical 4D CT data. Landmarks have been placed manually to mark
the tumor or a similar structure in the initial image whose position is then tracked over time. We achieve a
processing rate of up to 12 image volumes per second. The accuracy of the tracking after five time steps is
measured based on expert placed landmarks. We achieve a mean landmark error of less than 2 mm in each
dimension in a region with radius of 25 mm around the target structure.},
year = {2013},
doi = {10.1117/12.2006842},
URL = { http://dx.doi.org/10.1117/12.2006842},
eprint = {}
}

@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}}

@incollection{2013-BVM-RMHMW,
	Author = {Ruthotto, Lars and Mohammadi, Siawoosh and Heck, Constantin and Modersitzki, Jan and Weiskopf, Nikolaus},
	Booktitle = {Bildverarbeitung f{\"u}r die Medizin 2013},
	Doi = {10.1007/978-3-642-36480-8_60},
	Editor = {Meinzer, Hans-Peter and Deserno, Thomas Martin and Handels, Heinz and Tolxdorff, Thomas},
	Isbn = {978-3-642-36479-2},
	Language = {German},
	Pages = {344-349},
	Publisher = {Springer Berlin Heidelberg},
	Series = {Informatik aktuell},
	Title = {Hyperelastic Susceptibility Artifact Correction of DTI in SPM},
	Url = {http://dx.doi.org/10.1007/978-3-642-36480-8_60},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-36480-8_60}}

@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{BarendtModersitzkiIJCM2013,
  author = {Barendt, Sven and Modersitzki, Jan},
  title = {A variational model for SPECT reconstruction with a nonlinearly transformed attenuation prototype},
  journal = {International Journal of Computer Mathematics},
  volume = {90},
  number = {1},
  pages = {82-91},
  year = {2013}
}

@phdthesis{2013-PhD-Kainmueller,
  Author = {Dagmar Kainm\"uller},
  Title = {Deformable Meshes for Accurate Automatic Segmentation of Medical Image Data},
  School = {Institute of Mathematics and Image Computing, University of L\"ubeck},
  Year = {2013},
}

@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}
}

@phdthesis{OleschPhD201311_2,
title={Bildregistrierung f\"ur die navigierte Chirurgie},
author={Janine Olesch},
School = {Institute of Medical Informatics, University of L\"ubeck},
year={2013},
}

@article{BurgerEtAl2013,
  title={A hyperelastic regularization energy for image registration},
  author={Burger, M. and Modersitzki, J. and Ruthotto, L.},
  journal={SIAM Journal on Scientific Computing},
  volume={35},
  number={1},
  pages={B132--B148},
  year={2013},
  publisher={SIAM}
}

@article{PP2013,
	author = {Peter, Thomas and Plonka, Gerlind},
	title = {A Generalized Prony Method for Reconstruction of Sparse Sums of Eigenfunctions of Linear Operators. (revised preprint as download)},
        journal={Inverse Problems},
  volume={29},
  number={2},
	year = {2013},
	month = {January}	
}

@article{5c9d7318d40e4b20ad69ccaaba9f5e77,
title = "3D reconstruction of lung adenocarcinomas—one module for the development of mathematical multiscale models of lung cancer",
abstract = "Aims The BMBF-funded LungSysII consortium integrates information derived from molecular biology, cell biology, and histology using systems biology approaches to generate integrative multiscale-models of non-small cell lung cancer (NSCLC). In this context, we aim to define the three dimensional spatial relationship of the vascular system and the tumor mass in human pulmonary adenocarcinomas (ADC) as well as adjacent non-tumorous tissues based on histological data. We here report our most recent progress to generate a comprehensive 3-dimensional (3D) picture of ADC. Methods. Material was collected from freshly resected ADC patients and systematically cut into pieces of up to 1 cm in diameter. Samples were processed for optical projection tomography (OPT) scanning, utilizing tissue autofluorescence or specific epitope staining using directly labelled smooth muscle actin (SMA)-specific antibodies. In addition, alternate staining of serial sections derived from tumor samples were performed including H&E-, factor VIII (FVIII)-, and pan-cytokeratin (KL1) staining. Automated whole slide imaging was performed using the Hamamatsu NanoZoomer Digital Pathology system. The resulting 2D information was used to generate a 3D representation of the data by means of a non-linear elastic image registration. Results. Whole tissue OPT-scanning revealed the spatial distribution of bronchial and vasculature structures in the tumor and adjacent non-tumorous lung tissue. The image quality of the 3D vessel structure was improved solving a non-negatively constrained, L2-based reconstruction problem iteratively (MRNSD) on the raw-data produced by the OPT system. To reconstruct the serial sectioning data to a 3D volume, a special non-linear image registration algorithm was developed and applied. Specialization of the algorithm was needed due to cutting artefacts such as shape distortion and staining variation. The optimized non-linear algorithm was successfully applied on the H&E-, FVIII-, and KL1-staining. Conclusions. We here present approaches for 3D reconstruction of the vascular system and tumor mass in ADC as well as bordering healthy tissue. This quantitative information covers the range μm to cm and can be used for computational tissue modelling and for integration in mathematical multiscale models, which are currently under development.",
author = "B Mueller and J Olesch and J Lotz and S Barendt and O Sedlaczek and B Lahrmann and N Grabe and F Bestvater and U Kauczor and Schnabel, {P A} and H Hoffmann and B Fischer and P Schirmacher and A Warth and K Breuhahn",
year = "2013",
month = may,
day = "1",
doi = "10.1007/s00292-013-1765-2",
language = "English",
volume = "34 ",
pages = "6--163",
journal = "Der Pathologe",
issn = "1432-1963",
number = "Suppl 1",
}

@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{BarendtModersitzkiBVM2012,
  title={SPECT Reconstruction with a Transformed Attenuation Prototype at Multiple Levels},
  author={Barendt, Sven and Modersitzki, Jan},
 booktitle={Bildverarbeitung f{\"u}r die Medizin 2012},
 pages     = {352-357},
  year={2012},
  publisher={Springer}
}

@inproceedings{2012-DCEMRI-WBIR,
	title={Registration of Dynamic Contrast Enhanced {MRI} with Local Rigidity Constraint},
  	author={Ruthotto, L. and Hodneland, E. and  Modersitzki,J.},
 	booktitle={Biomedical Image Registration, 5th International Workshop {WBIR2012}},
  	year={2012},
	editor={Dawant B.M., Fitzpatrick J.M., Rueckert D., and Christensen G.E.},
  	publisher={Springer}
}

@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}}

@phdthesis{2012-PhD-Ruthotto,
  Author = {Lars Ruthotto},
  Title = {Hyperelastic Image Registration - Theory, Numerical Methods, and Applications},
  School = {Fachbereich Mathematik und Informatik, Westfälische Wilhelms-Universität Münster},
  Year = {2012},
}

@INPROCEEDINGS{2012-GigengackEtAl-NSS-MIC-B,
  author = {F. Gigengack and L. Ruthotto and T. K{\"o}sters and X. Jiang and
	J. Modersitzki and M. Burger and C.H. Wolters and K. Schäfers},
  title = {Pipeline for Motion Correction in Dual Gated PET},
  booktitle = {Nuclear Science Symposium and Medical Imaging Confereence (NSS/MIC), 2012 IEEE},
  year = {2012},
  pages = {2983--2984}
}

@INPROCEEDINGS{2012-BVM-SRKF,
   author = {Strehlow, Jan and R\"{u}haak, Jan and Kluck, Christina and Fischer, Bernd},
   booktitle = {Bildverarbeitung f{\"u}r die Medizin 2012},
   title = {Effiziente Verpunktung pulmonaler MR-Bilder zur Evaluierung von Registrierungsergebnissen},
   series = {Informatik aktuell},
   publisher = {Springer}
   year = {2012},   
   pages = {219-224},
}

@INPROCEEDINGS{2012-GigengackEtAl-MICCAI,
  author = {Gigengack, Fabian and Ruthotto, Lars and Jiang, Xiaoyi and Modersitzki,
	Jan and Burger, Martin and Hermann, Sven and Sch{\"a}fers, Klaus
	P.},
  title = {Atlas-Based Whole-Body {PET-CT} Segmentation using a Passive Contour
	Distance},
  booktitle = {Proceedings of the MICCAI Workshop on Medical Computer Vision 2012},
  year = {2012},
  pages = {1--10},
  publisher = {Springer LNCS}
}

@inproceedings{2012-VAMPIRE-BVM,
  title={A Simplified Pipeline for Motion Correction in Dual Gated Cardiac {PET}},
  author={Ruthotto, L. and Gigengack, F. and Burger, M. and Wolters, C.H., and Jiang, X. and Sch{\"a}fers, K. and           	
		  Modersitzki,J.},
 booktitle={Bildverarbeitung f{\"u}r die Medizin 2012},
  year={2012},
  publisher={Springer}
}

@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-VAMPIRE-IEEE,
author = {Gigengack, Fabian and Ruthotto, Lars and Burger, Martin and Wolters, Carsten H and Jiang, Xiaoyi and Sch{\"a}fers, Klaus P},
title = {{Motion Correction in Dual Gated Cardiac PET using Mass-Preserving Image Registration}},
journal = {IEEE Transactions on Medical Imaging},
year = {2012},
volume = {31},
number = {3},
pages = {698--712},
}

@article{RuthottoEtAl2012,
author = {Ruthotto, L and Kugel, H and Olesch, J and Fischer, B and Modersitzki, J and Burger, M and Wolters, CH},
title = {Diffeomorphic Susceptibility Artefact Correction of Diffusion-Weighted Magnetic Resonance Images},
journal = {Physics in Medicine and Biology},
year = {2012},
volume={57},
pages = {5715--5731},
url={http://stacks.iop.org/0031-9155/57/5715}
}

@ARTICLE{2011-Springer-CG,
  author = {M. Chung and B. Göbel},
  title = {Mathematical Modeling of the Human Energy Metabolism based on the
	Selfish Brain Theory},
  journal = {Advances in Systems Biology, Springer},
  year = {2011},
  volume = {(in press)},
  owner = {BrittaGoebel},
  timestamp = {2011.05.15}
}

@ARTICLE{2011-TB-GL,
  author = {B. G\"obel and D. Langemann},
  title = {Systemic investigation of a brain-centered model of the human energy
	metabolism},
  journal = {Theory Biosci},
  year = {2011},
  volume = {130},
  pages = {5-18},
  number = {1},
  owner = {BrittaGoebel},
  timestamp = {2010.12.09}
}

@inproceedings{2011-BVM-BM,
  author    = {Barendt, Sven and Modersitzki, Jan},
  title     = {SPECT Reconstruction with a Nonlinear Transformed Attenuation Prototype},
  booktitle = {Bildverarbeitung f{\"u}r die Medizin},
  year      = {2011},
  Series = {Informatik aktuell},
  }

@article{MOINCCBioTech2011,
  author = {J. Hamer and M. Kleine and S. Barendt and J. Krajewski and J. Konitzer and E. Gáspár and B. Meller and J. Knobloch and M. Russlies and I. Buchmann and J. Barkhausen and J. Modersitzki and G. Ebel and T. M. Buzug},
  title = {Molecular Imaging of Inflammations at Implant Interfaces (M4I) -
	Part of Molecular Imaging North Competence Center (MOIN CC)},
  journal = {Biomed Tech},
  year = {2011},
  volume = {56},
}

@phdthesis{2011-PhD-Lange,
  Author = {Thomas Lange},
  Title = {Modeling Prior Knowledge for Image Registration in Liver Surgery},
  School = {Institute of Mathematics and Image Computing, University of L\"ubeck},
  Year = {2011},
}

@phdthesis{2011-PhD-Goebel,
  Author = {Britta G\"obel},
  Title = {Mathematische Modellierung des menschlichen Energiestoffwechsels: Die zentrale Rolle des Gehirns},
  School = {Institute of Mathematics and Image Computing, University of L\"ubeck},
  Year = {2011},
}

@ARTICLE{2011-JBSE-CGPOM,
  author = {M. Chung and B. G\"obel and A. Peters and K.M. Oltmanns and A. Moser},
  title = {Mathematical modeling of the biphasic dopaminergic response to glucose},
  journal = {J Biomed Sci Eng},
  year = {2011},
  volume = {4},
  pages = {136-145},
  owner = {BrittaGoebel},
  timestamp = {2011.03.23}
}

@inproceedings{2011-VAPIRE-MICspline,
  title={Mass-Preserving Motion Correction of PET: Displacement Field vs. Spline Transformation},
  author={Gigengack, F. and Ruthotto, L. and Burger, M. and Wolters, C.H. and Jiang, X. and Sch{\"a}fers, K.P.},
 booktitle={Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), 2011 IEEE},
  year={2011},
   pages={3088--3090},
 organization={IEEE}
}

@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{2011-BVM-OF,
  author    = {Olesch, Janine and Fischer, Bernd},
  title     = {Focussed registration of tracked 2D US to 3D CT data of the liver},
  booktitle = {Bildverarbeitung f{\"u}r die Medizin},
  year      = {2011},
  Series = {Informatik aktuell},
  }

@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-BVM-ZPMF,
  author = {Zimmer, Veronika and Papenberg, Nils and Modersitzki, Jan and Fischer,
	Bernd},
  title = {Bildregistrierung zur Verbrennungsanalyse},
  booktitle = {Bildverarbeitung f\"ur die Medizin 2011},
  year = {2011},
  editor = {H Handels},
  pages = {159--163},
  publisher = {Springer}
}

@INPROCEEDINGS{2011-ISBI-MBRHBTHP,
	author = {Moltz, Jan Hendrik and Braunewell, Stefan and R\"{u}haak, Jan and Heckel, Frank and Barbieri, Sebastiano and Tautz, Lennart and Hahn, Horst Karl and Peitgen, Heinz-Otto},
	booktitle = {8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro},
	title = {Analysis of Variability in Manual Liver Tumor Delineation in CT Scans},
	year = {2011},
	address = {Chicago, Illinois, USA},
	month = {March}	
}

@INPROCEEDINGS{2011-SPIE-MRHP,
	author = {Moltz, Jan Hendrik and R\"{u}haak, Jan and Hahn, Horst Karl and Peitgen, Heinz-Otto},
	booktitle = {SPIE Medical Imaging 2011: Image Processing},
	title = {A Novel Adaptive Scoring System for Segmentation Validation with Multiple Reference Masks},
	year = {2011},
	address = {Lake Buena Vista, Florida, USA},
	month = {February}	
}