@article {7032,
	title = {A Digital 3D Reference Atlas Reveals Cellular Growth Patterns Shaping the Arabidopsis Ovule},
	journal = {eLife},
	year = {2021},
	doi = {10.7554/eLife.63262},
	author = {Vijayan, A. and Tofanelli, R and Strauss, S and Cerrone, L and Wolny, A and Strohmeier, J and Kreshuk, A and Fred A. Hamprecht and Smith, R S and Schneitz, K}
}
@article {7086,
	title = {Integration of Cell Growth and Asymmetric Division during Lateral Root Initiation in Arabidopsis thaliana},
	journal = {Plant and Cell Physiology},
	volume = {62},
	year = {2021},
	pages = {1269-1279},
	doi = {10.1093/pcp/pcab038},
	author = {Sch{\"u}tz, LM and Louveaux, M and Vilches-Barro, A and Bouziri, S and Cerrone, L and Wolny, A and Kreshuk, A and Hamprecht, FA and Maizel, A}
}
@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}
}
@conference {Radev2020,
	title = {BayesFlow: Learning complex stochastic models with invertible neural networks},
	year = {2020},
	abstract = {Estimating the parameters of mathematical models is a common problem in almost all branches of science. However, this problem can prove notably difficult when processes and model descriptions become increasingly complex and an explicit likelihood function is not available. With this work, we propose a novel method for globally amortized Bayesian inference based on invertible neural networks which we call BayesFlow. The method uses simulation to learn a global estimator for the probabilistic mapping from observed data to underlying model parameters. A neural network pre-trained in this way can then, without additional training or optimization, infer full posteriors on arbitrary many real data sets involving the same model family. In addition, our method incorporates a summary network trained to embed the observed data into maximally informative summary statistics. Learning summary statistics from data makes the method applicable to modeling scenarios where standard inference techniques with hand-crafted summary statistics fail. We demonstrate the utility of BayesFlow on challenging intractable models from population dynamics, epidemiology, cognitive science and ecology. We argue that BayesFlow provides a general framework for building reusable Bayesian parameter estimation machines for any process model from which data can be simulated.},
	url = {http://arxiv.org/abs/2003.06281},
	author = {Radev, Stefan T. and Mertens, Ulf K. and Voss, Andreass and Lynton Ardizzone and K{\"o}the, Ullrich}
}
@incollection {jaehne2020,
	title = {What controls air-sea gas exchange at extreme wind speeds? Evidence from laboratory experiments},
	year = {2020},
	pages = {133{\textendash}150},
	publisher = {Springer},
	doi = {10.1007/978-3-030-36371-0_10},
	author = {Bernd J{\"a}hne},
	editor = {P. Vlahos and E. Monahan}
}
@conference {Adler2019,
	title = {Out of Distribution Detection for Intra-operative Functional Imaging},
	booktitle = {MICCAI UNSURE Workshop 2019},
	volume = {11840 LNCS},
	year = {2019},
	pages = {75{\textendash}82},
	abstract = {Multispectral optical imaging is becoming a key tool in the operating room. Recent research has shown that machine learning algorithms can be used to convert pixel-wise reflectance measurements to tissue parameters, such as oxygenation. However, the accuracy of these algorithms can only be guaranteed if the spectra acquired during surgery match the ones seen during training. It is therefore of great interest to detect so-called out of distribution (OoD) spectra to prevent the algorithm from presenting spurious results. In this paper we present an information theory based approach to OoD detection based on the widely applicable information criterion (WAIC). Our work builds upon recent methodology related to invertible neural networks (INN). Specifically, we make use of an ensemble of INNs as we need their tractable Jacobians in order to compute the WAIC. Comprehensive experiments with in silico, and in vivo multispectral imaging data indicate that our approach is well-suited for OoD detection. Our method could thus be an important step towards reliable functional imaging in the operating room.},
	issn = {16113349},
	doi = {10.1007/978-3-030-32689-0_8},
	author = {Adler, Tim J and Ayala, Leonardo and Lynton Ardizzone and Kenngott, Hannes G and Vemuri, Anant and M{\"u}ller-Stich, Beat P and Carsten Rother and Ullrich K{\"o}the and Maier-Hein, Lena}
}
@mastersthesis {voigt2019,
	title = {Simulation and Measurement of the Water-sided Viscous Shear Stress without Waves},
	volume = {Bachelor},
	year = {2019},
	school = {Institut f{\"u}r Umweltphysik, Universit{\"a}t Heidelberg, Germany},
	type = {Bachelor{\textquoteright}s thesis},
	doi = {10.11588/heidok.00026653},
	author = {Philipp Voigt}
}
@conference {Hodan2018,
	title = {BOP: Benchmark for 6D object pose estimation},
	booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {11214 LNCS},
	year = {2018},
	month = {aug},
	pages = {19{\textendash}35},
	abstract = {We propose a benchmark for 6D pose estimation of a rigid object from a single RGB-D input image. The training data consists of a texture-mapped 3D object model or images of the object in known 6D poses. The benchmark comprises of: (i) eight datasets in a unified format that cover different practical scenarios, including two new datasets focusing on varying lighting conditions, (ii) an evaluation methodology with a pose-error function that deals with pose ambiguities, (iii) a comprehensive evaluation of 15 diverse recent methods that captures the status quo of the field, and (iv) an online evaluation system that is open for continuous submission of new results. The evaluation shows that methods based on point-pair features currently perform best, outperforming template matching methods, learning-based methods and methods based on 3D local features. The project website is available at bop.felk.cvut.cz.},
	isbn = {9783030012489},
	issn = {16113349},
	doi = {10.1007/978-3-030-01249-6_2},
	url = {http://arxiv.org/abs/1808.08319},
	author = {Hoda{\v n}, Tom{\'a}{\v s} and Michel, Frank and Brachmann, Eric and Kehl, Wadim and Buch, Anders Glent and Kraft, Dirk and Drost, Bertram and Vidal, Joel and Ihrke, Stephan and Zabulis, Xenophon and Sahin, Caner and Manhardt, Fabian and Tombari, Federico and Kim, Tae Kyun and Matas, Ji{\v r}{\'\i} and Carsten Rother}
}
@proceedings {6272,
	title = {Essentially No Barriers in Neural Network Energy Landscape},
	volume = {80},
	year = {2018},
	pages = {1308--1317},
	author = {Draxler, F and Veschgini, K and Salmhofer, M and Fred A. Hamprecht}
}
@conference {vianello2018,
	title = {Robust Hough transform based 3D reconstruction from circular light fields},
	booktitle = {Conference on Computer Vision and Pattern Recognition (CVPR)},
	year = {2018},
	doi = {10.1109/CVPR.2018.00765},
	author = {Alessandro Vianello and Jens Ackermann and Maximilian Diebold and Bernd J{\"a}hne}
}
@article {Vianello-etal-2017-TM,
	title = {3D reconstruction by a combined structure tensor and Hough transform light field approach},
	journal = {tm - Technisches Messen},
	year = {2017},
	abstract = {Disparity estimation using the structure tensor is a local approach to determine orientation in Epipolar Plane Images. A global extension would lead to more precise and robust estimations. In this work, a novel algorithm for 3D reconstruction from linear light fields is proposed. This method uses a modified version of the Progressive Probabilistic Hough Transform to extract orientations from Epipolar Plane Images, allowing to achieve high quality disparity maps. To this aim, the structure tensor estimates are used to speed up computation and improve the disparity estimation near occlusion boundaries. The new algorithm is evaluated on both synthetic and real light field datasets, and compared with classical local disparity estimation techniques based on the structure tensor.},
	doi = {10.1515/teme-2017-0010},
	author = {Alessandro Vianello and Giulio Manfredi and Maximilian Diebold and Bernd J{\"a}hne}
}
@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.}
}
@phdthesis {vianello207,
	title = {Robust 3D Surface Reconstruction from Light Fields},
	volume = {Dissertation},
	year = {2017},
	publisher = {IWR, Univ. Heidelberg},
	type = {phdDissertation},
	doi = {10.11588/heidok.00023819},
	author = {Alessandro Vianello}
}
@phdthesis {vonschmude2017,
	title = {Visual Localization with Lines},
	volume = {Dissertation},
	year = {2017},
	publisher = {IWR, Univ. Heidelberg},
	type = {phd},
	doi = {10.11588/heidok.00023524},
	author = {Najy von Schmude}
}
@proceedings {schilling-etal-2016-ForumBildverarbeitung,
	title = {3D Reconstruction by a Combined Structure Tensor and Hough Transform Light-Field Approach},
	year = {2016},
	abstract = {Disparity estimation using the structure tensor is a local approach to determine orientation in Epipolar Plane Images. A global extension would lead to more precise and robust estimations. In this work, a novel algorithm for 3D reconstruction from linear light fields is porposed. It uses a modified Progressive Probabilistic Hough Transform, in combination with the structure tensor, to extract orientations from Epipolar Plane Images edge maps, allowing to achieve high quality disparity maps.},
	isbn = {978-3-7315-0587-7},
	doi = {10.5445/KSP/1000059899},
	url = {https://doi.org/10.5445/KSP/1000059899},
	author = {Alessandro Vianello and Giulio Manfredi and Maximilian Diebold and Bernd J{\"a}hne}
}
@proceedings {6080,
	title = {Gaussian process density counting from weak supervision},
	volume = {LNCS 9905},
	year = {2016},
	pages = {365-380 },
	publisher = {Springer},
	doi = { 	10.1007/978-3-319-46448-0_22},
	author = {M. von Borstel and Kandemir, M and Schmidt, P and Rao, M and Rajamani, K and Fred A. Hamprecht}
}
@mastersthesis {6028,
	title = {Learning to Count from Weak Supervision},
	year = {2016},
	school = {University of Heidelberg},
	author = {M. von Borstel}
}
@conference {visapp16vonSchmude,
	title = {Relative Pose Estimation from Straight Lines using Parallel Line Clustering and its Application to Monocular Visual Odometry},
	booktitle = {Proceedings of the 11th Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications},
	year = {2016},
	abstract = {This paper tackles the problem of relative pose estimation between two monocular camera images in textureless scenes. Due to a lack of point matches, point-based approaches such as the 5-point algorithm often fail when used in these scenarios. Therefore we investigate relative pose estimation from line observations. We propose a new approach in which the relative pose estimation from lines is extended by a 3D line direction estimation step. The estimated line directions serve to improve the robustness and the efficiency of all processing phases: they enable us to guide the matching of line features and allow an efficient calculation of the relative pose. First, we describe in detail the novel 3D line direction estimation from a single image by clustering of parallel lines in the world. Secondly, we propose an innovative guided matching in which only clusters of lines with corresponding 3D line directions are considered. Thirdly, we introduce the new relative pose estimation based on 3 D line directions. Finally, we combine all steps to a visual odometry system. We evaluate the different steps on synthetic and real sequences and demonstrate that in the targeted scenarios we outperform the state-of-the-art in both accuracy and computation time.},
	isbn = {978-989-758-175-5},
	doi = {10.5220/0005661404210431},
	author = {Naja von Schmude and Pierre Lothe and Bernd J{\"a}hne}
}
@proceedings {6079,
	title = {Variational weakly-supervised Gaussian processes},
	year = {2016},
	author = {Kandemir, M and Manuel Hau{\ss}mann and Ferran Diego and Rajamani, K and van der Laak, J and Fred A. Hamprecht}
}
@conference {Biesdorf2015,
	title = {3D Segmentation of Vessels by Incremental Implicit Polynomial Fitting and Convex Optimization},
	booktitle = {Proc.~ISBI},
	year = {2015},
	author = {Biesdorf, A. and W{\"o}rz, S. and von Tengg-Kobligk, H. and Karl Rohr 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}
}
@conference {Kirillov2015a,
	title = {Inferring M-best diverse labelings in a single one},
	booktitle = {Proceedings of the IEEE International Conference on Computer Vision},
	volume = {2015 Inter},
	year = {2015},
	pages = {1814{\textendash}1822},
	abstract = {We consider the task of finding M-best diverse solutions in a graphical model. In a previous work by Batra et al. an algorithmic approach for finding such solutions was proposed, and its usefulness was shown in numerous applications. Contrary to previous work we propose a novel formulation of the problem in form of a single energy minimization problem in a specially constructed graphical model. We show that the method of Batra et al. can be considered as a greedy approximate algorithm for our model, whereas we introduce an efficient specialized optimization technique for it, based on alpha-expansion. We evaluate our method on two application scenarios, interactive and semantic image segmentation, with binary and multiple labels. In both cases we achieve considerably better error rates than state-of-the art diversity methods. Furthermore, we empirically discover that in the binary label case we were able to reach global optimality for all test instances.},
	isbn = {9781467383912},
	issn = {15505499},
	doi = {10.1109/ICCV.2015.211},
	author = {Kirillov, Alexander and Savchynskyy, Bogdan and Schlesinger, Dmitrij and Vetrov, Dmitry and Carsten Rother}
}
@conference {Kirillov2015,
	title = {M-best-diverse labelings for submodular energies and beyond},
	booktitle = {Advances in Neural Information Processing Systems},
	volume = {2015-Janua},
	year = {2015},
	pages = {613{\textendash}621},
	abstract = {We consider the problem of findingM best diverse solutions of energy minimization problems for graphical models. Contrary to the sequential method of Batra et al., which greedily finds one solution after another, we infer all M solutions jointly. It was shown recently that such jointly inferred labelings not only have smaller total energy but also qualitatively outperform the sequentially obtained ones. The only obstacle for using this new technique is the complexity of the corresponding inference problem, since it is considerably slower algorithm than the method of Batra et al. In this work we show that the joint inference of M best diverse solutions can be formulated as a submodular energy minimization if the original MAP-inference problem is submodular, hence fast inference techniques can be used. In addition to the theoretical results we provide practical algorithms that outperform the current state-of-the-art and can be used in both submodular and non-submodular case.},
	issn = {10495258},
	author = {Kirillov, Alexander and Schlesinger, Dmitrij and Vetrov, Dmitry and Carsten Rother and Savchynskyy, Bogdan}
}
@conference {Zheng2014,
	title = {Dense semantic image segmentation with objects and attributes},
	booktitle = {Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition},
	year = {2014},
	pages = {3214{\textendash}3221},
	abstract = {The concepts of objects and attributes are both important for describing images precisely, since verbal descriptions often contain both adjectives and nouns (e.g. {\textquoteright}I see a shiny red chair{\textquoteright}). In this paper, we formulate the problem of joint visual attribute and object class image segmentation as a dense multi-labelling problem, where each pixel in an image can be associated with both an object-class and a set of visual attributes labels. In order to learn the label correlations, we adopt a boosting-based piecewise training approach with respect to the visual appearance and co-occurrence cues. We use a filtering-based mean-field approximation approach for efficient joint inference. Further, we develop a hierarchical model to incorporate region-level object and attribute information. Experiments on the aPASCAL, CORE and attribute augmented NYU indoor scenes datasets show that the proposed approach is able to achieve state-of-the-art results.},
	keywords = {Attributes, Image segmentation, Object recognition, Scene Understanding},
	isbn = {9781479951178},
	issn = {10636919},
	doi = {10.1109/CVPR.2014.411},
	url = {http://www.robots.ox.ac.uk/\~{}tvg/http://tu-dresden.de/inf/cvld},
	author = {Zheng, Shuai and Cheng, Ming Ming and Warrell, Jonathan and Sturgess, Paul and Vineet, Vibhav and Carsten Rother and Torr, Philip H.S.}
}
@article {kandemir_14_multi-task,
	title = {Multi-task and multi-view learning of user state},
	journal = {Neurocomputing},
	volume = {139},
	year = {2014},
	pages = {97-106},
	doi = {10.1016/j.neucom.2014.02.057},
	author = {Kandemir, M. and Klami, A. and Gonen, M. and Vetek, A. and Kaski, S}
}
@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}
}
@conference {esparza2014,
	title = {Registration of a multi-camera system with a 3D laser range finder},
	booktitle = {9th Workshop Driver Assistance Systems (FAS2014), 26.-28.03.2014, Walting},
	year = {2014},
	pages = {37--46},
	url = {http://www.uni-das.de/de/Veranstaltungen/fas2014.php},
	author = {Esparza, Jose and Vepa, Leo and Helmle, Michael and Bernd J{\"a}hne}
}
@conference {Vineet2013,
	title = {Higher order priors for joint intrinsic image, objects, and attributes estimation},
	booktitle = {Advances in Neural Information Processing Systems},
	year = {2013},
	abstract = {Many methods have been proposed to solve the problems of recovering intrinsic scene properties such as shape, reflectance and illumination from a single image, and object class segmentation separately. While these two problems are mutually informative, in the past not many papers have addressed this topic. In this work we explore such joint estimation of intrinsic scene properties recovered from an image, together with the estimation of the objects and attributes present in the scene. In this way, our unified framework is able to capture the correlations between intrinsic properties (reflectance, shape, illumination), objects (table, tv-monitor), and materials (wooden, plastic) in a given scene. For example, our model is able to enforce the condition that if a set of pixels take same object label, e.g. table, most likely those pixels would receive similar reflectance values. We cast the problem in an energy minimization framework and demonstrate the qualitative and quantitative improvement in the overall accuracy on the NYU and Pascal datasets.},
	issn = {10495258},
	author = {Vineet, Vibhav and Carsten Rother and Torr, Philip H.S.}
}
@article {voss2012exp,
	title = {Bichromatic Particle Streak Velocimetry bPSV -- Interfacial, v3C3D velocimetry using a single camera},
	journal = {Exp. Fluids},
	year = {2012},
	note = {Submitted},
	author = {Bj{\"o}rn Voss and Julian Stapf and A. Berthe and Christoph S. Garbe}
}
@phdthesis {voss2012,
	title = {Novel Single Camera Techniques for 3D3C Lagrangian Trajectory Measurements in Interfacial Flows},
	year = {2012},
	note = {started 01.02.2009},
	publisher = {IWR, Fakult{\"a}t f{\"u}r Physik und Astronomie, Univ.\ Heidelberg},
	url = {http://www.ub.uni-heidelberg.de/archiv/13362},
	author = {Bj{\"o}rn Voss}
}
@incollection {garbe2012,
	title = {Plenoptic Particle Streak Velocimetry (pPSV): 3D3C fluid flow measurement from light fields with a single plenoptic camera},
	year = {2012},
	pages = {1-12},
	publisher = {Instituto Superior T{\'e}cnico},
	author = {Christoph S. Garbe and Bj{\"o}rn Voss and Julian Stapf}
}
@conference {Mansfield2012,
	title = {Visibility maps for improving seam carving},
	booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {6554 LNCS},
	number = {PART 2},
	year = {2012},
	pages = {131{\textendash}144},
	abstract = {In this paper, we present a new, improved seam carving algorithm. Seam carving efficiently removes pixels from an image to produce a retargeted image. It has proved popular with users and has been used as a component in many retargeting algorithms. We introduce the visibility map, a new framework for pixel removing image editing methods. This allows us to cast retargeting as a binary graph labelling problem. We derive a general algorithm which uses seam carving operations for efficient greedy optimization of a well defined energy, and compare this with forward energy seam carving and shift map image editing. We test this method with varying parameters on a large number of images, and present an improved seam carving algorithm which can demonstrably produce better results. We draw general conclusions about pixel removing methods for retargeting and motivate future directions of research. {\textcopyright} 2012 Springer-Verlag.},
	isbn = {9783642357398},
	issn = {03029743},
	doi = {10.1007/978-3-642-35740-4_11},
	url = {http://www.adobe.com/products/photoshop/photoshopextended/features/},
	author = {Mansfield, Alex and Gehler, Peter and Van Gool, Luc and Carsten Rother}
}
@conference {Vicente2011,
	title = {Object cosegmentation},
	booktitle = {Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition},
	year = {2011},
	pages = {2217{\textendash}2224},
	abstract = {Cosegmentation is typically defined as the task of jointly segmenting something similar in a given set of images. Existing methods are too generic and so far have not demonstrated competitive results for any specific task. In this paper we overcome this limitation by adding two new aspects to cosegmentation: (1) the "something" has to be an object, and (2) the "similarity" measure is learned. In this way, we are able to achieve excellent results on the recently introduced iCoseg dataset, which contains small sets of images of either the same object instance or similar objects of the same class. The challenge of this dataset lies in the extreme changes in viewpoint, lighting, and object deformations within each set. We are able to considerably outperform several competitors. To achieve this performance, we borrow recent ideas from object recognition: the use of powerful features extracted from a pool of candidate object-like segmentations. We believe that our work will be beneficial to several application areas, such as image retrieval. {\textcopyright} 2011 IEEE.},
	isbn = {9781457703942},
	issn = {10636919},
	doi = {10.1109/CVPR.2011.5995530},
	author = {Vicente, Sara and Carsten Rother and Kolmogorov, Vladimir}
}
@article {hanselmann_11_sima,
	title = {SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists},
	journal = {Bioinformatics},
	volume = {27 (7)},
	year = {2011},
	note = {1},
	pages = {987-993},
	doi = {10.1093/bioinformatics/btr051},
	author = {Hanselmann, M. and Bj{\"o}rn Voss and B. Y. Renard and Lindner, M. and Ullrich K{\"o}the and Kirchner, M. and Fred A. Hamprecht}
}
@conference {becker_11_variational,
	title = {Variational Recursive Joint Estimation of Dense Scene Structure and
Camera Motion from Monocular High Speed Traffic Sequences},
	booktitle = {2011 IEEE International Conference on Computer Vision ICCV},
	year = {2011},
	note = {1},
	pages = {1692-1699},
	doi = {10.1109/ICCV.2011.6126432},
	author = {Florian Becker and Frank Lenzen and J{\"o}rg H. Kappes and Christoph Schn{\"o}rr},
	editor = {Metaxas, D. N. and Quan, L. and Van Gool, L. J. and Sanfeliu, A.}
}
@conference {Vicente2010,
	title = {Cosegmentation revisited: Models and optimization},
	booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {6312 LNCS},
	number = {PART 2},
	year = {2010},
	pages = {465{\textendash}479},
	abstract = {The problem of cosegmentation consists of segmenting the same object (or objects of the same class) in two or more distinct images. Recently a number of different models have been proposed for this problem. However, no comparison of such models and corresponding optimization techniques has been done so far. We analyze three existing models: the L1 norm model of Rother et al. [1], the L2 norm model of Mukherjee et al. [2] and the "reward" model of Hochbaum and Singh [3]. We also study a new model, which is a straightforward extension of the Boykov-Jolly model for single image segmentation [4]. In terms of optimization, we use a Dual Decomposition (DD) technique in addition to optimization methods in [1,2]. Experiments show a significant improvement of DD over published methods. Our main conclusion, however, is that the new model is the best overall because it: (i) has fewest parameters; (ii) is most robust in practice, and (iii) can be optimized well with an efficient EM-style procedure. {\textcopyright} 2010 Springer-Verlag.},
	isbn = {3642155510},
	issn = {16113349},
	doi = {10.1007/978-3-642-15552-9_34},
	author = {Vicente, Sara and Kolmogorov, Vladimir and Carsten Rother}
}
@conference {voss2010,
	title = {A new approach for 3C3D measurements of aqueous boundary layer flows relative to the wind-wave undulated interface},
	booktitle = {6th Int. Symp. Gas Transfer at Water Surfaces, Kyoto, May 17--21, 2010},
	year = {2010},
	note = {poster},
	doi = {10.5281/zenodo.14930},
	author = {Bj{\"o}rn Voss and Alexander Heinlein and Bernd J{\"a}hne and Christoph S. Garbe}
}
@conference {voss2010a,
	title = {Novel strategy for water sided interfacial 3D3Cflow-visualization using a single camera},
	booktitle = {14th International Symposium on Flow Visualization},
	year = {2010},
	pages = {D1-018},
	author = {Bj{\"o}rn Voss and Christoph S. Garbe}
}
@article {Vlasenko-Schnoerr-10,
	title = {Physically Consistent and Efficient Variational Denoising of Image Fluid Flow Estimates},
	journal = {IEEE Trans.~Image Proc.},
	volume = {19},
	number = {3},
	year = {2010},
	pages = {586-595},
	author = {Vlasenko, A. and Christoph Schn{\"o}rr}
}
@article {Vlasenko-Schnoerr-10,
	title = {Physically Consistent and Efficient Variational Denoising of Image Fluid Flow Estimates},
	journal = {IEEE Trans. Image Proc.},
	volume = {19},
	number = {3},
	year = {2010},
	pages = {586-595},
	author = {Vlasenko, A. and Schn{\"o}rr, C.}
}
@conference {Mansfield2010,
	title = {Scene carving: Scene consistent image retargeting},
	booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
	volume = {6311 LNCS},
	number = {PART 1},
	year = {2010},
	pages = {143{\textendash}156},
	abstract = {Image retargeting algorithms often create visually disturbing distortion. We introduce the property of scene consistency, which is held by images which contain no object distortion and have the correct object depth ordering. We present two new image retargeting algorithms that preserve scene consistency. These algorithms make use of a user-provided relative depth map, which can be created easily using a simple GrabCut-style interface. Our algorithms generalize seam carving. We decompose the image retargeting procedure into (a) removing image content with minimal distortion and (b) re-arrangement of known objects within the scene to maximize their visibility. Our algorithms optimize objectives (a) and (b) jointly. However, they differ considerably in how they achieve this. We discuss this in detail and present examples illustrating the rationale of preserving scene consistency in retargeting. {\textcopyright} 2010 Springer-Verlag.},
	isbn = {3642155480},
	issn = {16113349},
	doi = {10.1007/978-3-642-15549-9_11},
	url = {www.fujifilm.com/products/3d/camera/finepix_},
	author = {Mansfield, Alex and Gehler, Peter and Van Gool, Luc and Carsten Rother}
}
@conference {lauer_09_continuous,
	title = {A Continuous Optimization Framework for Hybrid System Identification},
	booktitle = {submitted to Automatica},
	year = {2009},
	author = {Lauer, F. and Bloch, G. and Vidal, R.}
}
@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}
}
@conference {Vicente2009,
	title = {Joint optimization of segmentation and appearance models},
	booktitle = {Proceedings of the IEEE International Conference on Computer Vision},
	year = {2009},
	pages = {755{\textendash}762},
	abstract = {Many interactive image segmentation approaches use an objective function which includes appearance models as an unknown variable. Since the resulting optimization problem is NP-hard the segmentation and appearance are typically optimized separately, in an EM-style fashion. One contribution of this paper is to express the objective function purely in terms of the unknown segmentation, using higher-order cliques. This formulation reveals an interesting bias of the model towards balanced segmentations. Furthermore, it enables us to develop a new dual decomposition optimization procedure, which provides additionally a lower bound. Hence, we are able to improve on existing optimizers, and verify that for a considerable number of real world examples we even achieve global optimality. This is important since we are able, for the first time, to analyze the deficiencies of the model. Another contribution is to establish a property of a particular dual decomposition approach which involves convex functions depending on foreground area. As a consequence, we show that the optimal decomposition for our problem can be computed efficiently via a parametric maxflow algorithm. {\textcopyright}2009 IEEE.},
	isbn = {9781424444205},
	doi = {10.1109/ICCV.2009.5459287},
	author = {Vicente, Sara and Kolmogorov, Vladimir and Carsten Rother}
}
@incollection {Vlasenko-Schnoerr-09a,
	title = {Variational Approaches for Model-Based PIV and Visual Fluid Analysis},
	volume = {106},
	year = {2009},
	pages = {247-256},
	publisher = {Springer},
	author = {Vlasenko, A. and Christoph Schn{\"o}rr},
	editor = {W. Nitsche and C. Dobriloff}
}
@incollection {Vlasenko-Schnoerr-09a,
	title = {Variational Approaches for Model-Based PIV and Visual Fluid Analysis},
	volume = {106},
	year = {2009},
	pages = {247-256},
	publisher = {Springer},
	author = {Vlasenko, A. and Schn{\"o}rr, C.},
	editor = {Nitsche, W. and C. Dobriloff}
}
@mastersthesis {voss_08_alignment,
	title = {Alignment and Retention Time Correction of LC-MS Data in Proteomics},
	year = {2008},
	school = {University of Heidelberg},
	author = {Bj{\"o}rn Voss}
}
@article {Szeliski2008,
	title = {A comparative study of energy minimization methods for Markov random fields with smoothness-based priors},
	journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	volume = {30},
	number = {6},
	year = {2008},
	pages = {1068{\textendash}1080},
	publisher = {Springer-Verlag},
	abstract = {Among the most exciting advances in early vision has been the development of efficient energy minimization algorithms for pixel-labeling tasks such as depth or texture computation. It has been known for decades that such problems can be elegantly expressed as Markov random fields, yet the resulting energy minimization problems have been widely viewed as intractable. Recently, algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: for example, such methods form the basis for almost all the top-performing stereo methods. However, the tradeoffs among different energy minimization algorithms are still not well understood. In this paper we describe a set of energy minimization benchmarks and use them to compare the solution quality and running time of several common energy minimization algorithms. We investigate three promising recent methods graph cuts, LBP, and tree-reweighted message passing in addition to the well-known older iterated conditional modes (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching, interactive segmentation, and denoising. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods. Benchmarks, code, images, and results are available at http://vision.middlebury.edu/ MRF/. {\textcopyright} 2008 IEEE.},
	keywords = {Belief propagation, Global optimization, Graph Cuts, Markov random fields, Performance evaluation},
	issn = {01628828},
	doi = {10.1109/TPAMI.2007.70844},
	url = {http://vision.middlebury.edu/MRF.},
	author = {Szeliski, Richard and Zabih, Ramin and Scharstein, Daniel and Veksler, Olga and Kolmogorov, Vladimir and Agarwala, Aseem and Tappen, Marshall and Carsten Rother}
}
@article {Szeliski2008a,
	title = {A comparative study of energy minimization methods for Markov random fields with smoothness-based priors},
	journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	volume = {30},
	number = {6},
	year = {2008},
	month = {jun},
	pages = {1068{\textendash}1080},
	abstract = {Among the most exciting advances in early vision has been the development of efficient energy minimization algorithms for pixel-labeling tasks such as depth or texture computation. It has been known for decades that such problems can be elegantly expressed as Markov random fields, yet the resulting energy minimization problems have been widely viewed as intractable. Recently, algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: for example, such methods form the basis for almost all the top-performing stereo methods. However, the tradeoffs among different energy minimization algorithms are still not well understood. In this paper we describe a set of energy minimization benchmarks and use them to compare the solution quality and running time of several common energy minimization algorithms. We investigate three promising recent methods graph cuts, LBP, and tree-reweighted message passing in addition to the well-known older iterated conditional modes (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching, interactive segmentation, and denoising. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods. Benchmarks, code, images, and results are available at http://vision.middlebury.edu/ MRF/. {\textcopyright} 2008 IEEE.},
	keywords = {Belief propagation, Global optimization, Graph Cuts, Markov random fields, Performance evaluation},
	issn = {01628828},
	doi = {10.1109/TPAMI.2007.70844},
	author = {Szeliski, Richard and Zabih, Ramin and Scharstein, Daniel and Veksler, Olga and Kolmogorov, Vladimir and Agarwala, Aseem and Tappen, Marshall and Carsten Rother}
}
@conference {Vicente2008,
	title = {Graph cut based image segmentation with connectivity priors},
	booktitle = {26th IEEE Conference on Computer Vision and Pattern Recognition, CVPR},
	year = {2008},
	abstract = {Graph cut is a popular technique for interactive image segmentation. However, it has certain shortcomings. In particular, graph cut has problems with segmenting thin elongated objects due to the "shrinking bias". To overcome this problem, we propose to impose an additional connectivity prior, which is a very natural assumption about objects. We formulate several versions of the connectivity constraint and show that the corresponding optimization problems are all NP-hard. For some of these versions we propose two optimization algorithms: (i) a practical heuristic technique which we call DijkstraGC, and (ii) a slow method based on problem decomposition which provides a lower bound on the problem. We use the second technique to verify that for some practical examples DijkstraGC is able to find the global minimum. {\textcopyright}2008 IEEE.},
	isbn = {9781424422432},
	doi = {10.1109/CVPR.2008.4587440},
	author = {Vicente, Sara and Kolmogorov, Vladimir and Carsten Rother}
}
@conference {Vlasenko-et-al-08a,
	title = {Physically Consistent Variational Denoising of Image Fluid Flow Estimates},
	booktitle = {Pattern Recognition -- 30th DAGM Symposium},
	volume = {5096},
	year = {2008},
	pages = {406--415},
	publisher = {Springer Verlag},
	organization = {Springer Verlag},
	author = {Vlasenko, A. and Christoph Schn{\"o}rr}
}
@conference {Vlasenko-et-al-08a,
	title = {Physically Consistent Variational Denoising of Image Fluid Flow Estimates},
	booktitle = {Pattern Recognition {\textendash} 30th DAGM Symposium},
	series = {lncs},
	volume = {5096},
	year = {2008},
	pages = {406{\textendash}415},
	publisher = {Springer Verlag},
	organization = {Springer Verlag},
	author = {Vlasenko, A. and Schn{\"o}rr, C.}
}
@conference {friedrich2008,
	title = {Sarcomere Structure and Motor-Protein Function in an Animal Model of Duchenne Muscular Dystrophy (mdx mouse)},
	booktitle = {87th Annual Meeting of the German Physiological Society},
	year = {2008},
	author = {O. Friedrich and C. Weber and M. Both and Wegner, F. von and J. S. Chamberlain and Christoph S. Garbe and Rainer H. A. Fink}
}
@incollection {hara2007,
	title = {Estimation of air-sea gas and heat fluxes from infrared imagery based on near surface turbulence models},
	year = {2007},
	publisher = {Springer-Verlag},
	abstract = {Water surface infrared images were obtained during the GASEX2001 experiment in the South Equatorial Pacific waters and during the laboratory experiment in the AEOLOTRON wind wave tank at University of Heidelberg in October 2004. The infrared imagery during these experiments reveals coexistence of roller type turbulence and intermittent breaking events. Previous interpretations of the infrared images relied on the surface renewal model, in which the water surface is assumed to be occasionally renewed by bursts of turbulent eddies reaching the water surface. A new complementary model (eddy renewal model) based on stationary and spatially periodic turbulent eddies is developed to reinterpret the infrared images of near surface turbulence. The model predicts warm elongated patches bounded by cold streaks aligned with mean wind, being consistent with field and laboratory infrared images. The model yields bulk temperature estimates and mean heat flux estimates that are very close to those based on the surface renewal model.},
	doi = {10.1007/978-3-540-36906-6_17},
	author = {T. Hara and VanInwegen, E. and J. Wendelbo and Uwe Schimpf and Bernd J{\"a}hne and Nelson M. Frew and Bernd J{\"a}hne},
	editor = {Christoph S. Garbe and Christoph S. Garbe and Handler, R. A.}
}
@mastersthesis {vogel2006,
	title = {Spectroscopic Techniques for Gas-Exchange Measurements},
	year = {2006},
	school = {Institut f{\"u}r Umweltphysik, Fakult{\"a}t f{\"u}r Physik und Astronomie, Univ.\ Heidelberg},
	author = {Felix Vogel}
}
@incollection {banerjee2005,
	title = {High resolution optical measurement techniques in paper drying},
	volume = {4},
	year = {2005},
	pages = {16--22},
	author = {D. Banerjee and S. Schabel and Christoph S. Garbe and Uwe Schimpf and Bernd J{\"a}hne and Spiegel, W. von}
}
@unpublished {vogel2004,
	title = {Visualisierung von Gasaustauschprozessen durch Lumineszenzspektroskopie mit Ruthenium als Phosphoreszenzstoff},
	year = {2004},
	note = {Miniforschung vom 01.03. -- 05.04.2004},
	author = {Felix Vogel}
}
@incollection {hader_03_efficient,
	title = {Efficient Density Clustering},
	year = {2003},
	pages = {39-48},
	publisher = {Springer},
	doi = {10.1007/b13634},
	author = {S. Hader and Fred A. Hamprecht},
	editor = {Schader, M. and Gaul, W. and Vichi, M.}
}
@incollection {eisele_03_approach,
	title = {A new approach for defect detection in X-ray CT images},
	volume = {2449},
	year = {2003},
	pages = {345-352},
	publisher = {Springer},
	doi = {10.1007/3-540-45783-6},
	author = {H. Eisele and Fred A. Hamprecht},
	editor = {Luc Van Gool}
}
@article {hamprecht_02_chemical,
	title = {Chemical library subset selection algorithms: a unified derivation using spatial statistics},
	journal = {Journal of Chemical Information and Computer Sciences},
	volume = {42},
	year = {2002},
	pages = {414-428},
	author = {Fred A. Hamprecht and Thiel, W. and van Gunsteren, W. F.}
}
@conference {Bruhn-et-al-02b,
	title = {Combining the Advantages of Local and Global Optic Flow Methods},
	booktitle = {Pattern Recognition, Proc. 24th DAGM Symposium},
	series = {lncs},
	volume = {2449},
	year = {2002},
	pages = {454{\textendash}462},
	publisher = {Springer},
	organization = {Springer},
	address = {Z{\"u}rich, Switzerland},
	author = {Bruhn, Andr{\'e}s and Weickert, Joachim and Christoph Schn{\"o}rr},
	editor = {van Gool, L.}
}
@conference {spies2002b,
	title = {Dense parameter fields from total least squares},
	booktitle = {Proceedings of the 24th DAGM Symposium on Pattern Recognition},
	volume = {LNCS 2449},
	year = {2002},
	pages = {379--386},
	publisher = {Springer},
	organization = {Springer},
	abstract = {A method for the interpolation of parameter fields estimated by total least squares is presented. This is applied to the study of dynamic processes where the motion and further values such as divergence or brightness changes are parameterised in a partial differential equation. For the regularisation we introduce a constraint that restricts the solution only in the subspace determined by the total least squares procedure. The performance is illustrated on both synthetic and real test data.},
	doi = {10.1007/3-540-45783-6_46},
	author = {Hagen Spies and Christoph S. Garbe},
	editor = {Luc Van Gool}
}
@conference {Bruhn-et-al-02a,
	title = {Designing 3{\textendash}D Nonlinear Diffusion Filters for High Performance Cluster Computing},
	booktitle = {Pattern Recognition, Proc. 24th DAGM Symposium},
	series = {lncs},
	volume = {2449},
	year = {2002},
	pages = {290{\textendash}297},
	publisher = {Springer},
	organization = {Springer},
	address = {Z{\"u}rich, Switzerland},
	author = {Bruhn, Andr{\'e}s and Jakob, Tobias and Fischer, Markus and Kohlberger, Timo and Weickert, Joachim and Br{\"u}ning, Ulrich and Christoph Schn{\"o}rr},
	editor = {van Gool, L.}
}
@conference {garbe2002e,
	title = {Mixed OLS-TLS for the estimation of dynamic processes with a linear source term},
	booktitle = {Proceedings of the 24th DAGM Symposium on Pattern Recognition},
	volume = {2449},
	year = {2002},
	pages = {463--471},
	publisher = {Springer-Verlag},
	organization = {Springer-Verlag},
	abstract = {We present a novel technique to eliminate strong biases in parameter estimation were part of the data matrix is not corrupted by errors. Problems of this type occur in the simultaneous estimation of optical flow and the parameter of linear brightness change as well as in range flow estimation. For attaining highly accurate optical flow estimations under real world situations as required by a number of scientific applications, the standard brightness change constraint equation is violated. Very often the brightness change has to be modelled by a linear source term. In this problem as well as in range flow estimation, part of the data term consists of an exactly known constant. Total least squares (TLS) assumes the error in the data terms to be identically distributed, thus leading to strong biases in the equations at hand. The approach presented in this paper is based on a mixture of ordinary least squares (OLS) and total least squares, thus resolving the bias encountered in TLS alone. Apart from a thorough performance analysis of the novel estimator, a number of applications are presented.},
	doi = {10.1007/3-540-45783-6_56},
	author = {Christoph S. Garbe and Hagen Spies and Bernd J{\"a}hne},
	editor = {Luc Van Gool}
}
@article {gee_02_molecular,
	title = {A molecular dynamics simulation study of the conformational preferences of oligo-(3- hydroxyalcanoic acids) in chloroform solution},
	journal = {Helv. Chim. Acta},
	volume = {85},
	year = {2002},
	pages = {618-632},
	author = {Gee, P. J. and Fred A. Hamprecht and Schuler, L. D. and van Gunsteren, W. F. and Duchardt, E. and Schwalbe, H. and Albert, M. and Seebach, D.}
}
@conference {Cremers-Schnoerr-02,
	title = {Motion Competition: Variational Integration of Motion Segmentation and Shape Regularization},
	booktitle = {Pattern Recognition, Proc. 24th DAGM Symposium},
	series = {lncs},
	volume = {2449},
	year = {2002},
	pages = {472{\textendash}480},
	publisher = {Springer},
	organization = {Springer},
	address = {Z{\"u}rich, Switzerland},
	author = {Daniel Cremers and Christoph Schn{\"o}rr},
	editor = {van Gool, L.}
}
@conference {Keuchel-et-al-02b,
	title = {Unsupervised Image Partitioning with Semidefinite Programming},
	booktitle = {Pattern Recognition, Proc. 24th DAGM Symposium},
	series = {lncs},
	volume = {2449},
	year = {2002},
	pages = {141{\textendash}149},
	publisher = {Springer},
	organization = {Springer},
	address = {Z{\"u}rich, Switzerland},
	author = {Keuchel, J. and Schn{\"o}rr, C. and Schellewald, C. and Daniel Cremers},
	editor = {van Gool, L.}
}
@article {hamprecht_01_fibrillation,
	title = {Fibrillation power: An alternative method of ECG spectral analysis for prediction of countershock success in a porcine model of ventricular fibrillation},
	journal = {Resuscitation},
	volume = {50},
	year = {2001},
	pages = {287-296},
	author = {Fred A. Hamprecht and Achleitner, U. and Krismer, A. C. and Lindner, K. H. and Wenzel, V. and Strohmenger, H.-U. and Thiel, W. and van Gunsteren, W. F.}
}
@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.}
}
@article {uttenweiler2000,
	title = {Motion determination in actin filament fluorescence images with a spatio-temporal orientation analysis method.},
	journal = {Biophys J},
	volume = {78},
	number = {5},
	year = {2000},
	pages = {2709--2715},
	publisher = {Institut f{\"u}r Physiologie und Pathophysiologie, Ruprecht-Karls-Universit{\"a}t Heidelberg, 69120 Heidelberg, Germany. uttenweiler@urz.uni-heidelberg.de},
	abstract = {We present a novel approach of automatically measuring motion in series of microscopic fluorescence images. As a differential method, the three-dimensional structure tensor technique is used to calculate the displacement vector field for every image of the sequence, from which the velocities are subsequently derived. We have used this method for the analysis of the movement of single actin filaments in the in vitro motility assay, where fluorescently labeled actin filaments move over a myosin decorated surface. With its fast implementation and subpixel accuracy, this approach is, in general, very valuable for analyzing dynamic processes by image sequence analysis.},
	doi = {10.1016/S0006-3495(00)76815-9},
	author = {D. Uttenweiler and C. Veigel and R. Steubing and Carlo G{\"o}tz and Sven Mann and Horst Hau{\ss}ecker and Bernd J{\"a}hne and Rainer H. A. Fink}
}
@incollection {jaehne2000a,
	title = {Performance characteristics of low-level motion estimation in spatiotemporal images},
	year = {2000},
	note = {invited, Workshop Schloss Dagstuhl, March 16-20, 1998},
	pages = {pp. 139-152},
	publisher = {Kluwer, Dordrecht},
	doi = {10.1007/978-94-015-9538-4_12},
	author = {Bernd J{\"a}hne and Horst Hau{\ss}ecker},
	editor = {R. Klette and H. S. Stiehl and K. Vincken and M. Viergever}
}
@conference {spies2000a,
	title = {Regularised range flow},
	booktitle = {European Conference on Computer Vision (ECCV)},
	volume = {2},
	year = {2000},
	pages = {785--799},
	publisher = {Springer},
	organization = {Springer},
	abstract = {Extending a differential total least squares method for range flow estimation we present an iterative regularisation approach to compute dense range flow fields. We demonstrate how this algorithm can be used to detect motion discontinuities. This can can be used to segment the data into independently moving regions. The different types of aperture problem encountered are discussed. Our regularisation scheme then takes the various types of flow vectors and combines them into a smooth flow field within the previously segmented regions. A quantitative performance analysis is presented on both synthetic and real data. The proposed algorithm is also applied to range data from castor oil plants obtained with the Biris laser range sensor to study the 3-D motion of plant leaves.},
	doi = {10.1007/3-540-45053-X_50},
	author = {Hagen Spies and Bernd J{\"a}hne and John L. Barron},
	editor = {Vernon, D.}
}
@inbook {stoehr1999,
	title = {4D particle tracking velocimetry applied to gas-liquid reactors},
	booktitle = {In Scientific Computing in Chemical Engineering II - Simulation, Image Processing, Optimization and Control.},
	year = {1999},
	pages = {270--279},
	publisher = {Springer Verlag},
	organization = {Springer Verlag},
	author = {M. St{\"o}hr and Christoph S. Garbe and D. Engelmann and Peter Gei{\ss}ler and Gomes, S. and Frank Hering and Bernd J{\"a}hne and F. Keil and W. Mackens and H. Vo{\ss} and Wagner, H.-G..},
	editor = {J. Werther}
}
@conference {blom1999,
	title = {Quality classification and process control of micro-spot laser welding},
	booktitle = {Proceedings of the Ninth International FAIM Conference - Flexible Automation and Intelligent Manufacturing, Tilburg},
	year = {1999},
	pages = {929--941},
	publisher = {Begell House},
	organization = {Begell House},
	author = {Blom, A. H. M and Brassel, Jan-Oliver and Brocke, Martin von and Mittler, M.},
	editor = {Ashayeri, Jalal and Sullivan, William and Ahmad, Munir}
}
@article {hamprecht_97_generation,
	title = {Generation of pseudo-native protein structures for threading},
	journal = {Proteins},
	volume = {28},
	year = {1997},
	pages = {522-529},
	author = {Fred A. Hamprecht and Scott, W. R. P. and van Gunsteren, W. F.}
}
@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 {vliet1995,
	title = {Delft Hydraulics Large Wind-Wave Flume},
	booktitle = {Air-Water Gas Transfer---Selected Papers from the Third International Symposium of Air--Water Gas Transfer in Heidelberg},
	year = {1995},
	pages = {499--502},
	publisher = {AEON},
	organization = {AEON},
	doi = {10.5281/zenodo.10402},
	author = {van Vliet, P. and Frank Hering and Bernd J{\"a}hne and Bernd J{\"a}hne},
	editor = {E. C. Monahan}
}
@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}
}
@conference {halsema1992,
	title = {Comparisons of backscattering calculations with measurements made in a large wind/wave flume},
	booktitle = {Proc. IGARSS{\textquoteright}92},
	volume = {2},
	year = {1992},
	pages = {1451--1453},
	doi = {10.1109/IGARSS.1992.578480},
	author = {van Halsema, D. and C. J. Calkoen and W. A. Oost and P. Snoeij and J. Vogelzang and Bernd J{\"a}hne}
}
@conference {snoeij1992,
	title = {Microwave backscatter measurements made from the Dutch Ocean Research Tower {\textquoteright}Noordwijk{\textquoteright} compared with model predictions},
	booktitle = {Proc. IGARSS{\textquoteright}92},
	year = {1992},
	doi = {10.1109/IGARSS.1992.576808},
	author = {P. Snoeij and van Halsema, D. and W. A. Oost and C. J. Calkoen and Bernd J{\"a}hne and J. Vogelzang}
}
@conference {snoeij1991,
	title = {Comparison of microwave backscatter measurements and small-scale surface wave measurements made from the Dutch ocean research tower {\textquoteright}Noordwijk{\textquoteright}},
	booktitle = {Proceedings IGARSS {\textquoteright}91},
	volume = {3},
	year = {1991},
	pages = {1289--1292},
	doi = {10.1109/IGARSS.1991.579315},
	author = {P. Snoeij and van Halsema, D. and W. A. Oost and C. J. Calkoen and J. Vogelzang and Bernd J{\"a}hne}
}
@conference {halsema1991,
	title = {Dual-polarized scatterometer measurements of wind and mechanically generated waves in a very large wind/wave flume, the VIERS-1 project},
	booktitle = {Proc.\ 5th Int. Coll. Physical Measurements and Signatures in Remote Sensing, Courchevel, France},
	volume = {ESA SP-319},
	year = {1991},
	pages = {247--252},
	author = {van Halsema, D. and C. J. Calkoen and W. A. Oost and P. Snoeij and J. Vogelzang and Bernd J{\"a}hne}
}
@conference {calkoen1991a,
	title = {Evaluation of a two-scale model using extensive radar backscatter and wave measurements in a large wind-wave flume},
	booktitle = {Proceedings IGARSS {\textquoteright}91},
	volume = {2},
	year = {1991},
	pages = {885--888},
	doi = {10.1109/IGARSS.1991.580259},
	author = {Bernd J{\"a}hne and Bernd J{\"a}hne},
	editor = {C. J. Calkoen and P. Snoeij and van Halsema, D. and J. Vogelzang and W. A. Oost and C. J. Calkoen and P. Snoeij and J. Vogelzang and W. A. Oost and van Halsema, D.}
}
@conference {halsema1991a,
	title = {Modulation of the microwave backscatter by long gravity waves as measured in a very large wind/wave flume},
	booktitle = {Proc. IGARSS {\textquoteright}91},
	volume = {3},
	year = {1991},
	pages = {1293--1296},
	doi = {10.1109/IGARSS.1991.579316},
	author = {van Halsema, D. and P. Snoeij and C. J. Calkoen and W. A. Oost and J. Vogelzang and Bernd J{\"a}hne}
}
@conference {snoeij1990a,
	title = {Dual-polarized scatterometer measurements of generated Wind and Gravity Wave in a Very Large Wind/Wave Tank},
	booktitle = {Proc. IGARSS{\textquoteright}90},
	year = {1990},
	pages = {2157--2160},
	doi = {10.1109/IGARSS.1990.688958},
	author = {P. Snoeij and C. J. Calkoen and W. A. Oost and van Halsema, D. and J. Vogelzang and Bernd J{\"a}hne}
}
@conference {snoeij1990,
	title = {A high resolution scatterometer for radar backscatter measurements of wind generated waves in wind/wave tanks},
	booktitle = {European Micro Wave Conference 1990},
	year = {1990},
	abstract = {In February 1988, combined measurements of microwave backscatter, wind, waves and gas exchange have been carried out in the large Delft Hydraulics wind/wave tank, with wind generated waves. In March 1989 a second exaperiment took place in the huge outdoor wave tank, the Delta tank, with wind generated waves and mechanically generated waves. These experiments were perfonned in the framework of the VIERS-1 project. In this project a number of Dutch and German institutes cooperate. Main objective is to increase the knowledge about the physics involved in the interaction of microwaves and the ocean surface and, from that point, to an improvement of the algorithms used for determination of wind speed and direction from satelliteborne microwave scatterometers. A second objective is to study the relation between the gas exchange at the water surface and the microwave backscatter. To achieve these objectives two wind/wave tank experiments and one ocean based platform experiment are scheduled. In this paper, the VIERS-l program will be outlined. The features of a specially designed high resolution scatterometer will be described and some results of both tank expermnents will be shown.},
	doi = {10.1109/EUMA.1990.336154},
	author = {P. Snoeij and J. Vogelzang and C. J. Calkoen and W. A. Oost and van Halsema, D. and Bernd J{\"a}hne}
}
@conference {halsema1989b,
	title = {Comparisons of X-band Radar Backscatter Measurements with Area extended wave slop measurements made in a large Wind/Wave Tank},
	booktitle = {Proc. IGARSS{\textquoteright}89},
	volume = {5},
	year = {1989},
	pages = {2997--3001},
	doi = {10.1109/IGARSS.1989.575986},
	author = {van Halsema, D. and C. J. Calkoen and W. A. Oost and P. Snoeij and Bernd J{\"a}hne}
}
@conference {halsema1988,
	title = {VIERS-1: A Programme of Wind Scatterometry},
	booktitle = {Geoscience and Remote Sensing Symposium, Proc.\ IGARSS{\textquoteright}88},
	volume = {1},
	year = {1988},
	pages = {572},
	doi = {10.1109/IGARSS.1988.570207},
	author = {van Halsema, D. and de Loor, P. and Bernd J{\"a}hne}
}
