@article{LindowBaumHege2011, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Voronoi-Based Extraction and Visualization of Molecular Paths}, series = {IEEE Transactions on Visualization and Computer Graphics}, volume = {17}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {12}, doi = {10.1109/TVCG.2011.259}, pages = {2025 -- 2034}, year = {2011}, language = {en} } @article{SchmidtEhrenbergBaumHege2001, author = {Schmidt-Ehrenberg, Johannes and Baum, Daniel and Hege, Hans-Christian}, title = {Visually stunning - Molecular conformations}, series = {The Biochemist}, volume = {23}, journal = {The Biochemist}, number = {5}, pages = {22 -- 26}, year = {2001}, language = {en} } @inproceedings{SchmidtEhrenbergBaumHege2002, author = {Schmidt-Ehrenberg, Johannes and Baum, Daniel and Hege, Hans-Christian}, title = {Visualizing Dynamic Molecular Conformations}, 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.2002.1183780}, pages = {235 -- 242}, year = {2002}, language = {en} } @article{KozlikovaKroneFalketal., author = {Kozl{\´i}kov{\´a}, Barbora and Krone, Michael and Falk, Martin and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian}, title = {Visualization of Biomolecular Structures: State of the Art Revisited}, series = {Computer Graphics Forum}, volume = {36}, journal = {Computer Graphics Forum}, number = {8}, doi = {10.1111/cgf.13072}, pages = {178 -- 204}, abstract = {Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.}, language = {en} } @misc{KozlikovaKroneFalketal., author = {Kozlikova, Barbora and Krone, Michael and Falk, Martin and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian}, title = {Visualization of Biomolecular Structures: State of the Art}, issn = {1438-0064}, doi = {10.2312/eurovisstar.20151112}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57217}, abstract = {Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.}, language = {en} } @inproceedings{KozlikovaKroneLindowetal.2015, author = {Kozlikova, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian}, title = {Visualization of Biomolecular Structures: State of the Art}, series = {EuroVis 2015 STARS Proceedings}, booktitle = {EuroVis 2015 STARS Proceedings}, doi = {10.2312/eurovisstar.20151112}, pages = {61 -- 81}, year = {2015}, abstract = {Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.}, language = {en} } @misc{KroneKozlikovaLindowetal., author = {Krone, Michael and Kozlikova, Barbora and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Parulek, Julius and Hege, Hans-Christian and Viola, Ivan}, title = {Visual Analysis of Biomolecular Cavities: State of the Art}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60193}, abstract = {In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.}, language = {en} } @article{KroneKozlikovaLindowetal.2016, author = {Krone, Michael and Kozl{\´i}kov{\´a}, Barbora and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Parulek, Julius and Hege, Hans-Christian and Viola, Ivan}, title = {Visual Analysis of Biomolecular Cavities: State of the Art}, series = {Computer Graphics Forum}, volume = {35}, journal = {Computer Graphics Forum}, number = {3}, issn = {1467-8659}, doi = {10.1111/cgf.12928}, pages = {527 -- 551}, year = {2016}, abstract = {In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.}, language = {en} } @article{MahnkeArltBaumetal., author = {Mahnke, Heinz-Eberhard and Arlt, Tobias and Baum, Daniel and Hege, Hans-Christian and Herter, Felix and Lindow, Norbert and Manke, Ingo and Siopi, Tzulia and Menei, Eve and Etienne, Marc and Lepper, Verena}, title = {Virtual unfolding of folded papyri}, series = {Journal of Cultural Heritage}, volume = {41}, journal = {Journal of Cultural Heritage}, publisher = {Elsevier}, doi = {10.1016/j.culher.2019.07.007}, pages = {264 -- 269}, abstract = {The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent impro- vements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hid- den texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Mus{\´e}e du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for "Lord".}, language = {en} } @misc{MahnkeArltBaumetal., author = {Mahnke, Heinz-Eberhard and Arlt, Tobias and Baum, Daniel and Hege, Hans-Christian and Herter, Felix and Lindow, Norbert and Manke, Ingo and Siopi, Tzulia and Menei, Eve and Etienne, Marc and Lepper, Verena}, title = {Virtual unfolding of folded papyri}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74338}, abstract = {The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent impro- vements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hid- den texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Mus{\´e}e du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for "Lord".}, language = {en} } @inproceedings{ArltLindowBaumetal., author = {Arlt, Tobias and Lindow, Norbert and Baum, Daniel and Hilger, Andre and Mahnke, Ingo and Hege, Hans-Christian and Lepper, Verena and Siopi, Tzulia and Mahnke, Heinz.Eberhard}, title = {Virtual Access to Hidden Texts - Study of Ancient Papyri}, series = {Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany}, booktitle = {Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany}, abstract = {When physical unfolding/unrolling of papyri is not possible or too dangerous for preserving the precious object, tomographic approaches may be the ap- propriate alternative. Requirements are the resolution and the contrast to distinguish writing and substrate. The steps to be performed are the following: (1) Select the object of interest (archaeological arguments, cultural back- ground of the object, etc.). (2) Find the proper physical procedure, especially with respect to contrast, take the tomographic data, e.g. by absorption x-ray tomography. (3) Apply mathematical unfolding transformations to the tomographic data, in order to obtain a 2d-planar reconstruction of text.}, language = {en} } @article{HerterHegeHadwigeretal., author = {Herter, Felix and Hege, Hans-Christian and Hadwiger, Markus and Lepper, Verena and Baum, Daniel}, title = {Thin-Volume Visualization on Curved Domains}, series = {Computer Graphics Forum}, volume = {40}, journal = {Computer Graphics Forum}, number = {3}, publisher = {Wiley-Blackwell Publishing Ltd.}, address = {United Kingdom}, doi = {10.1111/cgf.14296}, pages = {147 -- 157}, abstract = {Thin, curved structures occur in many volumetric datasets. Their analysis using classical volume rendering is difficult because parts of such structures can bend away or hide behind occluding elements. This problem cannot be fully compensated by effective navigation alone, because structure-adapted navigation in the volume is cumbersome and only parts of the structure are visible in each view. We solve this problem by rendering a spatially transformed view into the volume so that an unobscured visualization of the entire curved structure is obtained. As a result, simple and intuitive navigation becomes possible. The domain of the spatial transform is defined by a triangle mesh that is topologically equivalent to an open disc and that approximates the structure of interest. The rendering is based on ray-casting in which the rays traverse the original curved sub-volume. In order to carve out volumes of varying thickness, the lengths of the rays as well as the position of the mesh vertices can be easily modified in a view-controlled manner by interactive painting. We describe a prototypical implementation and demonstrate the interactive visual inspection of complex structures from digital humanities, biology, medicine, and materials science. Displaying the structure as a whole enables simple inspection of interesting substructures in their original spatial context. Overall, we show that transformed views utilizing ray-casting-based volume rendering supported by guiding surface meshes and supplemented by local, interactive modifications of ray lengths and vertex positions, represent a simple but versatile approach to effectively visualize thin, curved structures in volumetric data.}, language = {en} } @inproceedings{BaumMahlowLameckeretal., author = {Baum, Daniel and Mahlow, Kristin and Lamecker, Hans and Zachow, Stefan and M{\"u}ller, Johannes and Hege, Hans-Christian}, title = {The Potential of Surface-based Geometric Morphometrics for Evolutionary Studies: An Example using Dwarf Snakes (Eirenis)}, series = {Abstract in DigitalSpecimen 2014}, booktitle = {Abstract in DigitalSpecimen 2014}, abstract = {Geometric morphometrics plays an important role in evolutionary studies. The state-of-the-art in this field are landmark-based methods. Since the landmarks usually need to be placed manually, only a limited number of landmarks are generally used to represent the shape of an anatomical structure. As a result, shape characteristics that cannot be properly represented by small sets of landmarks are disregarded. In this study, we present a method that is free of this limitation. The method takes into account the whole shape of an anatomical structure, which is represented as a surface, hence the term 'surface-based morphometrics'. Correspondence between two surfaces is established by defining a partitioning of the surfaces into homologous surface patches. The first step for the generation of a surface partitioning is to place landmarks on the surface. Subsequently, the landmarks are connected by curves lying on the surface. The curves, called 'surface paths', might either follow specific anatomical features or they can be geodesics, that is, shortest paths on the surface. One important requirement, however, is that the resulting surface path networks are topologically equivalent across all surfaces. Once the surface path networks have been defined, the surfaces are decomposed into patches according to the path networks. This approach has several advantages. One of them is that we can discretize the surface by as many points as desired. Thus, even fine shape details can be resolved if this is of interest for the study. Since a point discretization is used, another advantage is that well-established analysis methods for landmark-based morphometrics can be utilized. Finally, the shapes can be easily morphed into one another, thereby greatly supporting the understanding of shape changes across all considered specimens. To show the potential of the described method for evolutionary studies of biological specimens, we applied the method to the para-basisphenoid complex of the snake genus Eirenis. By using this anatomical structure as example, we present all the steps that are necessary for surface-based morphometrics, including the segmentation of the para-basisphenoid complex from micro-CT data sets. We also show some first results using statistical analysis as well as classification methods based on the presented technique.}, 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} } @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} } @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} } @inproceedings{HarthBastTroidletal., author = {Harth, Philipp and Bast, Arco and Troidl, Jakob and Meulemeester, Bjorge and Pfister, Hanspeter and Beyer, Johanna and Oberlaender, Marcel and Hege, Hans-Christian and Baum, Daniel}, title = {Rapid Prototyping for Coordinated Views of Multi-scale Spatial and Abstract Data: A Grammar-based Approach}, series = {Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)}, booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)}, doi = {10.2312/vcbm.20231218}, abstract = {Visualization grammars are gaining popularity as they allow visualization specialists and experienced users to quickly create static and interactive views. Existing grammars, however, mostly focus on abstract views, ignoring three-dimensional (3D) views, which are very important in fields such as natural sciences. We propose a generalized interaction grammar for the problem of coordinating heterogeneous view types, such as standard charts (e.g., based on Vega-Lite) and 3D anatomical views. An important aspect of our web-based framework is that user interactions with data items at various levels of detail can be systematically integrated and used to control the overall layout of the application workspace. With the help of a concise JSON-based specification of the intended workflow, we can handle complex interactive visual analysis scenarios. This enables rapid prototyping and iterative refinement of the visual analysis tool in collaboration with domain experts. We illustrate the usefulness of our framework in two real-world case studies from the field of neuroscience. Since the logic of the presented grammar-based approach for handling interactions between heterogeneous web-based views is free of any application specifics, it can also serve as a template for applications beyond biological research.}, language = {en} } @article{LindowBaumHege2012, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Perceptually Linear Parameter Variations}, series = {Computer Graphics Forum}, volume = {31}, journal = {Computer Graphics Forum}, number = {2}, doi = {10.1111/j.1467-8659.2012.03054.x target}, pages = {535 -- 544}, year = {2012}, language = {en} } @article{VohraHerreraTavhelidseSucketal., author = {Vohra, Sumit Kumar and Herrera, Kristian and Tavhelidse-Suck, Tinatini and Knoblich, Simon and Seleit, Ali and Boulanger-Weill, Jonathan and Chambule, Sydney and Aspiras, Ariel and Santoriello, Cristina and Randlett, Owen and Wittbrodt, Joachim and Aulehla, Alexander and Lichtman, Jeff W. and Fishman, Mark and Hege, Hans-Christian and Baum, Daniel and Engert, Florian and Isoe, Yasuko}, title = {Multi-species community platform for comparative neuroscience in teleost fish}, doi = {10.1101/2024.02.14.580400}, abstract = {Studying neural mechanisms in complementary model organisms from different ecological niches in the same animal class can leverage the comparative brain analysis at the cellular level. To advance such a direction, we developed a unified brain atlas platform and specialized tools that allowed us to quantitatively compare neural structures in two teleost larvae, medaka (Oryzias latipes) and zebrafish (Danio rerio). Leveraging this quantitative approach we found that most brain regions are similar but some subpopulations are unique in each species. Specifically, we confirmed the existence of a clear dorsal pallial region in the telencephalon in medaka lacking in zebrafish. Further, our approach allows for extraction of differentially expressed genes in both species, and for quantitative comparison of neural activity at cellular resolution. The web-based and interactive nature of this atlas platform will facilitate the teleost community's research and its easy extensibility will encourage contributions to its continuous expansion.}, language = {en} } @article{CourniaAllenAndricioaeietal.2015, author = {Cournia, Zoe and Allen, Toby W. and Andricioaei, Ioan and Antonny, Bruno and Baum, Daniel and Brannigan, Grace and Buchete, Nicolae-Viorel and Deckman, Jason T. and Delemotte, Lucie and del Val, Coral and Friedman, Ran and Gkeka, Paraskevi and Hege, Hans-Christian and H{\´e}nin, J{\´e}r{\^o}me and Kasimova, Marina A. and Kolocouris, Antonios and Klein, Michael L. and Khalid, Syma and Lemieux, Joanne and Lindow, Norbert and Roy, Mahua and Selent, Jana and Tarek, Mounir and Tofoleanu, Florentina and Vanni, Stefano and Urban, Sinisa and Wales, David J. and Smith, Jeremy C. and Bondar, Ana-Nicoleta}, title = {Membrane Protein Structure, Function and Dynamics: A Perspective from Experiments and Theory}, series = {Journal of Membrane Biology}, volume = {248}, journal = {Journal of Membrane Biology}, number = {4}, doi = {10.1007/s00232-015-9802-0}, pages = {611 -- 640}, year = {2015}, language = {en} } @article{LindowBaumHege2014, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Ligand Excluded Surface: A New Type of Molecular Surface}, series = {IEEE Transactions on Visualization and Computer Graphics}, volume = {20}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {12}, doi = {10.1109/TVCG.2014.2346404}, pages = {2486 -- 2495}, year = {2014}, abstract = {The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes - including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules.}, language = {en} } @misc{LindowBaumHege, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Ligand Excluded Surface: A New Type of Molecular Surface}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51194}, abstract = {The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes - including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules.}, language = {en} } @misc{LindowBaumLeborgneetal., author = {Lindow, Norbert and Baum, Daniel and Leborgne, Morgan and Hege, Hans-Christian}, title = {Interactive Visualization of RNA and DNA Structures}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-69704}, abstract = {The analysis and visualization of nucleic acids (RNA and DNA) play an increasingly important role due to the growing number of known 3-dimensional structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. For the first time, we present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization.}, language = {en} } @article{LindowBaumLeborgneetal., author = {Lindow, Norbert and Baum, Daniel and Leborgne, Morgan and Hege, Hans-Christian}, title = {Interactive Visualization of RNA and DNA Structures}, series = {IEEE Transactions on Visualization and Computer Graphics}, volume = {25}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {1}, doi = {10.1109/TVCG.2018.2864507}, pages = {967 -- 976}, abstract = {The analysis and visualization of nucleic acids (RNA and DNA) is playing an increasingly important role due to their fundamental importance for all forms of life and the growing number of known 3D structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. We present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables for the first time real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization.}, language = {en} } @article{LindowBaumHege2012, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Interactive Rendering of Materials and Biological Structures on Atomic and Nanoscopic Scale}, series = {Computer Graphics Forum}, volume = {31}, journal = {Computer Graphics Forum}, number = {3}, doi = {10.1111/j.1467-8659.2012.03128.x target}, pages = {1325 -- 1334}, year = {2012}, language = {en} } @inproceedings{KlindtBaumProhaskaetal.2012, author = {Klindt, Marco and Baum, Daniel and Prohaska, Steffen and Hege, Hans-Christian}, title = {iCon.text - a customizable iPad app for kiosk applications in museum exhibitions}, series = {EVA 2012 Berlin}, booktitle = {EVA 2012 Berlin}, publisher = {Gesellschaft zur F{\"o}rderung angewandter Informatik e.V.}, address = {Volmerstraße 3, 12489 Berlin}, pages = {150 -- 155}, year = {2012}, language = {en} } @misc{KlindtBaumProhaskaetal., author = {Klindt, Marco and Baum, Daniel and Prohaska, Steffen and Hege, Hans-Christian}, title = {iCon.text - a customizable iPad app for kiosk applications in museum exhibitions}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-17731}, abstract = {We present iCon.text, a kiosk platform for the iPad centered around artefacts, whose content and layout can be tailored without programming skills for specific museum exhibitions. The central metaphor to access information is a virtual postcard with one front and a customizable number of back sides that provide details about exhibits to museum visitors in textual and image form. Back sides can link to others cards. Access to these postcards is possible through one or more navigation views that can be navigated to from a navigation bar. The entry point to the application is designed as a multitouch interactive pile of cards in a playful manner that allows visitors of any age an easy approach to the presentation and interaction metaphor. To directly access a certain postcard, a mosaic view can be uitilized to provide an overview about all available exhibits. A category view groups postcards into themes. Locating artefacts on a zoomable map or exhibition floor plan allows for conveying information about spatial contexts between different objects and their location. Furthermore, contexts can be illustrated with a two stage view comprising an overview and corresponding detail views to provide further insights into the spatial, temporal, and thematic contexts of artefacts. The application scaffolding allows the design of bilingual presentations to support exhibitions with an international audience. The logo of the presenting institution or exhibition can be incorporated to display the the kiosk's corporate design branding and to access an imprint or further informations. Usage is logged into files to provide a basis for extracting statistical information about the usage. The details about the exhibits are presented as images and as such impose no limit to the design choices made by the content provider or exhibition designer. The application (enhanced with a panoramic view) has been integrated successfully into a large special exhibition about the ancient city of Pergamon 2011/2012 at the Pergamon Museum Berlin within the interdisciplinary project "Berlin Sculpture Network".}, language = {en} } @article{KramerNoackBaumetal., author = {Kramer, Tobias and Noack, Matthias and Baum, Daniel and Hege, Hans-Christian and Heller, Eric J.}, title = {Homogeneous dust emission and jet structure near active cometary nuclei: the case of 67P/Churyumov-Gerasimenko}, abstract = {We compute trajectories of dust grains starting from a homogeneous surface activity-profile on a irregularly shaped cometary nucleus. Despite the initially homogeneous dust distribution a collimation in jet-like structures becomes visible. The fine structure is caused by concave topographical features with similar bundles of normal vectors. The model incorporates accurately determined gravitational forces, rotation of the nucleus, and gas-dust interaction. Jet-like dust structures are obtained for a wide range of gas-dust interactions. For the comet 67P/Churyumov-Gerasimenko, we derive the global dust distribution around the nucleus and find several areas of agreement between the homogeneous dust emission model and the Rosetta observation of dust jets, including velocity-dependent bending of trajectories.}, language = {en} } @inproceedings{WeberMoellerVerbavatzetal.2011, author = {Weber, Britta and M{\"o}ller, Marit and Verbavatz, Jean-Marc and Baum, Daniel and Hege, Hans-Christian and Prohaska, Steffen}, title = {Fast Tracing of Microtubule Centerlines in Electron Tomograms}, series = {BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization}, booktitle = {BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization}, year = {2011}, language = {en} } @article{LindowBaumBondaretal.2013, author = {Lindow, Norbert and Baum, Daniel and Bondar, Ana-Nicoleta and Hege, Hans-Christian}, title = {Exploring cavity dynamics in biomolecular systems}, series = {BMC Bioinformatics}, volume = {14}, journal = {BMC Bioinformatics}, edition = {(Suppl 19):S5}, doi = {10.1186/1471-2105-14-S19-S5}, year = {2013}, language = {en} } @inproceedings{LindowBaumBondaretal.2012, author = {Lindow, Norbert and Baum, Daniel and Bondar, Ana-Nicoleta and Hege, Hans-Christian}, title = {Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization}, series = {Proceedings of IEEE Symposium on Biological Data Visualization (biovis'12)}, booktitle = {Proceedings of IEEE Symposium on Biological Data Visualization (biovis'12)}, doi = {10.1109/BioVis.2012.6378599}, pages = {99 -- 106}, year = {2012}, language = {en} } @misc{KramerNoackBaumetal.2017, author = {Kramer, Tobias and Noack, Matthias and Baum, Daniel and Hege, Hans-Christian and Heller, Eric J.}, title = {Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66338}, year = {2017}, abstract = {Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term obser- vations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial dis- tribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending.}, language = {en} } @article{KramerNoackBaumetal., author = {Kramer, Tobias and Noack, Matthias and Baum, Daniel and Hege, Hans-Christian and Heller, Eric J.}, title = {Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko}, series = {Advances in Physics: X}, volume = {3}, journal = {Advances in Physics: X}, number = {1}, doi = {10.1080/23746149.2017.1404436}, pages = {1404436}, abstract = {Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term obser- vations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial dis- tribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending.}, language = {en} } @misc{HombergBaumWiebeletal.2014, author = {Homberg, Ulrike and Baum, Daniel and Wiebel, Alexander and Prohaska, Steffen and Hege, Hans-Christian}, title = {Definition, Extraction, and Validation of Pore Structures in Porous Materials}, series = {Topological Methods in Data Analysis and Visualization III}, journal = {Topological Methods in Data Analysis and Visualization III}, editor = {Bremer, Peer-Timo and Hotz, Ingrid and Pascucci, Valerio and Peikert, Ronald}, publisher = {Springer}, doi = {10.1007/978-3-319-04099-8_15}, pages = {235 -- 248}, year = {2014}, language = {en} } @misc{HombergBaumWiebeletal., author = {Homberg, Ulrike and Baum, Daniel and Wiebel, Alexander and Prohaska, Steffen and Hege, Hans-Christian}, title = {Definition, Extraction, and Validation of Pore Structures in Porous Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42510}, abstract = {An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation.}, language = {en} } @inproceedings{KlindtProhaskaBaumetal.2012, author = {Klindt, Marco and Prohaska, Steffen and Baum, Daniel and Hege, Hans-Christian}, title = {Conveying Archaeological Contexts to Museum Visitors: Case Study Pergamon Exhibition}, series = {VAST12: The 13th International Symposium on Virtual Reality, Archaeology and Intelligent Cultural Heritage - Short Papers}, booktitle = {VAST12: The 13th International Symposium on Virtual Reality, Archaeology and Intelligent Cultural Heritage - Short Papers}, editor = {Arnold, David and Kaminski, Jaime and Niccolucci, Franco and Stork, Andre}, publisher = {Eurographics Association}, address = {Brighton, UK}, doi = {10.2312/PE/VAST/VAST12S/025-028}, pages = {25 -- 28}, year = {2012}, language = {en} } @article{WeberGreenanProhaskaetal.2012, author = {Weber, Britta and Greenan, Garrett and Prohaska, Steffen and Baum, Daniel and Hege, Hans-Christian and M{\"u}ller-Reichert, Thomas and Hyman, Anthony and Verbavatz, Jean-Marc}, title = {Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos}, series = {Journal of Structural Biology}, volume = {178}, journal = {Journal of Structural Biology}, number = {2}, doi = {10.1016/j.jsb.2011.12.004}, pages = {129 -- 138}, year = {2012}, language = {en} } @article{RigortGuentherHegerletal.2012, author = {Rigort, Alexander and G{\"u}nther, David and Hegerl, Reiner and Baum, Daniel and Weber, Britta and Prohaska, Steffen and Medalia, Ohad and Baumeister, Wolfgang and Hege, Hans-Christian}, title = {Automated segmentation of electron tomograms for a quantitative description of actin filament networks}, series = {Journal of Structural Biology}, volume = {177}, journal = {Journal of Structural Biology}, doi = {10.1016/j.jsb.2011.08.012}, pages = {135 -- 144}, year = {2012}, language = {en} } @misc{LindowBaumHege, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Atomic Accessibility Radii for Molecular Dynamics Analysis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-68468}, abstract = {In molecular structure analysis and visualization, the molecule's atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called atomic accessibility radius', that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely.}, language = {en} } @inproceedings{LindowBaumHege, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Atomic Accessibility Radii for Molecular Dynamics Analysis}, series = {Workshop on Molecular Graphics and Visual Analysis of Molecular Data}, booktitle = {Workshop on Molecular Graphics and Visual Analysis of Molecular Data}, publisher = {The Eurographics Association}, isbn = {978-3-03868-061-1}, doi = {10.2312/molva.20181101}, abstract = {In molecular structure analysis and visualization, the molecule's atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called atomic accessibility radius', that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely.}, language = {en} } @article{MikulaDoerffelBaumetal.2022, author = {Mikula, Natalia and D{\"o}rffel, Tom and Baum, Daniel and Hege, Hans-Christian}, title = {An Interactive Approach for Identifying Structure Definitions}, series = {Computer Graphics Forum}, volume = {41}, journal = {Computer Graphics Forum}, number = {3}, doi = {10.1111/cgf.14543}, pages = {321 -- 332}, year = {2022}, abstract = {Our ability to grasp and understand complex phenomena is essentially based on recognizing structures and relating these to each other. For example, any meteorological description of a weather condition and explanation of its evolution recurs to meteorological structures, such as convection and circulation structures, cloud fields and rain fronts. All of these are spatiotemporal structures, defined by time-dependent patterns in the underlying fields. Typically, such a structure is defined by a verbal description that corresponds to the more or less uniform, often somewhat vague mental images of the experts. However, a precise, formal definition of the structures or, more generally, concepts is often desirable, e.g., to enable automated data analysis or the development of phenomenological models. Here, we present a systematic approach and an interactive tool to obtain formal definitions of spatiotemporal structures. The tool enables experts to evaluate and compare different structure definitions on the basis of data sets with time-dependent fields that contain the respective structure. Since structure definitions are typically parameterized, an essential part is to identify parameter ranges that lead to desired structures in all time steps. In addition, it is important to allow a quantitative assessment of the resulting structures simultaneously. We demonstrate the use of the tool by applying it to two meteorological examples: finding structure definitions for vortex cores and center lines of temporarily evolving tropical cyclones. Ideally, structure definitions should be objective and applicable to as many data sets as possible. However, finding such definitions, e.g., for the common atmospheric structures in meteorology, can only be a long-term goal. The proposed procedure, together with the presented tool, is just a first systematic approach aiming at facilitating this long and arduous way.}, language = {en} } @article{LindowBaumProhaskaetal.2010, author = {Lindow, Norbert and Baum, Daniel and Prohaska, Steffen and Hege, Hans-Christian}, title = {Accelerated Visualization of Dynamic Molecular Surfaces}, series = {Comput. Graph. Forum}, volume = {29}, journal = {Comput. Graph. Forum}, doi = {10.1111/j.1467-8659.2009.01693.x}, pages = {943 -- 952}, year = {2010}, language = {en} } @article{VohraHarthIsoeetal., author = {Vohra, Sumit Kumar and Harth, Philipp and Isoe, Yasuko and Bahl, Armin and Fotowat, Haleh and Engert, Florian and Hege, Hans-Christian and Baum, Daniel}, title = {A Visual Interface for Exploring Hypotheses about Neural Circuits}, series = {IEEE Transactions on Visualization and Computer Graphics}, journal = {IEEE Transactions on Visualization and Computer Graphics}, doi = {10.1109/TVCG.2023.3243668}, abstract = {One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa.}, language = {en} } @misc{VohraHarthIsoeetal., author = {Vohra, Sumit Kumar and Harth, Philipp and Isoe, Yasuko and Bahl, Armin and Fotowat, Haleh and Engert, Florian and Hege, Hans-Christian and Baum, Daniel}, title = {A Visual Interface for Exploring Hypotheses about Neural Circuits}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-89932}, abstract = {One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa.}, language = {en} } @inproceedings{HarthVohraUdvaryetal., author = {Harth, Philipp and Vohra, Sumit and Udvary, Daniel and Oberlaender, Marcel and Hege, Hans-Christian and Baum, Daniel}, title = {A Stratification Matrix Viewer for Analysis of Neural Network Data}, series = {Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)}, booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)}, address = {Vienna, Austria}, doi = {10.2312/vcbm.20221194}, abstract = {The analysis of brain networks is central to neurobiological research. In this context the following tasks often arise: (1) understand the cellular composition of a reconstructed neural tissue volume to determine the nodes of the brain network; (2) quantify connectivity features statistically; and (3) compare these to predictions of mathematical models. We present a framework for interactive, visually supported accomplishment of these tasks. Its central component, the stratification matrix viewer, allows users to visualize the distribution of cellular and/or connectional properties of neurons at different levels of aggregation. We demonstrate its use in four case studies analyzing neural network data from the rat barrel cortex and human temporal cortex.}, language = {en} } @inproceedings{BaumHege2006, author = {Baum, Daniel and Hege, Hans-Christian}, title = {A Point-matching based algorithm for 3D surface alignment of drug-sized molecules}, series = {Computational Life Sciences II, Second International Symposium, CompLife 2006, Cambridge (UK), Sept. 2006}, volume = {4216}, booktitle = {Computational Life Sciences II, Second International Symposium, CompLife 2006, Cambridge (UK), Sept. 2006}, publisher = {Springer}, doi = {10.1007/11875741_18}, pages = {183 -- 193}, year = {2006}, language = {en} }