@article {7022,
	title = {Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera},
	journal = {BioEssays},
	volume = {43},
	year = {2021},
	doi = {10.1002/bies.202000257},
	author = {Pape, C and Remme, R and Wolny, A and Olberg, S and Wolf, S and Cerrone, L and Cortese, M and Klaus, S and Lucic, B and Ullrich, S and Anders-{\"O}sswein, M and Wolf, S and Cerikan, B and Neufeldt, C J and Ganter, M and Schnitzler, P and Merle, U and Lusic, M and Boulant, S and Stanifer, M and Bartenschlager, R and Hamprecht, F A and Kreshuk, A and Tischer, C and Kr{\"a}usslich, H.-G. and M{\"u}ller, B and Laketa, V}
}
@phdthesis {7065,
	title = {Scalable Instance Segmentation for Microscopy},
	year = {2021},
	publisher = {Heidelberg University},
	type = {PhD Thesis},
	author = {Pape, C}
}
@unpublished {7062,
	title = {Understanding Event-Generation Networks via Uncertainties},
	year = {2021},
	publisher = {arXiv preprint},
	url = {https://arxiv.org/abs/2104.04543v1},
	author = {Bellagente, M and Hau{\ss}mann, M and Luchmann, M and Plehn, T}
}
@article {7090,
	title = {Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution},
	journal = {eLife},
	volume = {9},
	year = {2020},
	doi = {10.7554/eLife.57613},
	author = {Wolny, A and Cerrone, L and Vijayan, A and Tofanelli, R and Vilches-Barro, A and Louveaux, M and Wenzel, C and Strauss, S and Wilson-Sanchez, D and Lymbouridou, R and Steigleder, SS and Pape, C and Bailoni, A and Duran-Nebreda, S and Bassel, GW and Lohmann, JU and Tsiantis, M and Hamprecht, FA and Schneitz, K and Maizel, A and Kreshuk, A}
}
@article {6319,
	title = {Deep-Learning Jets with Uncertainties and More},
	journal = {SciPost Phys},
	volume = {8},
	year = {2020},
	doi = {10.21468/SciPostPhys.8.1.006 },
	url = {https://scipost.org/10.21468/SciPostPhys.8.1.006},
	author = {Bollweg, S and Manuel Hau{\ss}mann and Kasieczka, G and Luchmann, M and Plehn, T and Thompson, J}
}
@article {Zeilmann:2020aa,
	title = {Geometric Numerical Integration of the Assignment Flow},
	journal = {Inverse Problems},
	volume = {36},
	number = {3},
	year = {2020},
	pages = {034004 (33pp)},
	author = {Zeilmann, A. and Savarino, F. and Petra, S. and Schn{\"o}rr, C.}
}
@article {Wolf2020,
	title = {The Mutex Watershed and its Objective: Efficient, Parameter-Free Graph Partitioning},
	journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	volume = {43},
	year = {2020},
	pages = {3724-3738},
	abstract = {Image partitioning, or segmentation without semantics, is the task of decomposing an image into distinct segments, or equivalently to detect closed contours. Most prior work either requires seeds, one per segment; or a threshold; or formulates the task as multicut / correlation clustering, an NP-hard problem. Here, we propose a greedy algorithm for signed graph partitioning, the "Mutex Watershed". Unlike seeded watershed, the algorithm can accommodate not only attractive but also repulsive cues, allowing it to find a previously unspecified number of segments without the need for explicit seeds or a tunable threshold. We also prove that this simple algorithm solves to global optimality an objective function that is intimately related to the multicut / correlation clustering integer linear programming formulation. The algorithm is deterministic, very simple to implement, and has empirically linearithmic complexity. When presented with short-range attractive and long-range repulsive cues from a deep neural network, the Mutex Watershed gives the best results currently known for the competitive ISBI 2012 EM segmentation benchmark.},
	doi = {10.1109/tpami.2020.2980827},
	author = {Wolf, Steffen and Bailoni, Alberto and Pape, Constantin and Rahaman, Nasim and Kreshuk, Anna and K{\"o}the, Ullrich and Hamprecht, Fred A.}
}
@proceedings {Haller2020,
	title = {A Primal-Dual Solver for Large-Scale Tracking-by-Assignment},
	year = {2020},
	abstract = {We propose a fast approximate solver for the combinatorial problem known as tracking-by-assignment, which we apply to cell tracking. The latter plays a key role in discovery in many life sciences, especially in cell and developmental biology. So far, in the most general setting this problem was addressed by off-the-shelf solvers like Gurobi, whose run time and memory requirements rapidly grow with the size of the input. In contrast, for our method this growth is nearly linear. Our contribution consists of a new (1) de-composable compact representation of the problem; (2) dual block-coordinate ascent method for optimizing the decomposition-based dual; and (3) primal heuristics that reconstructs a feasible integer solution based on the dual information. Compared to solving the problem with Gurobi, we observe an up to 60 times speed-up, while reducing the memory footprint significantly. We demonstrate the efficacy of our method on real-world tracking problems.},
	author = {Stefan Haller and Prakash, Mangal and Hutschenreiter, Lisa and Pietzsch, Tobias and Carsten Rother and Jug, Florian and Swoboda, Paul and Savchynskyy, Bogdan}
}
@proceedings {7005,
	title = {Proposal-Free Volumetric Instance Segmentation from Latent Single-Instance Masks},
	volume = {12544},
	year = {2020},
	pages = {331-344},
	publisher = {Springer},
	edition = {LNCS},
	doi = {10.1007/978-3-030-71278-5_24},
	author = {Bailoni, A and Pape, C and Wolf, S and Kreshuk, A. and Hamprecht, F A}
}
@proceedings {6990,
	title = {The Semantic Mutex Watershed for Efficient Bottom-Up Semantic Instance Segmentation},
	year = {2020},
	pages = {208-224},
	doi = {doi.org/10.1007/978-3-030-58539-6_13},
	author = {Wolf, S and Li, Y and Pape, C and Bailoni, A and Kreshuk, A and Hamprecht, F A}
}
@article {Censor:2020aa,
	title = {Superiorization vs. Accelerated Convex Optimization: The Superiorized/Regularized Least Squares Case},
	journal = {J. Appl. Numer. Optimization (in press; arXiv:1911.05498)},
	volume = {2},
	number = {1},
	year = {2020},
	pages = {15-62},
	url = {http://jano.biemdas.com/archives/1060},
	author = {Censor, Y. and Petra, S. and Schn{\"o}rr, C.}
}
@article {Zern:2020ab,
	title = {Unsupervised Assignment Flow: Label Learning on Feature Manifolds by Spatially Regularized Geometric Assignment},
	journal = {Journal of Mathematical Imaging and Vision},
	year = {2020},
	url = {https://doi.org/10.1007/s10851-019-00935-7},
	author = {Zern, A. and M. Zisler and Petra, S. and Schn{\"o}rr, C.}
}
@article {6290,
	title = {Bolus arrival time estimation in dynamic contrast-enhanced magnetic resonance imaging of small animals based on spline models, in press},
	journal = {Physics in Medicine and Biology},
	volume = {64},
	year = {2019},
	doi = {http://iopscience.iop.org/article/10.1088/1361-6560/aafce7},
	author = {Bendinger, AL and Debus, C and Glowa, C and Karger, CP and Peter, J and Martin Storath}
}
@article {Kleesiek2019,
	title = {Can Virtual Contrast Enhancement in Brain MRI Replace Gadolinium?: A Feasibility Study},
	journal = {Investigative Radiology},
	volume = {54},
	year = {2019},
	pages = {653{\textendash}660},
	abstract = {Objectives Gadolinium-based contrast agents (GBCAs) have become an integral part in daily clinical decision making in the last 3 decades. However, there is a broad consensus that GBCAs should be exclusively used if no contrast-free magnetic resonance imaging (MRI) technique is available to reduce the amount of applied GBCAs in patients. In the current study, we investigate the possibility of predicting contrast enhancement from noncontrast multiparametric brain MRI scans using a deep-learning (DL) architecture. Materials and Methods A Bayesian DL architecture for the prediction of virtual contrast enhancement was developed using 10-channel multiparametric MRI data acquired before GBCA application. The model was quantitatively and qualitatively evaluated on 116 data sets from glioma patients and healthy subjects by comparing the virtual contrast enhancement maps to the ground truth contrast-enhanced T1-weighted imaging. Subjects were split in 3 different groups: Enhancing tumors (n = 47), nonenhancing tumors (n = 39), and patients without pathologic changes (n = 30). The tumor regions were segmented for a detailed analysis of subregions. The influence of the different MRI sequences was determined. Results Quantitative results of the virtual contrast enhancement yielded a sensitivity of 91.8\% and a specificity of 91.2\%. T2-weighted imaging, followed by diffusion-weighted imaging, was the most influential sequence for the prediction of virtual contrast enhancement. Analysis of the whole brain showed a mean area under the curve of 0.969 {\textpm} 0.019, a peak signal-to-noise ratio of 22.967 {\textpm} 1.162 dB, and a structural similarity index of 0.872 {\textpm} 0.031. Enhancing and nonenhancing tumor subregions performed worse (except for the peak signal-to-noise ratio of the nonenhancing tumors). The qualitative evaluation by 2 raters using a 4-point Likert scale showed good to excellent (3-4) results for 91.5\% of the enhancing and 92.3\% of the nonenhancing gliomas. However, despite the good scores and ratings, there were visual deviations between the virtual contrast maps and the ground truth, including a more blurry, less nodular-like ring enhancement, few low-contrast false-positive enhancements of nonenhancing gliomas, and a tendency to omit smaller vessels. These "features" were also exploited by 2 trained radiologists when performing a Turing test, allowing them to discriminate between real and virtual contrast-enhanced images in 80\% and 90\% of the cases, respectively. Conclusions The introduced model for virtual gadolinium enhancement demonstrates a very good quantitative and qualitative performance. Future systematic studies in larger patient collectives with varying neurological disorders need to evaluate if the introduced virtual contrast enhancement might reduce GBCA exposure in clinical practice.},
	keywords = {Bayesian uncertainty, deep learning, gadolinium-based contrast agents, glioma, multiparametric MRI},
	issn = {15360210},
	doi = {10.1097/RLI.0000000000000583},
	author = {Kleesiek, Jens and Morshuis, Jan Nikolas and Isensee, Fabian and Deike-Hofmann, Katerina and Paech, Daniel and Kickingereder, Philipp and K{\"o}the, Ullrich and Rother, Carsten and Forsting, Michael and Wick, Wolfgang and Bendszus, Martin and Schlemmer, Heinz Peter and Radbruch, Alexander}
}
@mastersthesis {papst2019,
	title = {Development of a method for quantitative imaging of air-water gas exchange},
	volume = {Bachelors thesis},
	year = {2019},
	school = {Institut f{\"u}r Umweltphysik, Universit{\"a}t Heidelberg, Germany},
	type = {mastersMaster{\textquoteright}s thesis},
	doi = {10.11588/heidok.00027271},
	author = {Maximilian Papst}
}
@article {Zeilmann:2019aa,
	title = {Geometric Numerical Integration of the Assignment Flow},
	journal = {Inverse Problems},
	year = {2019},
	url = {https://doi.org/10.1088/1361-6420/ab2772},
	author = {Zeilmann, A. and Savarino, F. and Petra, S. and Schn{\"o}rr, C.}
}
@conference {HosseiniJafari2019,
	title = {iPose: Instance-Aware 6D Pose Estimation of Partly Occluded Objects},
	booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {11363 LNCS},
	year = {2019},
	pages = {477{\textendash}492},
	abstract = {We address the task of 6D pose estimation of known rigid objects from single input images in scenarios where the objects are partly occluded. Recent RGB-D-based methods are robust to moderate degrees of occlusion. For RGB inputs, no previous method works well for partly occluded objects. Our main contribution is to present the first deep learning-based system that estimates accurate poses for partly occluded objects from RGB-D and RGB input. We achieve this with a new instance-aware pipeline that decomposes 6D object pose estimation into a sequence of simpler steps, where each step removes specific aspects of the problem. The first step localizes all known objects in the image using an instance segmentation network, and hence eliminates surrounding clutter and occluders. The second step densely maps pixels to 3D object surface positions, so called object coordinates, using an encoder-decoder network, and hence eliminates object appearance. The third, and final, step predicts the 6D pose using geometric optimization. We demonstrate that we significantly outperform the state-of-the-art for pose estimation of partly occluded objects for both RGB and RGB-D input.},
	isbn = {9783030208929},
	issn = {16113349},
	doi = {10.1007/978-3-030-20893-6_30},
	author = {Omid Hosseini Jafari and Mustikovela, Siva Karthik and Pertsch, Karl and Brachmann, Eric and Carsten Rother}
}
@article {Huhnerbein:2019ab,
	title = {Learning Adaptive Regularization for Image Labeling Using Geometric Assignment},
	journal = {preprint: arXiv},
	year = {2019},
	url = {https://arxiv.org/abs/1910.09976},
	author = {H{\"u}hnerbein, R. and Savarino, F. and Petra, S. and Schn{\"o}rr, C.}
}
@conference {Huhnerbein:2019aa,
	title = {Learning Adaptive Regularization for Image Labeling Using Geometric Assignment},
	booktitle = {Proc. SSVM},
	year = {2019},
	publisher = {Springer},
	organization = {Springer},
	author = {H{\"u}hnerbein, R. and Savarino, F. and Petra, S. and Schn{\"o}rr, C.}
}
@phdthesis {6991,
	title = {Machine learning under test-time budget constraints},
	year = {2019},
	publisher = {Heidelberg University},
	author = {Peter, S}
}
@article {6315,
	title = {A Meta-Transfer Objective for Learning to Disentangle Causal Mechanisms},
	journal = {arXiv preprint arXiv:1901.10912},
	year = {2019},
	author = {Bengio, Y and Deleu, T and Rahaman, N and Ke, R and Lachapelle, S and Bilaniuk, O and Goyal, A and Pal, C}
}
@article {Zisler:2019ab,
	title = {Self-Assignment Flows for Unsupervised Data Labeling on Graphs},
	journal = {preprint: arXiv},
	year = {2019},
	url = {https://arxiv.org/abs/1911.03472},
	author = {M. Zisler and Zern, A. and Petra, S. and Schn{\"o}rr, C.}
}
@article {Censor:2019aa,
	title = {Superiorization vs. Accelerated Convex Optimization: The Superiorized/Regularized Least Squares Case},
	journal = {preprint: arXiv},
	year = {2019},
	url = {https://arxiv.org/abs/1911.05498},
	author = {Censor, Y. and Petra, S. and Schn{\"o}rr, C.}
}
@article {Zern:2019aa,
	title = {Unsupervised Assignment Flow: Label Learning on Feature Manifolds by Spatially Regularized Geometric Assignment},
	journal = {preprint: arXiv},
	year = {2019},
	url = {https://arxiv.org/abs/1904.10863},
	author = {Zern, A. and M. Zisler and Petra, S. and Schn{\"o}rr, C.}
}
@conference {Zisler:2019aa,
	title = {Unsupervised Labeling by Geometric and Spatially Regularized Self-Assignment},
	booktitle = {Proc. SSVM},
	year = {2019},
	publisher = {Springer},
	organization = {Springer},
	author = {M. Zisler and Zern, A. and Petra, S. and Schn{\"o}rr, C.}
}
@mastersthesis {6341,
	title = {Weakly Supervised Semantic Segmentation},
	year = {2019},
	school = {Heidelberg University},
	author = {Pandey, N}
}
@article {Zeilmann:2018aa,
	title = {Geometric Numerical Integration of the Assignment Flow},
	journal = {preprint: arXiv},
	year = {2018},
	url = {https://arxiv.org/abs/1810.06970},
	author = {Zeilmann, A. and Savarino, F. and Petra, S. and Schn{\"o}rr, C.}
}
@proceedings {6310,
	title = {iPose: Instance-Aware 6D Pose Estimation of Partly Occluded Objects},
	year = {2018},
	author = {Omid Hosseini Jafari and Mustikovela, S K and Pertsch, K and E Brachmann and Carsten Rother}
}
@proceedings {6275,
	title = {The Mutex Watershed: Efficient, Parameter-Free Image   Partitioning},
	year = {2018},
	pages = {571-587},
	publisher = {Springer},
	doi = {10.1007/978-3-030-01225-0_34},
	author = {Wolf, S and Pape, C and Bailoni, A and Rahaman, N and Kreshuk, A. and Ullrich K{\"o}the and Fred A. Hamprecht}
}
@conference {Wolf2018,
	title = {The Mutex Watershed: Efficient, Parameter-Free Image Partitioning},
	booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {11208 LNCS},
	year = {2018},
	month = {apr},
	pages = {571{\textendash}587},
	abstract = {Image partitioning, or segmentation without semantics, is the task of decomposing an image into distinct segments; or equivalently, the task of detecting closed contours in an image. Most prior work either requires seeds, one per segment; or a threshold; or formulates the task as an NP-hard signed graph partitioning problem. Here, we propose an algorithm with empirically linearithmic complexity. Unlike seeded watershed, the algorithm can accommodate not only attractive but also repulsive cues, allowing it to find a previously unspecified number of segments without the need for explicit seeds or a tunable threshold. The algorithm itself, which we dub {\textquotedblleft}Mutex Watershed{\textquotedblright}, is closely related to a minimal spanning tree computation. It is deterministic and easy to implement. When presented with short-range attractive and long-range repulsive cues from a deep neural network, the Mutex Watershed gives results that currently define the state-of-the-art in the competitive ISBI 2012 EM segmentation benchmark. These results are also better than those obtained from other recently proposed clustering strategies operating on the very same network outputs.},
	isbn = {9783030012243},
	issn = {16113349},
	doi = {10.1007/978-3-030-01225-0_34},
	url = {http://arxiv.org/abs/1904.12654},
	author = {Wolf, Steffen and Pape, Constantin and Bailoni, Alberto and Rahaman, Nasim and Kreshuk, Anna and Ullrich K{\"o}the and Fred A. Hamprecht}
}
@proceedings {6311,
	title = {Unsupervised Label Learning on Manifolds by Spatially Regularized Geometric Assignment},
	year = {2018},
	pages = {698-713},
	doi = {10.1007/978-3-030-12939-2_48},
	author = {Zern, A and M. Zisler and Freddie Astr{\"o}m and Petra, S and Schn{\"o}rr, C}
}
@conference {Zern:2018ac,
	title = {Unsupervised Label Learning on Manifolds by Spatially Regularized Geometric Assignment},
	booktitle = {GCPR},
	year = {2018},
	author = {Zern, A. and M. Zisler and Astr{\"o}m, F. and Petra, S. and Schn{\"o}rr, C.}
}
@conference {Dalitz2017,
	title = {Compressed Motion Sensing},
	booktitle = {Proc. SSVM},
	series = {LNCS},
	volume = {10302},
	year = {2017},
	publisher = {Springer},
	organization = {Springer},
	author = {Dalitz, R. and Petra, S. and Schn{\"o}rr, C.}
}
@proceedings {6204,
	title = {Cost-efficient Gradient Boosting},
	year = {2017},
	author = {Peter, S. and Ferran Diego and Fred A. Hamprecht and Nadler, B}
}
@conference {Ramos2017,
	title = {Detecting unexpected obstacles for self-driving cars: Fusing deep learning and geometric modeling},
	booktitle = {IEEE Intelligent Vehicles Symposium, Proceedings},
	year = {2017},
	month = {dec},
	pages = {1025{\textendash}1032},
	abstract = {The detection of small road hazards, such as lost cargo, is a vital capability for self-driving cars. We tackle this challenging and rarely addressed problem with a vision system that leverages appearance, contextual as well as geometric cues. To utilize the appearance and contextual cues, we propose a new deep learning-based obstacle detection framework. Here a variant of a fully convolutional network is proposed to predict a pixel-wise semantic labeling of (i) free-space, (ii) on-road unexpected obstacles, and (iii) background. The geometric cues are exploited using a state-of-The-Art detection approach that predicts obstacles from stereo input images via model-based statistical hypothesis tests. We present a principled Bayesian framework to fuse the semantic and stereo-based detection results. The mid-level Stixel representation is used to describe obstacles in a flexible, compact and robust manner. We evaluate our new obstacle detection system on the Lost and Found dataset, which includes very challenging scenes with obstacles of only 5 cm height. Overall, we report a major improvement over the state-of-The-Art, with a performance gain of 27.4\%. In particular, we achieve a detection rate of over 90\% for distances of up to 50 m. Our system operates at 22 Hz on our self-driving platform.},
	isbn = {9781509048045},
	doi = {10.1109/IVS.2017.7995849},
	url = {http://arxiv.org/abs/1612.06573},
	author = {Ramos, Sebastian and Gehrig, Stefan and Pinggera, Peter and Franke, Uwe and Carsten Rother}
}
@conference {Zisler2017a,
	title = {Gradient Flows on a Riemannian Submanifold for Discrete Tomography},
	booktitle = {Proc. GCPR},
	year = {2017},
	author = {M. Zisler and Savarino, F. and Petra, S. and Schn{\"o}rr, C.}
}
@article {Astroem2017,
	title = {Image Labeling by Assignment},
	journal = {J. Math. Imag. Vision},
	volume = {58},
	number = {2},
	year = {2017},
	pages = {211{\textendash}238},
	url = {Papers/Astroem2017.pdf},
	author = {Astr{\"o}m, F. and Petra, S. and Schmitzer, B. and Schn{\"o}rr, C.}
}
@conference {Zisler2017,
	title = {Image Reconstruction by Multilabel Propagation},
	booktitle = {Proc. SSVM},
	series = {LNCS},
	volume = {10302},
	year = {2017},
	publisher = {Springer},
	organization = {Springer},
	author = {M. Zisler and Astr{\"o}m, F. and Petra, S. and Schn{\"o}rr, C.}
}
@conference {Bodnariuc2017a,
	title = {A Local Spatio-Temporal Approach to Plane Wave Ultrasound Particle Image Velocimetry},
	booktitle = {Proc. GCPR},
	year = {2017},
	author = {Ecaterina Bodnariuc and Petra, S. and Schn{\"o}rr, C. and Voorneveld, J.}
}
@article {6122,
	title = {Multicut brings automated neurite segmentation closer to human performance},
	journal = {Nature Methods},
	volume = {14},
	year = {2017},
	pages = {101-102},
	doi = {10.1038/nmeth.4151},
	url = {http://rdcu.be/oVDQ},
	author = {Thorsten Beier and Pape, C and Rahaman, N and Prange, T and Stuart Berg and Bock, D and A. Cardona and G. W. Knott and Plaza, S M and Scheffer, L K and Ullrich K{\"o}the and Kreshuk, A and Fred A. Hamprecht}
}
@article {6213,
	title = {Solving Large Multicut Problems for Connectomics via Domain Decomposition},
	year = {2017},
	pages = {1-10},
	doi = { 10.1109/ICCVW.2017.7},
	author = {Pape, C and Thorsten Beier and Li, P and Jain, V and Brock, D. D. and Kreshuk, A.}
}
@proceedings {6205,
	title = {Sparse convolutional coding for neuronal assembly detection},
	year = {2017},
	author = {Peter, S. and Kirschbaum, E. and M. Both and Campbell, L. A. and Harvey, B. K. and Heins, C. and Durstewitz, D. and Ferran Diego and Fred A. Hamprecht}
}
@mastersthesis {pross2016,
	title = {Analysis of the Fetch Dependency of the Slope of Wind-Water Waves},
	year = {2016},
	school = {Institut f{\"u}r Umweltphysik, Universit{\"a}t Heidelberg, Germany},
	type = {mastersBachelor{\textquoteright}s thesis},
	abstract = {In this thesis mean square slope has been calculated from slope images which were recorded by the Imaging Slope Gauge (ISG) at the annular wind-wave tank Aeolotron in Heidelberg. The calculations have been realized using three different methods, which are, (i) calculation of the variance, (ii) integration of the slope power spectrum and (iii) fitting the probability distribution function of slope with a model function. The resulting values have been compared to each other and to the existing live evaluation of the ISG for a wide range of wind and fetch conditions. Also the fetch dependence of mean square slope has been analyzed, which obtains information about the evolution of a wave field. Additionally the slope images have been separated with the use of band pass filters into slope images of gravity waves and capillary waves. By separating gravity from capillary waves it was possible to analyze their slope probability distribution functions individually.},
	doi = {10.11588/heidok.00021613},
	author = {Pro{\ss}, Christin}
}
@conference {Astroem2016a,
	title = {The Assignment Manifold: A Smooth Model for Image Labeling},
	booktitle = {Proc. 2nd Int. Workshop on Differential Geometry in Computer Vision and Machine Learning (DIFF-CVML{\textquoteright}16; oral presentation; Grenander best paper award)},
	year = {2016},
	author = {Astr{\"o}m, F. and Petra, S. and Schmitzer, B. and Schn{\"o}rr, C.}
}
@mastersthesis {6075,
	title = {Automatic Segmentation of Neurites from Anisotropic EM-Imaging},
	year = {2016},
	school = {University of Heidelberg},
	author = {Pape, C}
}
@mastersthesis {6029,
	title = {Automatic Segmentation of Neurons in Electron Microscopy Data with Membrane Defects},
	year = {2016},
	school = {University of Heidelberg},
	author = {Prange, T.}
}
@conference {Zisler2016a,
	title = {Discrete Tomography by Continuous Multilabeling Subject to Projection Constraints},
	booktitle = {Proc. GCPR},
	year = {2016},
	author = {M. Zisler and Petra, S. and Schn{\"o}rr, Cl. and Christoph Schn{\"o}rr}
}
@conference {Astroem2016d,
	title = {A Geometric Approach to Image Labeling},
	booktitle = {Proc. ECCV},
	year = {2016},
	author = {Astr{\"o}m, F. and Petra, S. and Schmitzer, B. and Schn{\"o}rr, C.}
}
@booklet {Astroem2016,
	title = {Image Labeling by Assignment},
	year = {2016},
	note = {ArXiv, preprint},
	month = {March},
	url = {http://arxiv.org/abs/1603.05285},
	author = {Astr{\"o}m, F. and Petra, S. and Schmitzer, B. and Schn{\"o}rr, C.}
}
@article {6119,
	title = {Imagining the future of bioimage analysis},
	journal = {Nature Biotechnology},
	volume = {34},
	year = {2016},
	pages = {1250-1255},
	doi = {10.1038/nbt.3722},
	author = {Meijering, E and Carpenter, A E and Peng, Hanchuan and Fred A. Hamprecht and Olivo-Marin, J}
}
@conference {Pinggera2016,
	title = {Lost and found: Detecting small road hazards for self-driving vehicles},
	booktitle = {IEEE International Conference on Intelligent Robots and Systems},
	volume = {2016-Novem},
	year = {2016},
	pages = {1099{\textendash}1106},
	abstract = {Detecting small obstacles on the road ahead is a critical part of the driving task which has to be mastered by fully autonomous cars. In this paper, we present a method based on stereo vision to reliably detect such obstacles from a moving vehicle. The proposed algorithm performs statistical hypothesis tests in disparity space directly on stereo image data, assessing freespace and obstacle hypotheses on independent local patches. This detection approach does not depend on a global road model and handles both static and moving obstacles. For evaluation, we employ a novel lost-cargo image sequence dataset comprising more than two thousand frames with pixelwise annotations of obstacle and free-space and provide a thorough comparison to several stereo-based baseline methods. The dataset will be made available to the community to foster further research on this important topic4. The proposed approach outperforms all considered baselines in our evaluations on both pixel and object level and runs at frame rates of up to 20 Hz on 2 mega-pixel stereo imagery. Small obstacles down to the height of 5 cm can successfully be detected at 20 m distance at low false positive rates.},
	isbn = {9781509037629},
	issn = {21530866},
	doi = {10.1109/IROS.2016.7759186},
	url = {http://www.6d-vision.com/lostandfounddataset},
	author = {Pinggera, Peter and Ramos, Sebastian and Gehrig, Stefan and Franke, Uwe and Carsten Rother and Mester, Rudolf}
}
@article {Zisler2016,
	title = {Non-Binary Discrete Tomography by Continuous Non-Convex Optimization},
	journal = {IEEE Comp. Imaging},
	volume = {2},
	number = {3},
	year = {2016},
	pages = {335-347},
	author = {M. Zisler and Kappes, J.H. and Schn{\"o}rr, Cl. and Petra, S. and Christoph Schn{\"o}rr}
}
@conference {Bodnariuc2016,
	title = {Parametric Dictionary-Based Velocimetry for Echo PIV},
	booktitle = {Proc. CGPR},
	year = {2016},
	author = {Ecaterina Bodnariuc and Petra, S. and Poelma, C. and Schn{\"o}rr, C.}
}
@proceedings {6110,
	title = {Plane Wave Acoustic Superposition for Fast Ultrasound Imaging},
	year = {2016},
	author = {Ecaterina Bodnariuc and Martin F. Schiffner and Stefania Petra and Christoph Schn{\"o}rr}
}
@article {6033,
	title = {Virtual Raters for Reproducible and Objective Assessments in Radiology},
	journal = {Nature Scientific Reports},
	volume = {6},
	year = {2016},
	doi = {10.1038/srep25007},
	author = {Kleesiek, J. and Petersen, J. and D{\"o}ring, M. and Maier-Hein, K. and Ullrich K{\"o}the and Wick, W. and Fred A. Hamprecht and M. Bendszus and A. Biller}
}
@conference {Bodnariuc2015,
	title = {Adaptive Dictionary-Based Spatio-temporal Flow Estimation for Echo PIV},
	booktitle = {Proc.~EMMCVPR},
	volume = {8932},
	year = {2015},
	pages = {378--391},
	publisher = {Springer},
	organization = {Springer},
	author = {Ecaterina Bodnariuc and Gurung, A. and Stefania Petra and Christoph Schn{\"o}rr}
}
@conference {5977,
	title = {Adaptive Dictionary-Based Spatio-temporal Flow Estimation for Echo PIV},
	booktitle = {EMMCVPR},
	year = {2015},
	author = {Ecaterina Bodnariuc and Gurung, A. and Stefania Petra and Christoph Schn{\"o}rr}
}
@article {Krah2015a,
	title = {An advanced image processing method to improve the spatial resolution of ion radiographies},
	journal = {Physics in Medicine and Biology},
	volume = {60},
	year = {2015},
	pages = {8525},
	abstract = {We present an optimization method to improve the spatial resolution and the water equivalent thickness (WET) accuracy of ion radiographies. The method is designed for imaging systems measuring for each actively scanned beam spot the lateral position of the pencil beam and at the same time the Bragg curve (behind the target) in discrete steps without relying on tracker detectors to determine the ion trajectory before and after the irradiated volume. Specifically, the method was used for an imaging set-up consisting of a stack of 61 parallel-plate ionization chambers (PPIC) interleaved with absorber plates of polymethyl methacrylate (PMMA) working as a range telescope. The method uses not only the Bragg peak position, but approximates the entire measured Bragg curve as a superposition of differently shifted Bragg curves. Their relative weights allow to reconstruct the distribution of thickness around each scan spot of a heterogeneous phantom. The approach also allows merging the ion radiography with the geometric information of a co-registered x-ray radiography in order to increase its spatial resolution. The method was tested using Monte Carlo simulated and experimental proton radiographies of a PMMA step phantom and an anthropomorphic head phantom. For the step phantom, the effective spatial resolution was found to be 6 and 4 times higher than the nominal resolution for the simulated and experimental radiographies, respectively. For the head phantom, a gamma index was calculated to quantify the conformity of the simulated proton radiographies with a digitally reconstructed radiography (DRR) obtained from an x-ray CT and properly converted into WET. For a distance-to-agreement (DTA) of 2.5 mm and a relative WET difference (RWET) of 2.5\%, the passing ratio was 100\%/85\% for the optimized/non-optimized case, respectively. When the optimized proton radiography was merged with the co-registered DRR, the passing ratio was 100\% at DTA  =  1.3 mm and RWET  =  1.3\%. A special interpolation method allows to strongly reduce the dose by using a coarser grid of the measured beam spot position with a 5 times larger grid distance. We show that despite a dose reduction of 25 times (leading to a dose of 0.016 mGy for the current imaging set-up), the image quality of the optimized radiographies remains fairly unaffected for both the simulated and experimental case.},
	url = {http://stacks.iop.org/0031-9155/60/i=21/a=8525},
	author = {Nils Krah and M Testa and S Brons and O J{\"a}kel and K Parodi and Bj{\"o}rn Voss and I Rinaldi}
}
@article {kreshuk_15_automated,
	title = {Automated Tracing of Myelinated Axons and Detection of the Nodes of Ranvier in Serial Images of Peripheral Nerves},
	journal = {Journal of Microscopy},
	volume = {259 (2)},
	year = {2015},
	pages = {143-154},
	doi = {10.1111/jmi.12266},
	author = {Anna Kreshuk and Walecki, R. and Ullrich K{\"o}the and Gierthm{\"u}hlen, M. and Plachta, D. and Genoud, C. and Haastert-Talini, K. and Fred A. Hamprecht}
}
@conference {Zheng2015,
	title = {Object proposals estimation in depth image using compact 3D shape manifolds},
	booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {9358},
	year = {2015},
	pages = {196{\textendash}208},
	abstract = {Man-made objects, such as chairs, often have very large shape variations, making it challenging to detect them. In this work we investigate the task of finding particular object shapes from a single depth image. We tackle this task by exploiting the inherently low dimensionality in the object shape variations, which we discover and encode as a compact shape space. Starting from any collection of 3D models, we first train a low dimensional Gaussian Process Latent Variable Shape Space. We then sample this space, effectively producing infinite amounts of shape variations, which are used for training. Additionally, to support fast and accurate inference, we improve the standard 3D object category proposal generation pipeline by applying a shallow convolutional neural network-based filtering stage. This combination leads to considerable improvements for proposal generation, in both speed and accuracy. We compare our full system to previous state-of-the-art approaches, on four different shape classes, and show a clear improvement.},
	isbn = {9783319249469},
	issn = {16113349},
	doi = {10.1007/978-3-319-24947-6_16},
	author = {Zheng, Shuai and Prisacariu, Victor Adrian and Averkiou, Melinos and Cheng, Ming Ming and Mitra, Niloy J and Shotton, Jamie and Torr, Philip H.S. and Carsten Rother}
}
@article {Mitra2015,
	title = {Pacific Graphics 2015 DenseCut: Densely Connected CRFs for Realtime GrabCut},
	volume = {34},
	number = {7},
	year = {2015},
	abstract = {Figure-ground segmentation from bounding box input, provided either automatically or manually, has been ex-tremely popular in the last decade and influenced various applications. A lot of research has focused on high-quality segmentation, using complex formulations which often lead to slow techniques, and often hamper practi-cal usage. In this paper we demonstrate a very fast segmentation technique which still achieves very high quality results. We propose to replace the time consuming iterative refinement of global colour models in traditional GrabCut formulation by a densely connected CRF. To motivate this decision, we show that a dense CRF implicitly models unnormalized global colour models for foreground and background. Such relationship provides insightful analysis to bridge between dense CRF and GrabCut functional. We extensively evaluate our algorithm using two famous benchmarks. Our experimental results demonstrated that the proposed algorithm achieves an order of magnitude (10{\texttimes}) speed-up with respect to the closest competitor, and at the same time achieves a considerably higher accuracy.},
	keywords = {I46 [IMAGE PROCESSING AND COMPUTER VISION], partitioning, Segmentation{\textemdash}Region growing},
	url = {http://mftp.mmcheng.net/Papers/DenseCut.pdf},
	author = {Mitra, N J and Stam, J and Xu, K and Cheng, Ming-Ming and Prisacariu, Victor Adrian and Zheng, Shuai and Torr, Philip H S and Carsten Rother}
}
@mastersthesis {peter_15_spatio-temporal,
	title = {Spatio-Temporal Motif Deconvolution for Calcium Image Analysis},
	year = {2015},
	school = {University of Heidelberg},
	type = {Master Thesis},
	author = {Peter, S.}
}
@conference {Kappes2015b,
	title = {TomoGC: Binary Tomography by Constrained Graph Cuts},
	booktitle = {Proc.~GCPR},
	year = {2015},
	author = {J{\"o}rg H. Kappes and Stefania Petra and Christoph Schn{\"o}rr and M. Zisler}
}
@conference {Kappes2015b,
	title = {TomoGC: Binary Tomography by Constrained Graph Cuts},
	booktitle = {Proc. GCPR},
	year = {2015},
	author = {Kappes, J.H. and Petra, S. and Schn{\"o}rr, C. and M. Zisler}
}
@article {kauppi_15_towards,
	title = {Towards brain-activity-controlled information retrieval: Decoding image relevance from MEG signals},
	journal = {NeuroImage},
	volume = {112},
	year = {2015},
	note = {1},
	pages = {288-298},
	doi = {10.1016/j.neuroimage.2014.12.079},
	author = {Kauppi, J .P. and Kandemir, M. and Saarinen, V .M. and Hirvenkari, L. and Parkkonen, L. and Klami, A. and Hari, R. and Kaski, S.}
}
@article {kreshuk_14_automated,
	title = {Automated Detection of Synapses in Serial Section Transmission Electron Microscopy Image Stacks},
	journal = {PLoS ONE},
	volume = {9},
	year = {2014},
	note = {1},
	pages = {2},
	doi = {10.1371/journal.pone.0087351},
	author = {Anna Kreshuk and Ullrich K{\"o}the and Pax, E. and Bock, D. D. and Fred A. Hamprecht}
}
@article {Petra2014,
	title = {Average Case Recovery Analysis of Tomographic Compressive Sensing},
	journal = {Linear Algebra and its Applications},
	volume = {441},
	year = {2014},
	note = {Special issue on Sparse Approximate Solution of Linear Systems},
	pages = {168-198},
	author = {Stefania Petra and Christoph Schn{\"o}rr}
}
@conference {maierhein2014a,
	title = {Crowdsourcing for reference correspondence generation in endoscopic images},
	booktitle = {MICCAI},
	year = {2014},
	author = {Lena Maier-Hein and Sven Mersmann and Daniel Kondermann and C. Stock and Kenngott, H. and Sanchez, A. and Wagner, M. and Preukschas, A. and Wekerle, A. -L. and Helfert, S. and Bodenstedt, S. and Speidel, S.}
}
@article {Eyjolfsdottir2014,
	title = {Detection of social actions in fruit flies},
	journal = {Lecture Notes in Computer Science},
	volume = {8690},
	number = {September 2014},
	year = {2014},
	pages = {772{\textendash}787},
	publisher = {Springer International Publishing},
	address = {Cham},
	abstract = {Spatio-temporal detection of actions and events in video is a challenging problem. Besides the difficulties related to recognition, a major challenge for detection in video is the size of the search space defined by spatio-temporal tubes formed by sequences of bounding boxes along the frames. Recently methods that generate unsupervised detection proposals have proven to be very effective for object detection in still images. These methods open the possibility to use strong but computationally expensive features since only a relatively small number of detection hypotheses need to be assessed. In this paper we make two contributions towards exploiting detection proposals for spatio-temporal detection problems. First, we extend a recent 2D object proposal method, to produce spatio-temporal proposals by a randomized supervoxel merging process. We introduce spatial, temporal, and spatio-temporal pairwise supervoxel features that are used to guide the merging process. Second, we propose a new efficient supervoxel method. We experimentally evaluate our detection proposals, in combination with our new supervoxel method as well as existing ones. This evaluation shows that our supervoxels lead to more accurate proposals when compared to using existing state-of-the-art supervoxel methods.},
	isbn = {978-3-319-10604-5},
	issn = {16113349},
	doi = {10.1007/978-3-319-10605-2},
	url = {http://link.springer.com/10.1007/978-3-319-10605-2 http://www.ncbi.nlm.nih.gov/pubmed/31629782},
	author = {Eyjolfsdottir, Eyrun and Branson, Steve and Burgos-Artizzu, Xavier P. and Hoopfer, Eric D. and Schor, Jonathan and Anderson, David J. and Perona, Pietro},
	editor = {Fleet, David and Pajdla, Tomas and Schiele, Bernt and Tuytelaars, Tinne}
}
@conference {Denitiu2014,
	title = {An Entropic Perturbation Approach to TV-Minimization for Limited-Data Tomography},
	booktitle = {Discrete Geometry for Computer Imagery (DGCI) 2014},
	year = {2014},
	pages = {262--274},
	publisher = {Springer},
	organization = {Springer},
	author = {Andreea Denitiu and Stefania Petra and Schn{\"o}rr, Claudius and Christoph Schn{\"o}rr},
	editor = {Elena Barcucci and Frosini, Andrea and Eds Rinaldi, Simone}
}
@conference {Denitiu2014,
	title = {An Entropic Perturbation Approach to TV-Minimization for Limited-Data Tomography},
	booktitle = {Discrete Geometry for Computer Imagery (DGCI) 2014},
	series = {LNCS},
	year = {2014},
	pages = {262{\textendash}274},
	publisher = {Springer},
	organization = {Springer},
	author = {Andreea Denitiu and Petra, Stefania and Schn{\"o}rr, Claudius and Christoph Schn{\"o}rr},
	editor = {Elena Barcucci and Frosini,Andrea and Eds Rinaldi,Simone}
}
@incollection {Becker2014,
	title = {Optical Flow},
	year = {2014},
	note = {in press},
	publisher = {Springer},
	edition = {2nd},
	author = {Florian Becker and Petra, Stefania and Christoph Schn{\"o}rr},
	editor = {Scherzer, O.}
}
@article {Jug2014,
	title = {Optimal joint segmentation and tracking of escherichia coli in the mother machine},
	journal = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {8677},
	year = {2014},
	pages = {25{\textendash}36},
	abstract = {We introduce a graphical model for the joint segmentation and tracking of E. coli cells from time lapse videos. In our setup cells are grown in narrow columns (growth channels) in a so-called {\textquotedblleft}Mother Machine{\textquotedblright} [1]. In these growth channels, cells are vertically aligned, grow and divide over time, and eventually leave the channel at the top. The model is built on a large set of cell segmentation hypotheses for each video frame that we extract from data using a novel parametric max-flow variation. Possible tracking assignments between segments across time, including cell identity mapping, cell division, and cell exit events are enumerated. Each such assignment is represented as a binary decision variable with unary costs based on image and object features of the involved segments. We find a cost-minimal and consistent solution by solving an integer linear program. We introduce a new and important type of constraint that ensures that cells exit the Mother Machine in the correct order. Our method finds a globally optimal tracking solution with an accuracy of > 95\% (1.22 times the inter-observer error) and is on average 2 - 11 times faster than the microscope produces the raw data.},
	issn = {16113349},
	doi = {10.1007/978-3-319-12289-2_3},
	author = {Jug, Florian and Pietzsch, Tobias and Kainm{\"u}ller, Dagmar and Funke, Jan and Kaiser, Matthias and van Nimwegen, Erik and Carsten Rother and Myers, Gene}
}
@article {Denitiu2014a,
	title = {Phase Transitions and Cosparse Tomographic Recovery of Compound Solid Bodies from Few Projections},
	journal = {Fundamenta Informaticae},
	volume = {135},
	year = {2014},
	pages = {73--102},
	author = {Andreea Denitiu and Stefania Petra and Schn{\"o}rr, Cl. and Christoph Schn{\"o}rr}
}
@article {Denitiu2014a,
	title = {Phase Transitions and Cosparse Tomographic Recovery of Compound Solid Bodies from Few Projections},
	journal = {Fundamenta Informaticae},
	volume = {135},
	year = {2014},
	pages = {73{\textendash}102},
	author = {Andreea Denitiu and Petra, S. and Schn{\"o}rr, Cl. and Christoph Schn{\"o}rr}
}
@article {mikut_13_automated,
	title = {Automated Processing of Zebrafish Imaging Data: A Survey},
	journal = {Zebrafish},
	volume = {10 (3)},
	year = {2013},
	doi = {10.1089/zeb.2013.0886},
	author = {Mikut, R. and Dickmeis, T. and Driever, W. and Geurts, P. and Fred A. Hamprecht and Bernhard X. Kausler and Ledesma-Carbayo, M. and Marée, R. and Mikula, K. and Pantazis, P. and Ronneberger, O. and Santos, A. and Stotzka, R.}
}
@conference {petra_13_bsmart,
	title = {B-SMART: Bregman-Based First-Order Algorithms for Non-Negative
Compressed Sensing Problems},
	booktitle = {Proceedings of the 4th International Conference on Scale Space and
Variational Methods in Computer Vision SSVM},
	year = {2013},
	note = {1},
	pages = {110-124},
	doi = {10.1007/978-3-642-38267-3_10},
	author = {Stefania Petra and Christoph Schn{\"o}rr and Florian Becker and Frank Lenzen}
}
@conference {Petra-2013-bsmart,
	title = {B-SMART: Bregman-Based First-Order Algorithms for Non-Negative Compressed Sensing Problems},
	booktitle = {Proceedings of the 4th International Conference on Scale Space and Variational Methods in Computer Vision (SSVM) 2013},
	volume = {7893},
	year = {2013},
	pages = {110-124},
	publisher = {Springer},
	organization = {Springer},
	author = {Stefania Petra and Christoph Schn{\"o}rr and Florian Becker and Frank Lenzen}
}
@article {lenzen_13_class,
	title = {A Class of Quasi-Variational Inequalities for Adaptive Image Denoising
and Decomposition},
	journal = {Computational Optimization and Applications (COAP)},
	volume = {54 (2)},
	year = {2013},
	note = {1},
	pages = {371-398},
	doi = {10.1007/s10589-012-9456-0},
	author = {Frank Lenzen and Florian Becker and Lellmann, J. and Stefania Petra and Christoph Schn{\"o}rr}
}
@article {Lenzen-et-al-13,
	title = {A class of quasi-variational inequalities for adaptive image denoising and decomposition},
	journal = {Computational Optimization and Applications},
	volume = {54},
	number = {2},
	year = {2013},
	pages = {371-398},
	publisher = {Springer Netherlands},
	issn = {0926-6003},
	url = {http://dx.doi.org/10.1007/s10589-012-9456-0},
	author = {Frank Lenzen and Florian Becker and Lellmann, Jan and Stefania Petra and Christoph Schn{\"o}rr}
}
@article {Petra2013,
	title = {Critical Parameter Values and Reconstruction Propertiesof Discrete Tomography: Application to Experimental FluidDynamics},
	journal = {Fundamenta Informaticae},
	volume = {125},
	year = {2013},
	pages = {285--312},
	author = {Stefania Petra and Christoph Schn{\"o}rr and Schr{\"o}der, A.}
}
@conference {straehle_13_ksmallest,
	title = {K-smallest Spanning Tree Segmentations},
	booktitle = {German Conference on Pattern Recognition (DAGM/GCPR). Proceedings},
	number = {8142},
	year = {2013},
	note = {1},
	pages = {375-384},
	publisher = {Springer},
	organization = {Springer},
	doi = {10.1007/978-3-642-40602-7_40},
	author = {Christoph N. Straehle and Peter, S. and Ullrich K{\"o}the and Fred A. Hamprecht}
}
@booklet {Petra-Schnoerr-12b,
	title = {Critical Parameter Values and Reconstruction Properties of Discrete Tomography: Application to Experimental Fluid Dynamics},
	year = {2012},
	month = {September 19},
	url = {http://arxiv.org/abs/1209.4316},
	author = {Petra, S. and Schn{\"o}rr, C. and Schr{\"o}der, A.}
}
@conference {kondermann_12_on,
	title = {On Performance Analysis of Optical Flow Algorithms},
	booktitle = {Outdoor and Large-Scale Real-Worls Scene Analysis, Dagstuhl-Workshop
2011},
	volume = {LNCS},
	number = {7474},
	year = {2012},
	pages = {329-355},
	publisher = {Springer},
	organization = {Springer},
	doi = {10.1007/978-3-642-34091-8_15},
	author = {Daniel Kondermann and Steffen Abraham and W. F{\"o}rstner and Gehrig, S. and Imiya, A. and Bernd J{\"a}hne and Klose, F. and Magor, M. and Helmut Mayer and Mester, R. and Pajdla, T. and Reulke, R. and Zimmer, H.}
}
@article {Becker-et-al-11b,
	title = {Variational Adaptive Correlation Method for Flow Estimation},
	journal = {IEEE Transactions on Image Processing},
	volume = {21},
	number = {6},
	year = {2012},
	pages = {3053 -- 3065},
	doi = {10.1109/TIP.2011.2181524},
	author = {Florian Becker and Wieneke, Bernhard and Stefania Petra and Schr{\"o}der, Andreas and Christoph Schn{\"o}rr}
}
@article {Becker-et-al-11b,
	title = {Variational Adaptive Correlation Method for Flow Estimation},
	journal = {IEEE Transactions on Image Processing},
	volume = {21},
	number = {6},
	year = {2012},
	month = {June},
	pages = {3053 {\textendash} 3065},
	doi = {10.1109/TIP.2011.2181524},
	author = {Florian Becker and Wieneke, Bernhard and Petra, Stefania and Schr{\"o}der, Andreas and Christoph Schn{\"o}rr}
}
@conference {Lenzen-et-al-11,
	title = {Variational Image Denoising with Adaptive Constraint Sets},
	booktitle = {LNCS},
	year = {2012},
	pages = {206-217},
	publisher = {Springer},
	organization = {Springer},
	author = {Frank Lenzen and Florian Becker and Lellmann, Jan and Stefania Petra and Christoph Schn{\"o}rr}
}
@conference {Lenzen-et-al-11,
	title = {Variational Image Denoising with Adaptive Constraint Sets},
	booktitle = {Proceedings of the 3rd International Conference on Scale Space and Variational Methods in Computer Vision 2011},
	year = {2012},
	pages = {206-217},
	publisher = {Springer},
	organization = {Springer},
	author = {Lenzen, Frank and Florian Becker and Lellmann, Jan and Petra, Stefania and Christoph Schn{\"o}rr}
}
@conference {wanner_11_framework,
	title = {A Framework for Interactive Visualization and Classification of Dynamical Processes at the Water Surface},
	booktitle = {16th International Workshop on Vision, Modelling and Visualization},
	year = {2011},
	note = {1},
	pages = {199-206},
	publisher = {Eurographics Association, Germany},
	organization = {Eurographics Association, Germany},
	doi = {10.2312/PE/VMV/VMV11/199-206},
	author = {Sven Wanner and Christoph Sommer and Roland Rocholz and Fred A. Hamprecht and Bernd J{\"a}hne},
	editor = {Eisert, P. and Joachim Hornegger and Konrad Polthier}
}
@conference {wanner2011,
	title = {A framework for interactive visualization and classification of dynamical processes at the water surface},
	booktitle = {16th International Workshop on Vision, Modelling and Visualization},
	year = {2011},
	pages = {199--206},
	publisher = {Eurographics Association, Germany},
	organization = {Eurographics Association, Germany},
	doi = {10.2312/PE/VMV/VMV11/199-206},
	author = {Sven Wanner and Christoph Sommer and Roland Rocholz and Jung, M. and Fred A. Hamprecht and Bernd J{\"a}hne},
	editor = {Peter Eisert and Joachim Hornegger and Konrad Polthier}
}
@article {Nicola-et-al-2011,
	title = {A general extending and constraining procedure for linear iterative methods},
	journal = {Int.~J.~Comp.~Math.},
	year = {2011},
	note = {in press},
	url = {http://dx.doi.org/10.1080/00207160.2011.634002},
	author = {Nicola, A. and Stefania Petra and Popa, C. and Christoph Schn{\"o}rr}
}
@article {Nicola-et-al-2011,
	title = {A general extending and constraining procedure for linear iterative methods},
	journal = {Int. J. Comp. Math.},
	year = {2011},
	note = {in press},
	url = {http://dx.doi.org/10.1080/00207160.2011.634002},
	author = {Nicola, A. and Petra, S. and Popa, C. and Schn{\"o}rr, C.}
}
@conference {Rathke11,
	title = {Order Preserving and Shape Prior Constrained Intra-Retinal Layer Segmentation in Optical Coherence Tomography},
	booktitle = {MICCAI},
	volume = {6893},
	year = {2011},
	pages = {370--377},
	publisher = {Springer},
	organization = {Springer},
	author = {Rathke, Fabian and Schmidt, Stefan and Christoph Schn{\"o}rr},
	editor = {Fichtinger, Gabor and Martel, Anne L. and Peters, Terry M.}
}
@conference {Rathke11,
	title = {Order Preserving and Shape Prior Constrained Intra-Retinal Layer Segmentation in Optical Coherence Tomography},
	booktitle = {MICCAI},
	series = {Lecture Notes in Computer Science},
	volume = {6893},
	year = {2011},
	pages = {370{\textendash}377},
	publisher = {Springer},
	organization = {Springer},
	author = {Fabian Rathke and Stefan Schmidt and Christoph Schn{\"o}rr},
	editor = {Fichtinger, Gabor and Martel, Anne L. and Peters, Terry M.}
}
@conference {Pletscher2011,
	title = {Putting MAP back on the map},
	booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {6835 LNCS},
	year = {2011},
	pages = {111{\textendash}121},
	abstract = {Conditional Random Fields (CRFs) are popular models in computer vision for solving labeling problems such as image denoising. This paper tackles the rarely addressed but important problem of learning the full form of the potential functions of pairwise CRFs. We examine two popular learning techniques, maximum likelihood estimation and maximum margin training. The main focus of the paper is on models such as pairwise CRFs, that are simplistic (misspecified) and do not fit the data well. We empirically demonstrate that for misspecified models maximum-margin training with MAP prediction is superior to maximum likelihood estimation with any other prediction method. Additionally we examine the common belief that MLE is better at producing predictions matching image statistics. {\textcopyright} 2011 Springer-Verlag.},
	isbn = {9783642231223},
	issn = {03029743},
	doi = {10.1007/978-3-642-23123-0_12},
	author = {Pletscher, Patrick and Nowozin, Sebastian and Kohli, Pushmeet and Carsten Rother}
}
@conference {Pletscher2011a,
	title = {Putting MAP back on the map},
	booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {6835 LNCS},
	year = {2011},
	pages = {111{\textendash}121},
	abstract = {Conditional Random Fields (CRFs) are popular models in computer vision for solving labeling problems such as image denoising. This paper tackles the rarely addressed but important problem of learning the full form of the potential functions of pairwise CRFs. We examine two popular learning techniques, maximum likelihood estimation and maximum margin training. The main focus of the paper is on models such as pairwise CRFs, that are simplistic (misspecified) and do not fit the data well. We empirically demonstrate that for misspecified models maximum-margin training with MAP prediction is superior to maximum likelihood estimation with any other prediction method. Additionally we examine the common belief that MLE is better at producing predictions matching image statistics. {\textcopyright} 2011 Springer-Verlag.},
	isbn = {9783642231223},
	issn = {03029743},
	doi = {10.1007/978-3-642-23123-0_12},
	author = {Pletscher, Patrick and Nowozin, Sebastian and Kohli, Pushmeet and Carsten Rother}
}
@conference {lou_11_structured,
	title = {Structured Learning for Cell Tracking},
	booktitle = {NIPS 2011. Proceedings},
	year = {2011},
	note = {1},
	pages = {1296-1304},
	author = {Lou, X. and Fred A. Hamprecht},
	editor = {Shawe-Taylor, J. and Zemel, R.S. and Pereira, F.C.N. and Weinberger, K.Q. and Bartlett, P.}
}
@article {becker_11_variational2,
	title = {Variational Adaptive Correlation Method for Flow Estimation},
	journal = {IEEE Transactions on Image Processing},
	volume = {21, 6},
	year = {2011},
	note = {1},
	pages = {3053 - 3065},
	doi = {10.1109/TIP.2011.2181524},
	author = {Florian Becker and Wieneke, B. and Stefania Petra and Schr{\"o}der, A. and Christoph Schn{\"o}rr}
}
@conference {lenzen_11_variational,
	title = {Variational Image Denoising with Adaptive Constraint Sets},
	booktitle = {Proceedings of the 3nd International Conference on Scale Space and
Variational Methods in Computer Vision 2011, in press},
	volume = {6667},
	year = {2011},
	note = {1},
	pages = {206-217},
	publisher = {Springer},
	organization = {Springer},
	doi = {10.1007/978-3-642-24785-9_18},
	author = {Frank Lenzen and Florian Becker and Lellmann, J. and Stefania Petra and Christoph Schn{\"o}rr}
}
@article {pfannmoeller_11_visualizing,
	title = {Visualizing a homogeneous blend in bulk heterojunction polymer solar cells by analytical electron microscopy},
	journal = {Nano Letters},
	volume = {11},
	year = {2011},
	pages = {3099-3107},
	doi = {10.1021/nl201078t},
	author = {Pfannm{\"o}ller, M. and Fl{\"u}gge, H. and Benner, G. and Wacker, I. and Christoph Sommer and Hanselmann, M. and Schmale, S. and Schmidt, H. and Fred A. Hamprecht and Rabe, T. and Kowalsky, W. and Schr{\"o}der, R.}
}
@mastersthesis {platt2011,
	title = {Weiterentwicklung einer hochaufl{\"o}senden LIF-Methode zur Messung von Sauerstoffkonzentrationsprofilen in der wasserseitigen Grenzschicht},
	year = {2011},
	note = {started 11.04.2011},
	school = {Institut f{\"u}r Umweltphysik, Fakult{\"a}t f{\"u}r Physik und Astronomie, Univ.\ Heidelberg},
	author = {Tanja Platt}
}
@article {kirchner_10_computational,
	title = {Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments},
	journal = {Bioinformatics},
	volume = {26 (1)},
	year = {2010},
	note = {1},
	pages = {77-83},
	doi = {10.1093/bioinformatics/btp607},
	author = {Kirchner, M. and B. Y. Renard and Ullrich K{\"o}the and Pappin, D. J. and Fred A. Hamprecht and Judith A. J. Steen and Steen, H.}
}
@conference {Lellmann2010a,
	title = {Fast and Exact Primal-Dual Iterations for Variational Problems in Computer Vision},
	booktitle = {European Conference on Computer Vision (ECCV)},
	volume = {6312},
	year = {2010},
	pages = {494--505},
	publisher = {Springer Berlin / Heidelberg},
	organization = {Springer Berlin / Heidelberg},
	author = {Lellmann, J. and Breitenreicher, D. and Christoph Schn{\"o}rr},
	editor = {Daniilidis, K. and Maragos, P. and Paragios, N.}
}
@conference {Lellmann2010a,
	title = {Fast and Exact Primal-Dual Iterations for Variational Problems in Computer Vision},
	booktitle = {European Conference on Computer Vision (ECCV)},
	series = {LNCS},
	volume = {6312},
	year = {2010},
	pages = {494{\textendash}505},
	publisher = {Springer Berlin / Heidelberg},
	organization = {Springer Berlin / Heidelberg},
	author = {Lellmann, J. and Breitenreicher, D. and Schn{\"o}rr, C.},
	editor = {Daniilidis, K. and Maragos, P. and Paragios, N.}
}
@article {boerner_10_from,
	title = {From experimental setup to bioinformatics: An RNAi screening platform to identify host factors involved in HIV-1 replication},
	journal = {Biotechnology Journal},
	volume = {5},
	year = {2010},
	note = {1},
	pages = {39-49},
	doi = {10.1002/biot.200900226},
	author = {B{\"o}rner, K. and Hermle, J. and Christoph Sommer and Brown, N. P. and Knapp, B. and Glass, B. and Torralba, G. and Reymann, J. and Beil, N. and Beneke, J. and Pepperkok, R. and Schneider, R. and Ludwig, T.}
}
@conference {kappes_10_mrf,
	title = {MRF Inference by k-Fan Decomposition and Tight Lagrangian Relaxation},
	booktitle = {European Conference on Computer Vision (ECCV)},
	volume = {6313},
	year = {2010},
	note = {1},
	pages = {735--747},
	publisher = {Springer},
	organization = {Springer},
	doi = {10.1007/978-3-642-15558-1_53},
	author = {J{\"o}rg H. Kappes and Schmidt, S. and Christoph Schn{\"o}rr},
	editor = {Daniilidis, K. and Maragos, P. and Paragios, N.}
}
@conference {Kappes-ECCV2010,
	title = {MRF Inference by k-Fan Decomposition and Tight Lagrangian Relaxation},
	booktitle = {European Conference on Computer Vision (ECCV)},
	volume = {6313},
	year = {2010},
	pages = {735--747},
	publisher = {Springer Berlin / Heidelberg},
	organization = {Springer Berlin / Heidelberg},
	author = {J{\"o}rg H. Kappes and Schmidt, S. and Christoph Schn{\"o}rr},
	editor = {Daniilidis, K. and Maragos, P. and Paragios, N.}
}
@conference {Kappes-ECCV2010,
	title = {MRF Inference by k-Fan Decomposition and Tight Lagrangian Relaxation},
	booktitle = {European Conference on Computer Vision (ECCV)},
	volume = {6313},
	year = {2010},
	pages = {735{\textendash}747},
	publisher = {Springer Berlin / Heidelberg},
	organization = {Springer Berlin / Heidelberg},
	author = {Kappes, J. H. and Schmidt, S. and Schn{\"o}rr, C.},
	editor = {Daniilidis, K. and Maragos, P. and Paragios, N.}
}
@incollection {Petra-et-al-09a,
	title = {3D Tomography from Few Projections in Experimental Fluid Mechanics},
	volume = {106},
	year = {2009},
	pages = {63-72},
	publisher = {Springer},
	author = {Stefania Petra and Schr{\"o}der, A. and Christoph Schn{\"o}rr},
	editor = {W. Nitsche and C. Dobriloff}
}
@techreport {petra09b,
	title = {Accelerating Constrained SIRT with Applications in Tomographic Particle Image Reconstruction},
	year = {2009},
	institution = {IWR, University of Heidelberg},
	url = {http://www.ub.uni-heidelberg.de/archiv/9477},
	author = {Stefania Petra and Popa, C. and Christoph Schn{\"o}rr}
}
@article {hayn_09_analysing,
	title = {Analysing spatio-temporal patterns of the global NO<SUB>2</SUB>-distribution retrieved frome GOME satellite observations using a generalized additive model},
	journal = {Atmospheric Chemistry and Physics},
	volume = {9},
	number = {17},
	year = {2009},
	note = {1},
	pages = {9367-9398},
	doi = {10.5194/acp-9-6459-2009},
	author = {Hayn, M. and S. Beirle and Fred A. Hamprecht and Ulrich Platt and Bjoern H. Menze and T. Wagner}
}
@article {menze_09_comparison,
	title = {A Comparison of Random Forest and its Gini Importance with Standard Chemometric Methods for the Feature Selection and Classification of Spectral Data},
	journal = {BMC Bioinformatics},
	volume = {10:213},
	year = {2009},
	note = {1},
	doi = {10.1186/1471-2105-10-213},
	author = {Bjoern H. Menze and B. Michael Kelm and Masuch, R. and Himmelreich, U. and Bachert, P. and Petrich, W. and Fred A. Hamprecht}
}
@article {frank_09_denoising,
	title = {Denoising of Continuous-Wave Time-Of-Flight Depth Images Using Confidence Measures},
	journal = {Optical Engineering},
	volume = {48, 077003},
	year = {2009},
	note = {1},
	doi = {10.1117/1.3159869},
	author = {Mario Frank and Matthias Plaue and Fred A. Hamprecht}
}
@article {thieke_09_framework,
	title = {A framework and multi-application prototype for integrated radiological diagnostics and radiation therapy},
	journal = {Strahlentherapie und Onkologie},
	volume = {185},
	number = {Suppl. 1},
	year = {2009},
	pages = {81},
	author = {Thieke, C. and Nix, O. and Koehn, A. and Floca, R. and van Straaten, D. and Hahn, H. and Strauss, L. G. and Siems, U. and Graf, M. and Pruem, H. and Klein, J. and Laue, H. and F. O. Kaster}
}
@techreport {popa09,
	title = {On a general extending and constraining procedure for linear iterative methods},
	year = {2009},
	institution = {IWR, University of Heidelberg},
	url = {http://www.ub.uni-heidelberg.de/archiv/9761},
	author = {Nicola, A. and Stefania Petra and Popa, C. and Christoph Schn{\"o}rr}
}
@techreport {popa09,
	title = {On a general extending and constraining procedure for linear iterative methods},
	year = {2009},
	month = {August},
	institution = {IWR, University of Heidelberg},
	type = {Technical Report},
	url = {http://www.ub.uni-heidelberg.de/archiv/9761},
	author = {Nicola, A. and Petra, S. and Popa, C. and Schn{\"o}rr, C.}
}
@article {frank_09_theoretical,
	title = {Theoretical and Experimental Error Analysis of Continuous-Wave Time-Of-Flight Range Cameras},
	journal = {Optical Engineering},
	volume = {48, 013602},
	year = {2009},
	note = {1},
	doi = {10.1117/1.3070634},
	author = {Mario Frank and Matthias Plaue and Holger Rapp and Ullrich K{\"o}the and Bernd J{\"a}hne and Fred A. Hamprecht}
}
@article {frank2009,
	title = {Theoretical and experimental error analysis of continuous-wave time-of-flight range cameras},
	journal = {Opt. Eng.},
	volume = {48},
	year = {2009},
	pages = {013602},
	abstract = {We offer a formal investigation of the measurement principle of time-of-flight 3-D cameras using correlation of amplitude-modulated continuous-wave signals. These sensors can provide both depth maps and IR intensity pictures simultaneously and in real time. We examine the theory of the data acquisition in detail. The variance of the range measurements is derived in a concise way and we show that the computed range follows an offset normal distribution. The impact of quantization of that distribution is discussed. All theoretically investigated errors like the behavior of the variance, depth bias, saturation and quantization effects are supported by experimental results.},
	doi = {10.1117/1.3070634},
	author = {Mario Frank and Matthias Plaue and Holger Rapp and Ullrich K{\"o}the and Bernd J{\"a}hne and Fred A. Hamprecht}
}
@techreport {petra09c,
	title = {TomoPIV meets Compressed Sensing},
	year = {2009},
	institution = {IWR, University of Heidelberg},
	url = {http://www.ub.uni-heidelberg.de/archiv/9760},
	author = {Stefania Petra and Christoph Schn{\"o}rr}
}
@article {Petra-Schnoerr-PUMA-10,
	title = {TomoPIV meets Compressed Sensing},
	journal = {Pure Math.~Appl.},
	volume = {20},
	number = {1-2},
	year = {2009},
	pages = {49 -- 76},
	url = {http://www.mat.unisi.it/newsito/puma/public_html/contents.php},
	author = {Stefania Petra and Christoph Schn{\"o}rr}
}
@techreport {petra09c,
	title = {TomoPIV meets Compressed Sensing},
	year = {2009},
	month = {August},
	institution = {IWR, University of Heidelberg},
	type = {Technical Report},
	url = {http://www.ub.uni-heidelberg.de/archiv/9760},
	author = {Petra, S. and Schn{\"o}rr, C.}
}
@article {Petra-Schnoerr-PUMA-10,
	title = {TomoPIV meets Compressed Sensing},
	journal = {Pure Math. Appl.},
	volume = {20},
	number = {1-2},
	year = {2009},
	pages = {49 {\textendash} 76},
	url = {http://www.mat.unisi.it/newsito/puma/public_html/contents.php},
	author = {Petra, S. and Schn{\"o}rr, C.}
}
@phdthesis {pavlov2008,
	title = {Analysis of Motion in Scale Space},
	year = {2008},
	publisher = {IWR, Fakult{\"a}t f{\"u}r Mathematik und Informatik, Univ.\ Heidelberg},
	abstract = {This work includes some new aspects of motion estimation by the optic flow method in scale spaces. The usual techniques for motion estimation are limited to the application of coarse to fine strategies. The coarse to fine strategies can be successful only if there is enough information in every scale. In this work we investigate the motion estimation in the scale space more basically. The wavelet choice for scale space decomposition of image sequences is discussed in the first part of this work. We make use of the continuous wavelet transform with rotationally symmetric wavelets. Bandpass decomposed sequences allow the replacement of the structure tensor by the phase invariant energy operator. The structure tensor is computationally more expensive because of its spatial or spatio-temporal averaging. The energy operator needs in general no further averaging. The numerical accuracy of the motion estimation with the energy operator is compared to the results of usual techniques, based on the structure tensor. The comparison tests are performed on synthetic and real life sequences. Another practical contribution is the accuracy measurement for motion estimation by adaptive smoothed tensor fields. The adaptive smoothing relies on nonlinear anisotropic diffusion with discontinuity and curvature preservation. We reached an accuracy gain under properly chosen parameters for the diffusion filter. A theoretical contribution from mathematical point of view is a new discontinuity and curvature preserving regularization for motion estimation. The convergence of solutions for the isotropic case of the nonlocal partial differential equation is shown. For large displacements between two consecutive frames the optic flow method is systematically corrupted because of the violence of the sampling theorem. We developed a new method for motion analysis by scale decomposition, which allows to circumvent the systematic corruption without using the coarse to fine strategy. The underlying assumption is, that in a certain neighborhood the grey value undergoes the same displacement. If this is fulfilled, then the same optic flow should be measured in all scales. If there arise inconsistencies in a pixel across the scale space, so they can be detected and the scales containing this inconsistencies are not taken into account.},
	url = {http://www.ub.uni-heidelberg.de/archiv/9378},
	author = {Pavel Pavlov}
}
@article {steen_08_different,
	title = {Different Phosphorylation States of the Anaphase Promoting Complex in Response to Anti-Mitotic Drugs: A Quantitative Proteomic Analysis},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {105},
	number = {16},
	year = {2008},
	note = {1},
	pages = {6069-6074},
	doi = {10.1073/pnas.0709807104},
	author = {Judith A. J. Steen and Steen, H. and Georgi, A. and Kenneth C. Parker and Springer, M. and Kirchner, M. and Fred A. Hamprecht and Kirschner, M. W.}
}
@conference {petra-wmm08,
	title = {Enhancing Sparsity by Constraining Strategies: Constrained SIRT versus Spectral Projected Gradient Methods},
	booktitle = {Proc. 7th Workshop on Modelling of Environmental and Life Sciences Problems (WMM 08)},
	year = {2008},
	month = {Oct. 22-Oct. 25},
	publisher = {Ed Acad Romane, Bucuresti},
	organization = {Ed Acad Romane, Bucuresti},
	address = {Constanta, Romania},
	author = {Petra, S. and Popa, C. and Schn{\"o}rr, C.}
}
@conference {Petra-et-al-08b,
	title = {Enhancing Sparsity by Constraining Strategies: Constrained SIRT versus Spectral Projected Gradient Methods},
	booktitle = {Proc. 7th Workshop on Modelling of Environmental and Life Sciences Problems (WMM 08)},
	series = {Ed Acad Romane},
	year = {2008},
	address = {Bucharest, Romania},
	author = {Petra, S. and Popa, C. and Schn{\"o}rr, C.}
}
@techreport {Petra-et-al08b,
	title = {Extended and Constrained Cimmino-type Algorithms with Applications in Tomographic Image Reconstruction},
	year = {2008},
	institution = {IWR, University of Heidelberg},
	url = {http://www.ub.uni-heidelberg.de/archiv/8798/},
	author = {Stefania Petra and Popa, Constantin and Christoph Schn{\"o}rr}
}
@techreport {Petra-et-al08b,
	title = {Extended and Constrained Cimmino-type Algorithms with Applications in Tomographic Image Reconstruction},
	year = {2008},
	month = {November},
	institution = {IWR, University of Heidelberg},
	type = {Technical Report},
	url = {http://www.ub.uni-heidelberg.de/archiv/8798/},
	author = {Stefania Petra and Constantin Popa and Christoph Schn{\"o}rr}
}
@incollection {acker2008,
	title = {Inverse Problems and Parameter Identification in Image Processing},
	year = {2008},
	pages = {111--151},
	publisher = {Springer},
	abstract = {Many problems in imaging are actually inverse problems. One reason for this is that conditions and parameters of the physical processes underlying the actual image acquisition are usually not known. Examples for this are the inhomogeneities of the magnetic field in magnetic resonance imaging (MRI) leading to nonlinear deformations of the anatomic structures in the recorded images, material parameters in geological structures as unknown parameters for the simulation of seismic wave propagation with sparse measurement on the surface, or temporal changes in movie sequences given by intensity changes or moving image edges and resulting from deformation, growth and transport processes with unknown fluxes. The underlying physics is mathematically described in terms of variational problems or evolution processes. Hence, solutions of the forward problem are naturally described by partial differential equations. These forward models are reflected by the corresponding inverse problems as well. Beyond these concrete, direct modeling links to continuum mechanics abstract concepts from physical modeling are successfully picked up to solve general perceptual problems in imaging. Examples are visually intuitive methods to blend between images showing multiscale structures at different resolution or methods for the analysis of flow fields.},
	doi = {10.1007/978-3-540-75632-3_4},
	author = {Jens F. Acker and Benjamin Berkels and Kristian Bredies and Mamadou S. Diallo and Marc Droske and Christoph S. Garbe and Matthias Holschneider and Jaroslav Hron and Claudia Kondermann and Michail Kulesh and Peter Maass and Nadine Olischl{\"a}ger and Heinz-Otto Peitgen},
	editor = {R. Dahlhaus and J. Kurths and Timmer, J. and Peter Maass}
}
@incollection {garbe_08_nonlinear,
	title = {Nonlinear Analysis of Multi-Dimensional Signals},
	year = {2008},
	note = {1},
	pages = {231-288},
	publisher = {Springer},
	doi = {10.1007/978-3-540-75632-3_7},
	author = {Christoph S. Garbe and Kai Krajsek and Pavel Pavlov and Bj{\"o}rn Andres and Matthias M{\"u}hlich and Ingo Stuke and Cicero Mota and Martin B{\"o}hme and Martin Haker and Schuchert, T. and Hanno Scharr and Til Aach and Erhardt Barth},
	editor = {R. Dahlhaus and J. Kurths and Timmer, J. and Peter Maass}
}
@incollection {garbe2008,
	title = {Nonlinear analysis of multi-dimensional signals: local adaptive estimation of complex motion and orientation patterns},
	year = {2008},
	pages = {231-288},
	publisher = {Springer},
	abstract = {We consider the general task of accurately detecting and quantifying orientations in n-dimensional signals s. The main emphasis will be placed on the estimation of motion, which can be thought of as orientation in spatiotemporal signals. Associated problems such as the optimization of matched kernels for deriving isotropic and highly accurate gradients from the signals, optimal integration of local models, and local model selection will also be addressed.},
	doi = {10.1007/978-3-540-75632-3_7},
	author = {Christoph S. Garbe and Kai Krajsek and Pavel Pavlov and Bj{\"o}rn Andres and Matthias M{\"u}hlich and Ingo Stuke and Cicero Mota and Martin B{\"o}hme and Martin Haker and Tobias Schucher and Hanno Scharr and Til Aach and Erhardt Barth},
	editor = {R. Dahlhaus and J. Kurths and Timmer, J. and Peter Maass}
}
@article {koenig_08_robust,
	title = {Robust Prediction of the MASCOT Score for an Improved Quality Assessment in Mass Spectrometric Proteomics},
	journal = {Journal of Proteome Research},
	volume = {7},
	number = {9},
	year = {2008},
	note = {1},
	pages = {3708-3717},
	doi = {10.1021/pr700859x},
	author = {K{\"o}nig, T. and Bjoern H. Menze and Kirchner, M. and Monigatti, F. and Kenneth C. Parker and Patterson, T. and Judith Jebanthirajah Steen and Fred A. Hamprecht and Steen, H.}
}
@conference {Petra-et-al-08,
	title = {On Sparsity Maximization in Tomographic Particle Image Reconstruction},
	booktitle = {Pattern Recognition -- 30th DAGM Symposium},
	volume = {5096},
	year = {2008},
	pages = {294--303},
	publisher = {Springer Verlag},
	organization = {Springer Verlag},
	author = {Stefania Petra and Schr{\"o}der, A. and Wieneke, B. and Christoph Schn{\"o}rr}
}
@conference {Petra-et-al-08,
	title = {On Sparsity Maximization in Tomographic Particle Image Reconstruction},
	booktitle = {Pattern Recognition {\textendash} 30th DAGM Symposium},
	series = {lncs},
	volume = {5096},
	year = {2008},
	pages = {294{\textendash}303},
	publisher = {Springer Verlag},
	organization = {Springer Verlag},
	author = {Petra, S. and Schr{\"o}der, A. and Wieneke, B. and Schn{\"o}rr, C.}
}
@incollection {jaehne2007f,
	title = {The influence of intermittency on air/water gas transfer measurements},
	year = {2007},
	publisher = {Springer-Verlag},
	abstract = {This paper theoretically investigates the influence of intermittency on determining average transfer velocities using different measuring techniques. It is shown that all measuring techniques can significantly be biased by intermittency. Mass balance and eddy correlation measurements are only biased when the concentration difference between the air and the water is spatially or temporally inhomogeneous over the measurement interval. Mean transfer velocities calculated either from mean boundary layer thicknesses or from thermographic techniques, which compute the mean transfer velocity either from concentration differences of from time constants, are biased toward lower values. The effects can be large and a simple stochastic bimodal model is used to estimate the effect.},
	doi = {10.1007/978-3-540-36906-6_18},
	author = {Bernd J{\"a}hne and Christopher Popp and Uwe Schimpf and Christoph S. Garbe and Bernd J{\"a}hne},
	editor = {Christoph S. Garbe and Handler, R. A.}
}
@article {Gall-et-al-07,
	title = {Interacting and Annealing Particle Filters: Mathematics and a Recipe for Applications},
	journal = {J.~Math.~Imag.~Vision},
	volume = {28},
	year = {2007},
	pages = {1--18},
	author = {Gall, J{\"u}rgen and Potthoff, J{\"u}rgen and Christoph Schn{\"o}rr and Rosenhahn, Bodo and Hans-Peter Seidel}
}
@article {Gall-et-al-07,
	title = {Interacting and Annealing Particle Filters: Mathematics and a Recipe for Applications},
	journal = {J. Math. Imag. Vision},
	volume = {28},
	year = {2007},
	pages = {1{\textendash}18},
	author = {Gall, J{\"u}rgen and Potthoff, J{\"u}rgen and Christoph Schn{\"o}rr and Rosenhahn, Bodo and Seidel, Hans-Peter}
}
@article {menze_07_multivariate,
	title = {Multivariate feature selection and hierarchical classification for infrared spectroscopy: serum-based detection of bovine spongiform encephalopathy},
	journal = {Analytical and Bioanalytical Chemistry},
	volume = {387},
	number = {5},
	year = {2007},
	note = {1},
	pages = {1801-1807},
	doi = {10.1007/s00216-006-1070-5},
	author = {Bjoern H. Menze and Petrich, W. and Fred A. Hamprecht}
}
@article {preusser2007,
	title = {A phase field method for joint denoising, edge detection, and motion estimation in image sequence processing.},
	journal = {SIAM Journal of Applied Mathematics},
	volume = {68},
	year = {2007},
	pages = {599-618},
	abstract = {The estimation of optical flow fields from image sequences is incorporated in a Mumford/Shah approach for image denoising and edge detection. Possibly noisy image sequences are considered as input and a piecewise smooth image intensity, a piecewise smooth motion field, and a joint discontinuity set are obtained as minimizers of the functional. The method simultaneously detects image edges and motion field discontinuities in a rigorous and robust way. It is able to handle information on motion that is concentrated on edges. Inherent to it is a natural multiscale approximation that is closely related to the phase field approximation for edge detection by Ambrosio and Tortorelli. We present an implementation for two-dimensional image sequences with finite elements in space and time. This leads to three linear systems of equations, which have to be solved in a suitable iterative minimization procedure. Numerical results and different applications underline the robustness of the approach presented.},
	doi = {10.1137/060677409},
	author = {Preusser, T. and Marc Droske and Christoph S. Garbe and Martin Rumpf and Alexandru Telea}
}
@conference {Schmidt-et-al-07,
	title = {Spine Detection and Labeling Using a Parts-Based Graphical Model},
	booktitle = {Proc. 20th International Conference on Information Processing in Medical Imaging (IPMI 2007)},
	volume = {4584},
	year = {2007},
	pages = {122-133},
	publisher = {Springer},
	organization = {Springer},
	author = {Schmidt, S. and J{\"o}rg H. Kappes and Bergtholdt, M. and Pekar, V. and Dries, S. and Bystrov, D. and Christoph Schn{\"o}rr}
}
@conference {Schmidt-et-al-07,
	title = {Spine Detection and Labeling Using a Parts-Based Graphical Model},
	booktitle = {Proc. 20th International Conference on Information Processing in Medical Imaging (IPMI 2007)},
	series = {LCNS},
	volume = {4584},
	year = {2007},
	pages = {122-133},
	publisher = {Springer},
	organization = {Springer},
	author = {Schmidt, S. and Kappes, J. H. and Bergtholdt, M. and Pekar, V. and Dries, S. and Bystrov, D. and Schn{\"o}rr, C.}
}
@conference {petra-wmm07,
	title = {Tomographic Image Reconstruction in Experimental Fluid Dynamics: Synopsis and Problems},
	booktitle = {Proc. 6th Workshop on Modelling of Environmental and Life Sciences Problems (WMM 07)},
	year = {2007},
	month = {Sept. 5-Sept. 9},
	publisher = {Ed Acad Romane, Bucuresti},
	organization = {Ed Acad Romane, Bucuresti},
	address = {Constanta, Romania},
	author = {Petra, S. and Schn{\"o}rr, C. and A. Schr{\"o}der and B. Wieneke}
}
@conference {schimpf2006,
	title = {Active thermography: a local and fast method to investigate heat and gas exchange between ocean and atmosphere},
	booktitle = {Verhandlungen der Deutschen Physikalischen Gesellschaft, Spring Conference, Heidelberg, 15.-17.03.2006},
	year = {2006},
	publisher = {Deutsche Physikalische Gesellschaft},
	organization = {Deutsche Physikalische Gesellschaft},
	url = {http://www.dpg-verhandlungen.de/2006/heidelberg/up.html},
	author = {Uwe Schimpf and Christopher Popp and Bernd J{\"a}hne}
}
@inbook {carlsohn_06_spectral,
	title = {Color image processing},
	volume = {7(17)},
	year = {2006},
	pages = {393-419},
	publisher = {CRC Press},
	organization = {CRC Press},
	chapter = {Spectral Imaging and Applications},
	author = {Carlsohn, M. F. and Bjoern H. Menze and B. Michael Kelm and Fred A. Hamprecht and Kercek, A. and Leitner, R. and Polder, G.},
	editor = {Lukac, R. and Plataniotis, K.N.}
}
@conference {kelm_06_combining,
	title = {Combining Generative and Discriminative Methods for Pixel Classification with Multi-Conditional Learning.},
	booktitle = {ICPR 2006},
	volume = {2},
	year = {2006},
	note = {1},
	pages = {828-832},
	doi = {10.1109/ICPR.2006.384},
	author = {B. Michael Kelm and Pal, C. and McCallum, A.}
}
@phdthesis {popp2006,
	title = {Untersuchung von Austauschprozessen an der Wasseroberfl{\"a}che aus Infrarot-Bildsequenzen mittels frequenzmodulierter W{\"a}rmeeinstrahlung},
	year = {2006},
	publisher = {Institut f{\"u}r Umweltphysik, Fakult{\"a}t f{\"u}r Physik und Astronomie, Univ.\ Heidelberg},
	abstract = {The study presents a new technique for measuring the gas transfer rate at a free water surface with high temporal and spatial resolution, a method suitable for field experiments. The approach is based on the Controlled Flux Technique (CFT) using heat as a proxy tracer for gas exchange. A periodically varying heat flux at water surface is used. The heat flux is generated by a 100 W CO2-laser, while a highly sensitive infrared camera measures the temperature response of the water surface. Heat - and consequently gas transfer rates - can be deduced from the analysis of the spectral amplitude attenuation at water surface. Furthermore, the approach presented allows direct insight into the transport mechanisms of gas exchange processes by an analysis of the phase shift observed at water surface. A first series of measurements at the Heidelberg wind wave facility AEOLOTRON shows that the spectral amplitude attenuation is in keeping with model predictions. The calculated transfer rates for CO2 are also well in accordance with results from other laboratory and field experiments. Contrary to the amplitude attenuation, the calculated phase shifts differ signicantly from model predictions, especially for high wind speeds. This effect, observed for the first time, can be interpreted as being caused by the intermittence of transfer processes. This would indicate that stochastic processes play a larger role in gas transfer than assumed so far.},
	url = {http://www.ub.uni-heidelberg.de/archiv/6489},
	author = {Christopher Popp}
}
@conference {telea2006,
	title = {A variational approach to joint denoising, edge detection and motion estimation},
	booktitle = {Proceedings of the 28th DAGM Symposium on Pattern Recognition},
	year = {2006},
	pages = {525--535},
	url = {http://numod.ins.uni-bonn.de/research/papers/public/PrDrGa06.pdf},
	author = {Alexandru Telea and Tobias Preu{\ss}er and Christoph S. Garbe and Marc Droske and Martin Rumpf}
}
@conference {jaehne2005,
	title = {Air-Sea Gas Transfer; Schmidt Number dependency and intermittency},
	booktitle = {Presented at: International Liege Colloquium on Ocean Dynamics, Gas Transfer at Water Surfaces},
	year = {2005},
	author = {Bernd J{\"a}hne and Nielsen, R. and Christopher Popp and Uwe Schimpf and Christoph S. Garbe}
}
@article {wenig2005,
	title = {Operator representation as a new differential optical absorption spectroscopy formalism},
	journal = {Appl. Optics},
	volume = {44},
	year = {2005},
	pages = {3246-3253},
	abstract = {UV-visible absorption spectroscopy with extraterrestrial light sources is a widely used technique for the measurement of stratospheric and tropospheric trace gases. We focus on differential optical absorption spectroscopy (DOAS) and present an operator notation as a new formalism to describe the different processes in the atmosphere and the simplifying assumptions that compose the advantage of DOAS. This formalism provides tools to classify and reduce possible error sources of DOAS applications.},
	doi = {10.1364/AO.44.003246},
	author = {Mark Wenig and Bernd J{\"a}hne and Ulrich Platt}
}
@article {Ruhnau-et-al-05b,
	title = {A variational approach for particle tracking velocimetry},
	journal = {Meas. Science and Techn.},
	volume = {16},
	year = {2005},
	pages = {1449-1458},
	author = {Ruhnau, P. and G{\"u}tter, C. and Putze, T. and Schn{\"o}rr, C.}
}
@proceedings {Paragios-et-al-05,
	title = {Variational, Geometric and Level Sets in Computer Vision (VLSM{\textquoteright}05)},
	volume = {3752},
	year = {2005},
	month = {Oct. 16},
	publisher = {Springer},
	address = {Beijing, China},
	editor = {Paragios, N. and Faugeras, O. and Chan, T. and Schn{\"o}rr, C.}
}
@incollection {Bergtholdt-et-al-05,
	title = {Variational Segmentation with Shape Priors},
	year = {2005},
	pages = {147-160},
	publisher = {Springer},
	chapter = {9},
	author = {Bergtholdt, Martin and Daniel Cremers and Christoph Schn{\"o}rr},
	editor = {Paragios, N. and Chen, Y. and Faugeras, O.}
}
@conference {Giebel-et-al-04,
	title = {A Bayesian Framework for Multi-cue 3D Object Tracking},
	booktitle = {Computer Vision {\textendash} ECCV 2004},
	series = {lncs},
	volume = {3024},
	year = {2004},
	pages = {241-252},
	publisher = {Springer},
	organization = {Springer},
	author = {Giebel, J. and Gavrila, D. M. and Schn{\"o}rr, C.},
	editor = {Pajdla, T. and Matas, J.}
}
@conference {jaehne2004e,
	title = {Exchange processes at the ocean surface: their role in coupling atmosphere and ocean, a contribution to the SOLAS project},
	booktitle = {Verhandlungen der Deutschen Physikalischen Gesellschaft, Spring Conference, Munich, 22.-26.03.2004},
	year = {2004},
	publisher = {Deutsche Physikalische Gesellschaft},
	organization = {Deutsche Physikalische Gesellschaft},
	abstract = {Der Stoffaustausch zwischen Atmosph{\"a}re und Ozean ist trotz seiner Bedeutung f{\"u}r die globalen Stoffkreisl{\"a}ufe immer noch wenig verstanden und experimentell schwer zug{\"a}nglich. In den letzten Jahre wurde eine neue Technik entwickelt, die es mittels aktiver Thermographie erlaubt, die Antwortfunktion des Transports durch die wasserseitige viskose Grenzschicht sowohl im Labor als auch im Feld zu messen. Damit ist es nicht nur m{\"o}glich, innerhalb weniger Minuten die Transfergeschwindigkeit f{\"u}r Gase zu messen, sondern auch verschiedene Modelle zu unterscheiden und die Schmidtzahlabh{\"a}ngigkeit zu bestimmen. Dies bedeutet f{\"u}r zuk{\"u}nftige Messungen im Feld, dass Messungen der Konzentrationen von beliebigen Tracern im Wasser und der Atmosph{\"a}re ausreichend sind, um Flussraten relevanter Tracer zwischen Atmosph{\"a}re und Ozean zu bestimmen. Es sind keine aufwendigen und unsicheren direkten Flussraten (z.B. durch Eddykorrelations- oder -akkumulationsmessungen) mehr notwendig. Die neue Technik soll ein wesentliches Bindeglied zwischen den atmosph{\"a}rischen und ozeanographischen Untersuchungen des internationalen SOLAS-Projekt werden.},
	url = {http://old.dpg-tagungen.de/archive/2004/up_1.html},
	author = {Bernd J{\"a}hne and Uwe Schimpf and Christopher Popp and Christoph S. Garbe}
}
@conference {Cremers-et-al-04,
	title = {Multiphase Dynamic Labeling for Variational Recognition-Driven Image Segmentation},
	booktitle = {Computer Vision {\textendash} ECCV 2004},
	series = {lncs},
	volume = {3024},
	year = {2004},
	pages = {74-86},
	publisher = {Springer},
	organization = {Springer},
	author = {Daniel Cremers and Sochen, Nir and Christoph Schn{\"o}rr},
	editor = {Pajdla, T. and Matas, J.}
}
@conference {Kohlberger-et-al-04a,
	title = {Parallel Variational Motion Estimation by Domain Decomposition and Cluster Computing},
	booktitle = {Computer Vision {\textendash} ECCV 2004},
	series = {lncs},
	volume = {3024},
	year = {2004},
	pages = {205-216},
	publisher = {Springer},
	organization = {Springer},
	author = {Kohlberger, T. and Schn{\"o}rr, C. and Bruhn, A. and Weickert, J.},
	editor = {Pajdla, T. and Matas, J.}
}
@article {wenig2004,
	title = {Retrieval and analysis of stratospheric NO$_2$ from the Global Ozone Monitoring Experiment},
	journal = {J. Geophys. Res.},
	volume = {109},
	number = {D4},
	year = {2004},
	pages = {D04315, 1--11},
	abstract = {We describe the retrieval of stratospheric NO2 vertical column densities from the Global Ozone Monitoring Experiment (GOME) aboard the ERS-2 satellite. Different differential optical absorption spectroscopy (DOAS) evaluations are compared in order to investigate uncertainties caused by the diffuser plate. An improved version of our algorithm to separate the tropospheric and stratospheric fraction of NO2 from GOME satellite data is described and is used to extract a long term data set of stratospheric NO2 (1996-2000). In addition, the average seasonal variation in the global distribution is determined, which allows us to monitor and investigate specific aspects of stratospheric chemistry, in particular the interhemispheric comparison of stratospheric NO2. In contrast to other satellite observations (e.g., SAGE II, OSIRIS), GOME observations of stratospheric NO2 include the lower stratosphere. In general, our observations are in agreement with previous measurements and confirm the current knowledge of stratospheric nitrogen chemistry.},
	issn = {0148-0227},
	doi = {10.1029/2003JD003652},
	author = {Mark Wenig and Kuhl, S. and S. Beirle and Bucsela, E. and Bernd J{\"a}hne and Ulrich Platt and Gleason, J. and T. Wagner}
}
@incollection {scholes2003,
	title = {Biosphere-Atmosphere Interactions},
	year = {2003},
	pages = {19--71},
	publisher = {Springer},
	chapter = {2},
	doi = {10.1007/978-3-642-18984-5_2},
	author = {Mary C. Scholes and Patricia A. Matrai and Meinrat O. Andreae and Keith A. Smith and Martin R. Manning and Paulo Artaxo and Leonard A. Barrie and Timothy S. Bates and James H. Butler and Paolo Ciccioli and Stanislaw A. Cieslik and Robert J. Delmas and Frank J. Dentener},
	editor = {Guy P. Brasseur and Ronald G. Prinn and Alexander A. P. Pszenny}
}
@conference {Neumann-et-al-03a,
	title = {Feasible Adaption Criteria for Hybrid Wavelet {\textendash} Large Margin Classifiers},
	booktitle = {Proc. Computer Analysis of Images and Patterns (CAIP{\textquoteright}03)},
	series = {LNCS},
	volume = {2756},
	year = {2003},
	pages = {588{\textendash}595},
	publisher = {Springer},
	organization = {Springer},
	author = {Neumann, J. and Schn{\"o}rr, C. and Steidl, G.},
	editor = {Petkov, N. and Westenberg, M.A.}
}
@article {wenig2003,
	title = {Intercontinental transport of nitrogen oxide pollution plumes},
	journal = {Atmos. Chem. Phys.},
	volume = {3},
	year = {2003},
	pages = {387--393},
	doi = {10.5194/acp-3-387-2003},
	author = {Mark Wenig and N. Spichtinger and A. Stohl and G. Held and S. Beirle and T. Wagner and Bernd J{\"a}hne and Ulrich Platt}
}
@conference {Bruhn-et-al-03a,
	title = {Real-Time Optic Flow Computation with Variational Methods},
	booktitle = {Proc. Computer Analysis of Images and Patterns (CAIP{\textquoteright}03)},
	series = {LNCS},
	volume = {2756},
	year = {2003},
	pages = {222-229},
	publisher = {Springer},
	organization = {Springer},
	author = {Bruhn, Andr{\'e}s and Weickert, Joachim and Feddern, Christian and Kohlberger, Timo and Christoph Schn{\"o}rr},
	editor = {Petkov, N. and Westenberg, M.A.}
}
@article {wenig2002,
	title = {Intercontinental transport of nitrogen oxide pollution plumes},
	journal = {acpd},
	volume = {3},
	year = {2002},
	pages = {2151--2165},
	doi = {10.5194/acpd-2-2151-2002},
	author = {Mark Wenig and N. Spichtinger and A. Stohl and G. Held and S. Beirle and T. Wagner and Bernd J{\"a}hne and Ulrich Platt}
}
@conference {wenig2001a,
	title = {Image sequence analysis of satellite NO$_2$ concnetration maps},
	booktitle = {Pattern Recognition, 23rd DAGM Symposium Munich},
	volume = {2191},
	year = {2001},
	pages = {223--230},
	publisher = {Springer},
	organization = {Springer},
	abstract = {Here we describe a new method for the quantification of a global NOx budget from image sequences of the GOME instrument on the ERS-2. The focus of this paper is on image processing techniques to separate tropospheric and stratospheric NO2-colums using normalized convolution with infinite impulse response filters (IIR) to interpolate gaps in the data and average the cloud coverage of the earth, the estimation the NO2 life time and the determination of regional NOx source strengths.},
	doi = {10.1007/3-540-45404-7_30},
	author = {Mark Wenig and Carsten Leue and S. Kraus and T. Wagner and Ulrich Platt and Bernd J{\"a}hne},
	editor = {B. Radig and S. Florczyk}
}
@article {wagner2001a,
	title = {Monitoring of the stratospheric chlorine activation by Global Ozone Monitoring Experiment (GOME) OClO measurements in the austral and boreal winters 1995 through 1999},
	journal = {J. Geophys. Res.},
	volume = {106},
	number = {D6},
	year = {2001},
	pages = {4971-4986},
	abstract = {Measurements of OClO total column amounts by means of the Global Ozone Monitoring Experiment (GOME) instrument conducted in the austral and boreal winter stratospheres from 1995 through 1999 are presented, GOME is a four-channel UV/visible spectrometer (240-790 nm) deployed on the polar orbiting European ERS-2 satellite since April 1995. Previous studies have shown that the observations of OClO, the symmetric chlorine dioxide formed in a side channel of the reaction of BrO + ClO, can serve as an indicator for a stratospheric chlorine activation. GOME{\textquoteright}s 3-day coverage of the global atmosphere allows us to infer the first global data set of OClO, and to study continuous time series of its occurrence in both winter stratospheres. It is found that, while OClO regularly occurs over Antarctica in similar amounts and seasonal timing during the different winters, its occurrence is much more variable in the Arctic winter stratosphere, primarily because of the larger dynamic activity that result in warmer temperatures there. About 40\% higher OClO column amounts are found in the Antarctic polar stratosphere than in its northern counterpart, a further indication for a significantly more efficient chlorine activation in the Antarctic than the Arctic late winter and spring stratosphere.},
	doi = {10.1029/2000JD900458},
	author = {T. Wagner and Carsten Leue and Klaus Pfeilsticker and Ulrich Platt}
}
@article {leue2001,
	title = {Quantitative analysis of NO$_x$ emissions from Global Ozone Monitoring Experiment satellite image sequences},
	journal = {J. Geophys. Res.},
	volume = {106},
	number = {D6},
	year = {2001},
	pages = {5493--5505},
	abstract = {Nitric oxides (NOx) play a very important role among the anthropogenic trace gases. They affect human health and have an impact on ozone chemistry and climatic change. Here we describe a new method for the quantification of the global NOx budget from image sequences of the Global Ozone Monitoring Experiment (GOME) spectrometer on board the ERS 2 satellite. In contrast to measurements using ground-based or balloon- or aircraft-borne sensors, this instrument provides, for the first time, the possibility of observing global maps of NO2 column densities. As part of this work, algorithms were developed to analyze GOME spectra numerically and to extract physically relevant parameters from the resulting maps using image-processing techniques. Column densities of NO x were determined using differential optical absorption spectroscopy (DOAS) [Platt, 1994]. By the combined use of an efficient B-spline interpolation and an inversion algorithm based on Householder transformations, the numerical algorithms accelerate the retrievals by a factor of 26 with respect to previous methods. Moreover, techniques are presented for separating tropospheric and stratospheric NO2 colums and estimating the lifetime of NO2 in the troposphere. This allows determination of regional NOx source strengths. Independent of traditional methods, a global source strength of (43 {\textpm} 20) Tg N yr-1 is estimated. The accuracy of this method is comparable to that of established statistical approaches.},
	doi = {10.1029/2000JD900572},
	author = {Carsten Leue and Mark Wenig and T. Wagner and Klimm, O. and Ulrich Platt and Bernd J{\"a}hne}
}
@article {wagner2001,
	title = {Spatial and temporal distribution of enhanced boundary layer BrO concentrations measured by the GOME instrument aboard ERS-2},
	journal = {J. Geophys. Res.},
	volume = {106},
	number = {D6},
	year = {2001},
	pages = {24225--24235},
	abstract = {The temporal and spatial distribution of enhanced boundary layer BrO concentrations in both hemispheres during 1997 is presented using observations of the Global Ozone Monitoring Experiment (GOME) on board the European research satellite ERS-2. BrO concentrations (up to 50 ppt) are the major cause for catalytic boundary layer ozone destruction typically observed during polar spring in both hemispheres. While autocatalytic mechanisms are most probably responsible for the release of the observed high concentrations of reactive bromine compounds, uncertainties still remain with respect to the primary release mechanisms and whether the autocatalytic reactions are taking place on sea-salt aerosol or the surface of sea ice. We find that enhanced boundary layer BrO concentrations correlate very well with ozone depletion events. Enhanced BrO concentrations are always found over or near to areas of frozen salt water (above sea ice or also above the frozen surface of the Caspian Sea) consistent with the assumption that such conditions are a prerequisite for the autocatalytic release of high BrO concentrations to the troposphere.},
	doi = {10.1029/2000JD000201},
	author = {T. Wagner and Carsten Leue and Mark Wenig and Klaus Pfeilsticker and Ulrich Platt}
}
@article {hamprecht_01_strategy,
	title = {A strategy for analysis of (molecular) equilibrium simulations: configuration space density estimation, clustering and visualization},
	journal = {Journal of Chemical Physics},
	volume = {114},
	year = {2001},
	pages = {2079-2089},
	author = {Fred A. Hamprecht and Peter, C. and Daura, X. and Thiel, W. and van Gunsteren, W. F.}
}
@mastersthesis {prokop2000,
	title = {Bestimmung Physiologischer Parameter von Pflanzen mittels Digitaler Bildverarbeitung},
	year = {2000},
	school = {IWR, Fakult{\"a}t f{\"u}r Physik und Astronomie, Univ.\ Heidelberg},
	author = {Prokop, M.}
}
@incollection {wenig2000,
	title = {Cloud classification analyzing image sequences},
	year = {2000},
	pages = {652--653},
	publisher = {Academic Press},
	chapter = {A22},
	author = {Mark Wenig and Carsten Leue and Ulrich Platt and Bernd J{\"a}hne and Horst Hau{\ss}ecker}
}
@conference {scharr2000c,
	title = {Flame front analysis in turbulent combustion},
	booktitle = {Mustererkennung 2000},
	year = {2000},
	pages = {325--332},
	publisher = {Springer},
	organization = {Springer},
	doi = {10.1007/978-3-642-59802-9_41},
	author = {Hanno Scharr and Bernd J{\"a}hne and S. B{\"o}ckle and J. Kazenwadel and T. Kunzelmann and C. Schulz and N. Kr{\"u}ger},
	editor = {G. Sommer and Ch. Perwasser}
}
@incollection {leue2000,
	title = {NOX Emissions Retrieved from Satellite Images},
	year = {2000},
	pages = {654--655},
	publisher = {Academic Press},
	chapter = {A23},
	author = {Carsten Leue and Mark Wenig and Ulrich Platt and Bernd J{\"a}hne and Horst Hau{\ss}ecker}
}
@article {Peckar-et-al-99,
	title = {Parameter-Free Elastic Deformation Approach for 2D and 3D Registration Using Prescribed Displacements},
	journal = {J. Math. Imaging and Vision},
	volume = {10},
	number = {2},
	year = {1999},
	pages = {143{\textendash}162},
	author = {Peckar, W. and Schn{\"o}rr, C. and Rohr, K. and Stiehl, H.{\textendash}S.}
}
@incollection {leue1999a,
	title = {Retrieval of Atmospheric Trace Gas Concentrations},
	volume = {3: Systems and Applications},
	year = {1999},
	pages = {783-805},
	publisher = {Academic Press},
	chapter = {37},
	author = {Carsten Leue and Mark Wenig and Ulrich Platt and Bernd J{\"a}hne and Peter Gei{\ss}ler and Horst Hau{\ss}ecker}
}
@article {leue1998a,
	title = {GOME mi{\ss}t atmosph{\"a}rische Stickoxide. Globale Biomassenverbrennung und Industrieemissionen},
	journal = {Physik in unserer Zeit},
	volume = {29},
	number = {4},
	year = {1998},
	pages = {179},
	doi = {10.1002/piuz.19980290410},
	author = {Carsten Leue and Mark Wenig and Bernd J{\"a}hne and Ulrich Platt}
}
@article {Peckar-et-al-98,
	title = {Linear and Incremental Estimation of Elastic Deformations in Medical Registration Using Prescribed Displacements},
	journal = {Machine Graphics \& Vision},
	volume = {7},
	number = {4},
	year = {1998},
	pages = {807{\textendash}829},
	author = {Peckar, W. and Schn{\"o}rr, C. and Rohr, K. and Stiehl, H.{\textendash}S. and Spetzger, U.}
}
@conference {Peckar-et-al-98a,
	title = {Non-Rigid Image Registration Using a Parameter-Free Elastic Model},
	booktitle = {9th British Machine Vision Conference (BMVC{\textquoteleft}98)},
	year = {1998},
	month = {Sept. 14{\textendash}17},
	pages = {134{\textendash}143},
	address = {Southampton/UK},
	author = {Peckar, W. and Schn{\"o}rr, C. and Rohr, K. and Stiehl, H.S.},
	editor = {Carter, J.N. and Nixon, M.S.}
}
@article {leue1998,
	title = {Quantitative observation of biomass-burning plumes from GOME},
	journal = {ESA Publications EOQ},
	volume = {58},
	year = {1998},
	pages = {33--35},
	url = {http://esapub.esrin.esa.it/eoq/eoq58},
	author = {Carsten Leue and Mark Wenig and Bernd J{\"a}hne and Ulrich Platt}
}
@conference {scharr1997,
	title = {Numerische Isotropieoptimierung von FIR-Filtern mittels Quergl{\"a}ttung},
	booktitle = {Proceedings of the 19th DAGM Symposium on Pattern Recognition, Braunschweig},
	year = {1997},
	pages = {199--208},
	doi = {10.1007/978-3-642-60893-3_39},
	author = {Hanno Scharr and K{\"o}rkel, S. and Bernd J{\"a}hne},
	editor = {E. Paulus and F. M. Wahl}
}
@conference {reinecke1997a,
	title = {Rekonstruktion von Schreiberkurven},
	booktitle = {Mustererkennung 1997},
	year = {1997},
	pages = {527--536},
	publisher = {Springer},
	organization = {Springer},
	author = {Reinecke, H. and N. L. Fantana and Horst Hau{\ss}ecker and Bernd J{\"a}hne},
	editor = {E. Paulus and F. M. Wahl}
}
@incollection {liss1997,
	title = {Report Group 1 - Physical processes in the microlayer and the air-sea exchange of trace gases},
	year = {1997},
	pages = {1--33},
	publisher = {Cambridge University Press},
	doi = {10.1017/CBO9780511525025.002},
	author = {Peter S. Liss and A. J. Watson and E. J. Bock and Bernd J{\"a}hne and William E. Asher and Nelson M. Frew and L. Hasse and Gerald M. Korenowski and L. Merlivat and L. F. Phillips and P. Schl{\"u}ssel and D. K. Woolf},
	editor = {Peter S. Liss and Robert A. Duce}
}
@conference {jaehne1997j,
	title = {The research unit (Forschergruppe) Image Sequence Processing to Study Dynamical Processes},
	booktitle = {Proc.\ 3D Image Analysis and Synthesis{\textquoteright}97, Erlangen (Germany), November 17--18, 1997},
	year = {1997},
	pages = {107--114},
	publisher = {infix},
	organization = {infix},
	author = {Bernd J{\"a}hne and Horst Hau{\ss}ecker and Ulrich Platt and Ulrich Schurr and Mark Stitt},
	editor = {Hans-Peter Seidel and B. Girod and H. Niemann}
}
@conference {haussecker1997,
	title = {A tensor approach for precise computation of dense displacement vector fields},
	booktitle = {Proceedings of the 19th DAGM Symposium on Pattern Recognition, Braunschweig},
	year = {1997},
	note = {DAGM award},
	pages = {199--208},
	publisher = {Springer},
	organization = {Springer},
	doi = {10.1007/978-3-642-60893-3_20},
	author = {Horst Hau{\ss}ecker and Bernd J{\"a}hne},
	editor = {E. Paulus and F. M. Wahl}
}
@conference {Peckar-et-al-97a,
	title = {Two-Step Parameter-Free Elastic Image Registration with Prescribed Point Displacements},
	booktitle = {Proc. 9th Int. Conf. on Image Analysis and Processing (ICIAP{\textquoteright}97)},
	year = {1997},
	month = {Sept. 17{\textendash}19},
	address = {Florence, Italy},
	author = {Peckar, W. and Schn{\"o}rr, C. and Rohr, K. and Stiehl, H.S.}
}
@conference {waas1996,
	title = {Combined height/slope/curvature measurements of short ocean wind waves},
	booktitle = {Proc.\ The Air-Sea Interface, Radio and Acoustic Sensing, Turbulence and Wave Dynamics, Marseille, 24--30. June 1993},
	year = {1996},
	pages = {383--388},
	publisher = {RSMAS, University of Miami},
	organization = {RSMAS, University of Miami},
	doi = {10.5281/zenodo.14000},
	author = {Stefan Waas and Bernd J{\"a}hne},
	editor = {M. A. Donelan and W. H. Hui and W. J. Plant}
}
@conference {hering1996b,
	title = {Combined wave and flow field visualization for investigation of short-wave/long-wave interaction},
	booktitle = {Proc.\ The Air-Sea Interface, Radio and Acoustic Sensing, Turbulence and Wave Dynamics, Marseille, 24--30. June 1993},
	year = {1996},
	pages = {133--138},
	publisher = {RSMAS, University of Miami},
	organization = {RSMAS, University of Miami},
	doi = {10.5281/zenodo.14002},
	author = {Frank Hering and Dietmar Wierzimok and W. K. Melville and Bernd J{\"a}hne},
	editor = {M. A. Donelan and W. H. Hui and W. J. Plant}
}
@conference {spedding1996,
	title = {Estimating $\omega(k)$ in an unsteady, wind-generated surface wave field from the 2D complex wavelet transform of the surface slope},
	booktitle = {Proc.\ The Air-Sea Interface, Radio and Acoustic Sensing, Turbulence and Wave Dynamics, Marseille, 24--30. June 1993},
	year = {1996},
	pages = {373--382},
	publisher = {RSMAS, University of Miami},
	organization = {RSMAS, University of Miami},
	doi = {10.5281/zenodo.14564},
	author = {G. R. Spedding and J. Klinke and S. R. Long},
	editor = {M. A. Donelan and W. H. Hui and W. J. Plant}
}
@conference {muensterer1996a,
	title = {A fluorescence technique to measure concentration profiles in the aqueous mass boundary layer},
	booktitle = {Proc.\ The Air-Sea Interface, Radio and Acoustic Sensing, Turbulence and Wave Dynamics, Marseille, 24--30. June 1993},
	year = {1996},
	pages = {517--522},
	publisher = {RSMAS, University of Miami},
	organization = {RSMAS, University of Miami},
	doi = {10.5281/zenodo.13995},
	author = {Thomas M{\"u}nsterer and Bernd J{\"a}hne},
	editor = {M. A. Donelan and W. H. Hui and W. J. Plant}
}
@conference {jaehne1996b,
	title = {Measurements of the modulation of short waves from image sequences},
	booktitle = {Proc.\ The Air-Sea Interface, Radio and Acoustic Sensing, Turbulence and Wave Dynamics, Marseille, 24--30. June 1993},
	year = {1996},
	pages = {389--394},
	publisher = {RSMAS, University of Miami},
	organization = {RSMAS, University of Miami},
	doi = {10.5281/zenodo.13996},
	author = {Bernd J{\"a}hne},
	editor = {M. A. Donelan and W. H. Hui and W. J. Plant}
}
@conference {jaehne1996a,
	title = {The role of active vision in exploring growth, transport, and exchange processes},
	booktitle = {Aktives Sehen in technischen und biologischen Systemen, Workshop der GI-Fachgruppe 1.0.4. Bildverstehen Hamburg, 3--4. December 1996},
	volume = {4},
	year = {1996},
	pages = {194--202},
	publisher = {infix},
	organization = {infix},
	author = {Bernd J{\"a}hne and Horst Hau{\ss}ecker and Frank Hering and G{\"u}nther Balschbach and J. Klinke and Martin Lell and Dominik Schmund and Michael Schultz and Ulrich Schurr and Mark Stitt and Ulrich Platt},
	editor = {B Mertsching}
}
@article {schurr1996,
	title = {Structural and functional evidence for xylem-mediated water transport and high tranpiration in Agrobacterium tumefaciens-induced tumors of Ricinus communis},
	journal = {Botanica Acta},
	volume = {109},
	year = {1996},
	pages = {405--412},
	doi = {10.1111/j.1438-8677.1996.tb00590.x},
	author = {Ulrich Schurr and B. Schuberth and R. Aloni and K. S. Pradel and Dominik Schmund and Bernd J{\"a}hne and C. I. Ullrich}
}
@conference {janssen1996,
	title = {The VIERS scatterometer algorithm},
	booktitle = {Proc.\ The Air-Sea Interface, Radio and Acoustic Sensing, Turbulence and Wave Dynamics, Marseille, 24--30. June 1993},
	year = {1996},
	pages = {749--754},
	publisher = {RSMAS, University of Miami},
	organization = {RSMAS, University of Miami},
	doi = {10.5281/zenodo.13994},
	author = {J. A. M. Janssen and C. J. Calkoen and van Halsema, D. and Bernd J{\"a}hne and P. A. E. M. Janssen and W. A. Oost and P. Snoeij and J. Vogelzang and H. Wallbrink},
	editor = {M. A. Donelan and W. H. Hui and W. J. Plant}
}
@conference {klinke1996a,
	title = {Wave number spectra of short wind waves: implications from laboratory studies},
	booktitle = {Proc.\ The Air-Sea Interface, Radio and Acoustic Sensing, Turbulence and Wave Dynamics, Marseille, 24--30. June 1993},
	year = {1996},
	pages = {367--372},
	publisher = {RSMAS, University of Miami},
	organization = {RSMAS, University of Miami},
	doi = {10.5281/zenodo.14001},
	author = {J. Klinke and Bernd J{\"a}hne},
	editor = {M. A. Donelan and W. H. Hui and W. J. Plant}
}
@conference {jaehne1995a,
	title = {An imaging optical technique for bubble measurements},
	booktitle = {Proc. Sea Surface Sound {\textquoteright}94},
	year = {1995},
	pages = {290--296},
	publisher = {World Scientific},
	organization = {World Scientific},
	doi = {10.1142/9789814447102_0019},
	author = {Bernd J{\"a}hne and Peter Gei{\ss}ler},
	editor = {Buckingham, M. J. and Potter, J. R.}
}
@conference {Schnoerr-Peckar-95,
	title = {Motion-Based Identification of Deformable Templates},
	booktitle = {Proc. 6th Int. Conf. on Computer Analysis of Images and Patterns (CAIP {\textquoteright}95)},
	series = {Lect. Notes in Comp. Sci.},
	volume = {970},
	year = {1995},
	month = {Sept. 6-8},
	pages = {122-129},
	publisher = {Springer Verlag},
	organization = {Springer Verlag},
	address = {Prague, Czech Republic},
	author = {Schn{\"o}rr, C. and Peckar, W.},
	editor = {V. Hlav{\'a}{\v c}, R. {\v S}{\'a}ra}
}
@conference {scheuermann1995,
	title = {Oberfl{\"a}chenkonturvermessung mikroskopischer Objekte durch Projektion statistischer Rauschmuster},
	booktitle = {Proc. 17. DAGM-Symposium Mustererkennung, Bielefeld, 13.-15. September 1995},
	year = {1995},
	pages = {319--326},
	author = {Scheuermann, T. and Pfundt, G. and Eyerer, P. and Bernd J{\"a}hne}
}
@conference {geissler1993a,
	title = {Depth-from-focus zur Bestimmung der Konzentration und Gr{\"o}{\ss}e von Gasblasen},
	booktitle = {Proc. 15. DAGM-Symposium Mustererkennung},
	year = {1993},
	note = {DAGM award},
	pages = {560--567},
	publisher = {Springer},
	organization = {Springer},
	author = {Peter Gei{\ss}ler and Bernd J{\"a}hne and S. J. P{\"o}ppl},
	editor = {H. Handels}
}
@conference {Sprengel-Schnoerr-dagm-93,
	title = {Nichtlineare Diffusion zur Integration visueller Daten - Anwendung auf Kernspintomogramme},
	booktitle = {Mustererkennung 1993, 15. DAGM-Symposium},
	year = {1993},
	pages = {134{\textendash}141},
	publisher = {Springer Verlag},
	organization = {Springer Verlag},
	author = {Sprengel, R. and Schn{\"o}rr, C.},
	editor = {P{\"o}ppl, S.J. and Handels, H.}
}
@conference {janssen1993,
	title = {The VIERS scatterometer algorithm},
	booktitle = {Proc. The Air-Sea Interface, Radio and Acoustic Sensing, Turbulence and Wave Dynamics, Marseille, 24--30. June 1993},
	year = {1993},
	pages = {749--754},
	publisher = {University of Miami},
	organization = {University of Miami},
	doi = {10.5281/zenodo.13994},
	author = {J. A. M. Janssen and C. J. Calkoen and van Halsema, D. and Bernd J{\"a}hne and P. A. E. M. Janssen and W. A. Oost and P. Snoeij and J. Vogelzang and H. Wallbrink},
	editor = {M. A. Donelan and W. H. Hui and W. J. Plant}
}
@article {jaehne1989a,
	title = {Investigating the transfer process across the free aqueous boundary layer by the controlled flux method},
	journal = {Tellus},
	volume = {41B},
	number = {2},
	year = {1989},
	pages = {177--195},
	abstract = {Theory and experimental results of a new method are described directly investigating the transfer processes across the aqueous viscous boundary layer. The method is based on a known and controllable flux density being applied at the interface. Then the local transfer velocity can be determined by monitoring the tracer concentration at the water surface within minutes. Moreover, the time constant for the transport across the boundary layer ("surface renewal time") can be measured directly. Comparison of the theoretical and measured frequency response of the boundary layer yields significant deviations. The technique is put into operation for heat transfer measurements. Direct comparisons with gas exchange measurements in several wind/wave facilities verify that the gas transfer velocity can be accurately extrapolated from the heat transfer measurements. A new way is opened both for detailed studies of the transfer processes in wind/wave facilities and the urgently needed direct parameterization of the transfer velocity as a function of windshear, wave parameters, and water turbulence in natural systems as rivers, lakes and the ocean. This paper includes (as a first example) measurements on the fetch dependency of the transfer process.},
	doi = {10.1111/j.1600-0889.1989.tb00135.x},
	author = {Bernd J{\"a}hne and P. Libner and Fischer, R. and Thomas Billen and Erich J. Plate}
}
@conference {wierzimok1987,
	title = {Bildfolgenanalyse dreidimensionaler turbulenter Str{\"o}mungen},
	booktitle = {Proc. 9. DAGM-Symposium zur Mustererkennung 1987},
	volume = {149},
	year = {1987},
	pages = {288},
	publisher = {Springer},
	organization = {Springer},
	doi = {10.1007/978-3-662-22205-8_71},
	author = {Dietmar Wierzimok and Bernd J{\"a}hne and J. Dengler},
	editor = {E. Paulus}
}
@article {libner1987a,
	title = {Ein neue Methode zur lokalen und momentanen Bestimmung der Wiederbel{\"u}ftungsraten von Gew{\"a}ssern},
	journal = {Wasserwirtschaft},
	volume = {77},
	number = {5},
	year = {1987},
	pages = {230--235},
	doi = {10.5281/zenodo.13129},
	author = {P. Libner and Bernd J{\"a}hne and Erich J. Plate}
}
@conference {jaehne1987c,
	title = {Neue Ans{\"a}tze zur Bildfolgenanalyse},
	booktitle = {Proc. 9. DAGM-Symposium zur Mustererkennung 1987},
	volume = {149},
	year = {1987},
	pages = {287},
	publisher = {Springer},
	organization = {Springer},
	doi = {10.1007/978-3-662-22205-8_70},
	author = {Bernd J{\"a}hne},
	editor = {E. Paulus}
}
