@article{AllenGoodaleLanfermannetal.1999, author = {Allen, Gabrielle and Goodale, Tom and Lanfermann, Gerd and Seidel, Edward and Benger, Werner and Hege, Hans-Christian and Merzky, Andr{\´e} and Masso, Joan and Shalf, John}, title = {Solving Einstein's Equations on Supercomputers}, series = {IEEE Computer}, journal = {IEEE Computer}, doi = {10.1109/2.809251}, pages = {52 -- 59}, year = {1999}, language = {en} } @inproceedings{vonFunckWeinkaufTheiseletal.2008, author = {von Funck, Wolfram and Weinkauf, Tino and Theisel, Holger and Hege, Hans-Christian}, title = {Smoke Surfaces: An Interactive Flow Visualization Technique Inspired by Real-World Flow Experiments}, series = {IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization 2008)}, volume = {14}, booktitle = {IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization 2008)}, number = {6}, doi = {10.1109/TVCG.2008.163}, pages = {1396 -- 1403}, year = {2008}, language = {en} } @inproceedings{KaehlerAbelHege2007, author = {K{\"a}hler, Ralf and Abel, Tom and Hege, Hans-Christian}, title = {Simultaneous GPU-Assisted Raycasting of Unstructured Point Sets and Volumetric Grid Data}, series = {Proceedings of IEEE/EG International Symposium on Volume Graphics 2007}, booktitle = {Proceedings of IEEE/EG International Symposium on Volume Graphics 2007}, publisher = {A K Peters}, address = {Prague, Czech Republic}, pages = {49 -- 56}, year = {2007}, language = {en} } @article{BoeltsHarthGaoetal., author = {Boelts, Jan and Harth, Philipp and Gao, Richard and Udvary, Daniel and Yanez, Felipe and Baum, Daniel and Hege, Hans-Christian and Oberlaender, Marcel and Macke, Jakob H}, title = {Simulation-based inference for efficient identification of generative models in connectomics}, series = {bioRxiv}, journal = {bioRxiv}, doi = {10.1101/2023.01.31.526269}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-89890}, abstract = {Recent advances in connectomics research enable the acquisition of increasing amounts of data about the connectivity patterns of neurons. How can we use this wealth of data to efficiently derive and test hypotheses about the principles underlying these patterns? A common approach is to simulate neural networks using a hypothesized wiring rule in a generative model and to compare the resulting synthetic data with empirical data. However, most wiring rules have at least some free parameters and identifying parameters that reproduce empirical data can be challenging as it often requires manual parameter tuning. Here, we propose to use simulation-based Bayesian inference (SBI) to address this challenge. Rather than optimizing a single rule to fit the empirical data, SBI considers many parametrizations of a wiring rule and performs Bayesian inference to identify the parameters that are compatible with the data. It uses simulated data from multiple candidate wiring rules and relies on machine learning methods to estimate a probability distribution (the `posterior distribution over rule parameters conditioned on the data') that characterizes all data-compatible rules. We demonstrate how to apply SBI in connectomics by inferring the parameters of wiring rules in an in silico model of the rat barrel cortex, given in vivo connectivity measurements. SBI identifies a wide range of wiring rule parameters that reproduce the measurements. We show how access to the posterior distribution over all data-compatible parameters allows us to analyze their relationship, revealing biologically plausible parameter interactions and enabling experimentally testable predictions. We further show how SBI can be applied to wiring rules at different spatial scales to quantitatively rule out invalid wiring hypotheses. Our approach is applicable to a wide range of generative models used in connectomics, providing a quantitative and efficient way to constrain model parameters with empirical connectivity data.}, language = {en} } @article{BoeltsHarthGaoetal., author = {Boelts, Jan and Harth, Philipp and Gao, Richard and Udvary, Daniel and Yanez, Felipe and Baum, Daniel and Hege, Hans-Christian and Oberlaender, Marcel and Macke, Jakob H.}, title = {Simulation-based inference for efficient identification of generative models in computational connectomics}, series = {PLOS Computational Biology}, volume = {19}, journal = {PLOS Computational Biology}, number = {9}, doi = {10.1371/journal.pcbi.1011406}, abstract = {Recent advances in connectomics research enable the acquisition of increasing amounts of data about the connectivity patterns of neurons. How can we use this wealth of data to efficiently derive and test hypotheses about the principles underlying these patterns? A common approach is to simulate neuronal networks using a hypothesized wiring rule in a generative model and to compare the resulting synthetic data with empirical data. However, most wiring rules have at least some free parameters, and identifying parameters that reproduce empirical data can be challenging as it often requires manual parameter tuning. Here, we propose to use simulation-based Bayesian inference (SBI) to address this challenge. Rather than optimizing a fixed wiring rule to fit the empirical data, SBI considers many parametrizations of a rule and performs Bayesian inference to identify the parameters that are compatible with the data. It uses simulated data from multiple candidate wiring rule parameters and relies on machine learning methods to estimate a probability distribution (the 'posterior distribution over parameters conditioned on the data') that characterizes all data-compatible parameters. We demonstrate how to apply SBI in computational connectomics by inferring the parameters of wiring rules in an in silico model of the rat barrel cortex, given in vivo connectivity measurements. SBI identifies a wide range of wiring rule parameters that reproduce the measurements. We show how access to the posterior distribution over all data-compatible parameters allows us to analyze their relationship, revealing biologically plausible parameter interactions and enabling experimentally testable predictions. We further show how SBI can be applied to wiring rules at different spatial scales to quantitatively rule out invalid wiring hypotheses. Our approach is applicable to a wide range of generative models used in connectomics, providing a quantitative and efficient way to constrain model parameters with empirical connectivity data.}, language = {en} } @inproceedings{GladilinZachowDeuflhardetal.2002, author = {Gladilin, Evgeny and Zachow, Stefan and Deuflhard, Peter and Hege, Hans-Christian}, title = {Shape-based Modeling Approach for the Estimation of Individual Facial Mimics in Craniofacial Surgery Planning}, series = {Proc. SPIE Medical Imaging 2002: Visualization, Image-Guided Procedures, and Display}, volume = {4681}, booktitle = {Proc. SPIE Medical Imaging 2002: Visualization, Image-Guided Procedures, and Display}, editor = {Mun, Seong}, address = {San Diego, USA target}, pages = {242 -- 248}, year = {2002}, language = {en} } @article{OberleithnerSieberNayerietal.2010, author = {Oberleithner, Kilian and Sieber, Moritz and Nayeri, Christian and Paschereit, Christian and Petz, Christoph and Hege, Hans-Christian and Noack, Bernd and Wygnanski, Israel}, title = {Self Excited Oscillations in Swirling Jets: Stability Analysis and Empirical Mode Construction}, series = {Bulletin of the American Physical Society}, volume = {55}, journal = {Bulletin of the American Physical Society}, number = {16}, pages = {GE.00008}, year = {2010}, language = {en} } @inproceedings{StallingZoecklerHege1998, author = {Stalling, Detlev and Z{\"o}ckler, Malte and Hege, Hans-Christian}, title = {Segmentation of 3D Medical Images with Subvoxel Accuracy}, series = {Proc. CARS '98 Computer Assisted Radiology and Surgery}, booktitle = {Proc. CARS '98 Computer Assisted Radiology and Surgery}, address = {Tokyo}, pages = {137 -- 142}, year = {1998}, language = {en} } @incollection{CoconuColditzHegeetal.2005, author = {Coconu, Liviu and Colditz, Carsten and Hege, Hans-Christian and Deussen, Oliver}, title = {Seamless integration of stylized renditions in computer-generated landscape visualization}, series = {Trends in Real-Time Landscape Visualization and Participation}, booktitle = {Trends in Real-Time Landscape Visualization and Participation}, editor = {Buhmann, Erich and Paar, Philip and Bishop, Ian and Lange, Eckart}, publisher = {Wichmann Verlag}, address = {Heidelberg}, pages = {88 -- 96}, year = {2005}, language = {en} } @inproceedings{DeuflhardHege1994, author = {Deuflhard, Peter and Hege, Hans-Christian}, title = {Scientific Computing in der Theoretischen Physik - Collected Abstracts}, series = {Tagung organisiert von der DMV-Fachgruppe Scientific Computing in Kooperation mit dem GAMM Fachausschuss Scientific Computing}, booktitle = {Tagung organisiert von der DMV-Fachgruppe Scientific Computing in Kooperation mit dem GAMM Fachausschuss Scientific Computing}, address = {Berlin}, year = {1994}, language = {en} } @article{HegeBengerMerzkyetal.2000, author = {Hege, Hans-Christian and Benger, Werner and Merzky, Andr{\´e} and Kasper, Friedbert and Radke, Thomas and Seidel, Edward}, title = {Schwarze L{\"o}cher in Sicht - Immersive {\"U}berwachung und Steuerung von Remote-Simulationen}, series = {DFN-Mitteilungen}, volume = {52}, journal = {DFN-Mitteilungen}, number = {2}, pages = {4 -- 6}, year = {2000}, language = {en} } @article{Hege1994, author = {Hege, Hans-Christian}, title = {Scaling study of pure SU(3) theory - the QCD-TARO collaboration}, series = {Nucl. Phys. B Proc. Suppl.}, volume = {34}, journal = {Nucl. Phys. B Proc. Suppl.}, doi = {10.1016/0920-5632(94)90358-1}, pages = {246 -- 252}, year = {1994}, language = {en} } @inproceedings{TheiselWeinkaufHegeetal.2003, author = {Theisel, Holger and Weinkauf, Tino and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {Saddle Connectors - An Approach to Visualizing the Topological Skeleton of Complex 3D Vector Fields}, series = {Proc. IEEE Visualization 2003}, booktitle = {Proc. IEEE Visualization 2003}, address = {Seattle}, doi = {10.1109/VISUAL.2003.1250376}, pages = {225 -- 232}, year = {2003}, language = {en} } @article{BaumLindowHegeetal.2017, author = {Baum, Daniel and Lindow, Norbert and Hege, Hans-Christian and Lepper, Verena and Siopi, Tzulia and Kutz, Frank and Mahlow, Kristin and Mahnke, Heinz-Eberhard}, title = {Revealing hidden text in rolled and folded papyri}, series = {Applied Physics A}, volume = {123}, journal = {Applied Physics A}, number = {3}, doi = {10.1007/s00339-017-0808-6}, pages = {171}, year = {2017}, abstract = {Ancient Egyptian papyri are often folded, rolled up or kept as small packages, sometimes even sealed. Physically unrolling or unfolding these packages might severely damage them. We demonstrate a way to get access to the hidden script without physical unfolding by employing computed tomography and mathematical algorithms for virtual unrolling and unfolding. Our algorithmic approaches are combined with manual interaction. This provides the necessary flexibility to enable the unfolding of even complicated and partly damaged papyrus packages. In addition, it allows us to cope with challenges posed by the structure of ancient papyrus, which is rather irregular, compared to other writing substrates like metallic foils or parchment. Unfolding of packages is done in two stages. In the first stage, we virtually invert the physical folding process step by step until the partially unfolded package is topologically equivalent to a scroll or a papyrus sheet folded only along one fold line. To minimize distortions at this stage, we apply the method of moving least squares. In the second stage, the papyrus is simply flattened, which requires the definition of a medial surface. We have applied our software framework to several papyri. In this work, we present the results of applying our approaches to mockup papyri that were either rolled or folded along perpendicular fold lines. In the case of the folded papyrus, our approach represents the first attempt to address the unfolding of such complicated folds.}, language = {en} } @misc{BaumLindowHegeetal., author = {Baum, Daniel and Lindow, Norbert and Hege, Hans-Christian and Lepper, Verena and Siopi, Tzulia and Kutz, Frank and Mahlow, Kristin and Mahnke, Heinz-Eberhard}, title = {Revealing hidden text in rolled and folded papyri}, issn = {1438-0064}, doi = {10.1007/s00339-017-0808-6}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-61826}, abstract = {Ancient Egyptian papyri are often folded, rolled up or kept as small packages, sometimes even sealed. Physically unrolling or unfolding these packages might severely damage them. We demonstrate a way to get access to the hidden script without physical unfolding by employing computed tomography and mathematical algorithms for virtual unrolling and unfolding. Our algorithmic approaches are combined with manual interaction. This provides the necessary flexibility to enable the unfolding of even complicated and partly damaged papyrus packages. In addition, it allows us to cope with challenges posed by the structure of ancient papyrus, which is rather irregular, compared to other writing substrates like metallic foils or parchment. Unfolding of packages is done in two stages. In the first stage, we virtually invert the physical folding process step by step until the partially unfolded package is topologically equivalent to a scroll or a papyrus sheet folded only along one fold line. To minimize distortions at this stage, we apply the method of moving least squares. In the second stage, the papyrus is simply flattened, which requires the definition of a medial surface. We have applied our software framework to several papyri. In this work, we present the results of applying our approaches to mockup papyri that were either rolled or folded along perpendicular fold lines. In the case of the folded papyrus, our approach represents the first attempt to address the unfolding of such complicated folds.}, language = {en} } @article{GoubergritsSchallerKertzscheretal., author = {Goubergrits, Leonid and Schaller, Jens and Kertzscher, Ulrich and Petz, Christoph and Hege, Hans-Christian and Spuler, Andreas}, title = {Reproducibility of Image-Based Analysis of Cerebral Aneurysm Geometry and Hemodynamics: An In-Vitro Study of Magnetic Resonance Imaging, Computed Tomography, and Three-Dimensional Rotational Angiography}, series = {Journal of Neurological Surgery, Part A: Central European Neurosurgery}, volume = {74}, journal = {Journal of Neurological Surgery, Part A: Central European Neurosurgery}, number = {5}, doi = {10.1055/s-0033-1342937}, pages = {294 -- 302}, language = {en} } @inproceedings{KaehlerCoxPattersonetal.2002, author = {K{\"a}hler, Ralf and Cox, Donna and Patterson, Robert and Levy, Stuart and Hege, Hans-Christian and Abel, Tom}, title = {Rendering The First Star in The Universe - A Case Study}, series = {Proceedings of IEEE Visualization 2002}, booktitle = {Proceedings of IEEE Visualization 2002}, editor = {J. Moorhead, Robert and Gross, Markus and I. Joy, Kenneth}, publisher = {IEEE Computer Society Press}, address = {Boston MA, USA}, doi = {10.1109/VISUAL.2002.1183824}, pages = {537 -- 540}, year = {2002}, language = {en} } @misc{HoerthBaumKnoeteletal., author = {Hoerth, Rebecca M. and Baum, Daniel and Kn{\"o}tel, David and Prohaska, Steffen and Willie, Bettina M. and Duda, Georg and Hege, Hans-Christian and Fratzl, Peter and Wagermaier, Wolfgang}, title = {Registering 2D and 3D Imaging Data of Bone during Healing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53426}, abstract = {Purpose/Aims of the Study: Bone's hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro computed tomography (μCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. Materials and Methods: We investigated bone during healing by means of μCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue's calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. Results: We present an approach for the registration of 2D data in a 3D μCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into μCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. Conclusions: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.}, language = {en} } @article{HoerthBaumKnoeteletal., author = {Hoerth, Rebecca M. and Baum, Daniel and Kn{\"o}tel, David and Prohaska, Steffen and Willie, Bettina M. and Duda, Georg and Hege, Hans-Christian and Fratzl, Peter and Wagermaier, Wolfgang}, title = {Registering 2D and 3D Imaging Data of Bone during Healing}, series = {Connective Tissue Research}, volume = {56}, journal = {Connective Tissue Research}, number = {2}, publisher = {Taylor \& Francis}, doi = {10.3109/03008207.2015.1005210}, pages = {133 -- 143}, language = {en} } @misc{GowinSaparinFelsenbergetal.2002, author = {Gowin, Wolfgang and Saparin, Peter and Felsenberg, Dieter and Kurths, J{\"u}rgen and Zaikin, Alexei and Prohaska, Steffen and Hege, Hans-Christian}, title = {Regional Structural Skeletal Discordance Assessed by Measures of Complexity}, year = {2002}, language = {en} }