@article{HochWesselAscheetal.2014, author = {Hoch, Hannelore and Wessel, Andreas and Asche, Manfred and Baum, Daniel and Beckmann, Felix and Br{\"a}unig, Peter and Ehrig, Karsten and M{\"u}hlethaler, Roland and Riesemeier, Heinrich and Staude, Andreas and Stelbrink, Bj{\"o}rn and Wachmann, Ekkehard and Weintraub, Phyllis and Wipfler, Benjamin and Wolff, Carsten and Zilch, Mathias}, title = {Non-Sexual Abdominal Appendages in Adult Insects Challenge a 300 Million Year Old Bauplan}, volume = {24}, journal = {Current Biology}, number = {1}, doi = {10.1016/j.cub.2013.11.040}, pages = {R16 -- R17}, year = {2014}, language = {en} } @misc{LindowBaumLeborgneetal.2018, 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}, year = {2018}, 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.2019, author = {Lindow, Norbert and Baum, Daniel and Leborgne, Morgan and Hege, Hans-Christian}, title = {Interactive Visualization of RNA and DNA Structures}, volume = {25}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {1}, doi = {10.1109/TVCG.2018.2864507}, pages = {967 -- 976}, year = {2019}, 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} } @misc{KnoetelBeckerScholtzetal.2018, author = {Kn{\"o}tel, David and Becker, Carola and Scholtz, Gerhard and Baum, Daniel}, title = {Global and Local Mesh Morphing for Complex Biological Objects from microCT Data}, issn = {1438-0064}, doi = {10.2312/vcbm.20181243}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-70618}, year = {2018}, abstract = {We show how biologically coherent mesh models of animals can be created from μCT data to generate artificial yet naturally looking intermediate objects. The whole pipeline of processing algorithms is presented, starting from generating topologically equivalent surface meshes, followed by solving the correspondence problem, and, finally, creating a surface morphing. In this pipeline, we address all the challenges that are due to dealing with complex biological, non-isometric objects. For biological objects it is often particularly important to obtain deformations that look as realistic as possible. In addition, spatially non-uniform shape morphings that only change one part of the surface and keep the rest as stable as possible are of interest for evolutionary studies, since functional modules often change independently from one another. We use Poisson interpolation for this purpose and show that it is well suited to generate both global and local shape deformations.}, language = {en} } @inproceedings{KnoetelBeckerScholtzetal.2018, author = {Kn{\"o}tel, David and Becker, Carola and Scholtz, Gerhard and Baum, Daniel}, title = {Global and Local Mesh Morphing for Complex Biological Objects from microCT Data}, booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)}, address = {Granada, Spain}, doi = {10.2312/vcbm.20181243}, pages = {179 -- 183}, year = {2018}, abstract = {We show how biologically coherent mesh models of animals can be created from μCT data to generate artificial yet naturally looking intermediate objects. The whole pipeline of processing algorithms is presented, starting from generating topologically equivalent surface meshes, followed by solving the correspondence problem, and, finally, creating a surface morphing. In this pipeline, we address all the challenges that are due to dealing with complex biological, non-isometric objects. For biological objects it is often particularly important to obtain deformations that look as realistic as possible. In addition, spatially non-uniform shape morphings that only change one part of the surface and keep the rest as stable as possible are of interest for evolutionary studies, since functional modules often change independently from one another. We use Poisson interpolation for this purpose and show that it is well suited to generate both global and local shape deformations.}, 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}, 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.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}, issn = {1438-0064}, doi = {10.1007/s00339-017-0808-6}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-61826}, 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} } @inproceedings{PaetschBaumEhrigetal.2012, author = {Paetsch, Olaf and Baum, Daniel and Ehrig, Karsten and Meinel, Dietmar and Prohaska, Steffen}, title = {Vergleich automatischer 3D-Risserkennungsmethoden f{\"u}r die quantitative Analyse der Schadensentwicklung in Betonproben mit Computer-Tomographie}, booktitle = {Tagungsband der DACH Jahrestagung 2012}, year = {2012}, language = {de} } @inproceedings{PaetschBaumBressleretal.2013, author = {Paetsch, Olaf and Baum, Daniel and Breßler, David and Ehrig, Karsten and Meinel, Dietmar and Prohaska, Steffen}, title = {3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben}, booktitle = {Tagungsband der DGZfP Jahrestagung 2013}, year = {2013}, language = {de} } @inproceedings{PaetschBaumEhrigetal.2012, author = {Paetsch, Olaf and Baum, Daniel and Ehrig, Karsten and Meinel, Dietmar and Prohaska, Steffen}, title = {Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography}, booktitle = {Proceedings of Conference on Industrial Computed Tomography}, pages = {321 -- 330}, year = {2012}, language = {en} } @misc{KroneKozlikovaLindowetal.2016, 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}, 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{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}, 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} } @misc{DeanHosnySeideletal.2016, author = {Dean, Mason N. and Hosny, Ahmed and Seidel, Ronald and Baum, Daniel}, title = {Biological strategies for fatique and wear avoidance: lessons from stingray skeletons and teeth}, journal = {Poster, Tomography for Scientific Advancement symposium (ToScA)}, year = {2016}, language = {en} } @article{TitschackFinkBaumetal.2016, author = {Titschack, J{\"u}rgen and Fink, Hiske G. and Baum, Daniel and Wienberg, Claudia and Hebbeln, Dierk and Freiwald, Andr{\´e}}, title = {Mediterranean cold-water corals - an important regional carbonate factory?}, volume = {2}, journal = {The Depositional Record}, number = {1}, doi = {10.1002/dep2.14}, pages = {74 -- 96}, year = {2016}, language = {en} } @inproceedings{BaumTitschack2016, author = {Baum, Daniel and Titschack, J{\"u}rgen}, title = {Cavity and Pore Segmentation in 3D Images with Ambient Occlusion}, booktitle = {EuroVis 2016 - Short Papers}, publisher = {The Eurographics Association}, doi = {10.2312/eurovisshort.20161171}, year = {2016}, language = {en} } @misc{BaumTitschack2016, author = {Baum, Daniel and Titschack, J{\"u}rgen}, title = {Cavity and Pore Segmentation in 3D Images with Ambient Occlusion}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59151}, year = {2016}, abstract = {Many natural objects contain pores and cavities that are filled with the same material that also surrounds the object. When such objects are imaged using, for example, computed tomography, the pores and cavities cannot be distinguished from the surrounding material by considering gray values and texture properties of the image. In this case, morphological operations are often used to fill the inner region. This is efficient, if the pore and cavity structures are small compared to the overall size of the object and if the object's shape is mainly convex. If this is not the case, the segmentation might be very difficult and may result in a lot of noise. We propose the usage of ambient occlusion for the segmentation of pores and cavities. One nice property of ambient occlusion is that it generates smooth scalar fields. Due to this smoothness property, a segmentation based on those fields will result in smooth boundaries at the pore and cavity openings. This is often desired, particularly when dealing with natural objects.}, language = {en} } @article{KramerNoackBaumetal.2015, 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}, arxiv = {http://arxiv.org/abs/1505.08041}, year = {2015}, 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} } @misc{LindowBaumHege2018, 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}, year = {2018}, 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{LindowBaumHege2018, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Atomic Accessibility Radii for Molecular Dynamics Analysis}, 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}, year = {2018}, 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{NyakaturaBaumgartenBaumetal.2019, author = {Nyakatura, John and Baumgarten, Roxane and Baum, Daniel and Stark, Heiko and Youlatos, Dionisios}, title = {Muscle internal structure revealed by contrast-enhanced μCT and fibre recognition: The hindlimb extensors of an arboreal and a fossorial squirrel}, volume = {99}, journal = {Mammalian Biology}, doi = {10.1016/j.mambio.2019.10.007}, pages = {71 -- 80}, year = {2019}, abstract = {In individuals of similar body mass representing closely related species with different lifestyles, muscle architectural properties can be assumed to reflect adaptation to differing, lifestyle-related functional demands. We here employ a fiber recognition algorithm on contrast-enhanced micro-computed tomography (μCT) scans of one specimen each of an arboreal (Sciurus vulgaris) and a fossorial (Spermophilus citellus) sciuromorph rodent. The automated approach accounts for potential heterogeneity of architectural properties within a muscle by analyzing all fascicles that compose a muscle. Muscle architectural properties (volume, fascicle length, and orientation, and force-generating capacity) were quantified in 14 hindlimb (hip, knee, and ankle) extensor muscles and compared between specimens. We expected the arboreal squirrel to exhibit greater force-generating capacity and a greater capacity for length change allowing more powerful hindlimb extension. Generally and mostly matching our expectations, the S. vulgaris specimen had absolutely and relatively larger extensor muscles than the S. citellus specimen which were thus metabolically more expensive and demonstrate the relatively larger investment into powerful hindlimb extension necessary in the arboreal context. We conclude that detailed quantitative data on hindlimb muscle internal structure as was gathered here for a very limited sample further lends support to the notion that muscle architecture reflects adaptation to differential functional demands in closely related species with different locomotor behaviors and lifestyles.}, language = {en} } @article{MohrAltenburgUlbrichtetal.2020, author = {Mohr, Gunther and Altenburg, Simon J. and Ulbricht, Alexander and Heinrich, Philipp and Baum, Daniel and Maierhofer, Christiane and Hilgenberg, Kai}, title = {In-situ defect detection in laser powder bed fusion by using thermography and optical tomography - comparison to computed tomography}, volume = {10}, journal = {Metals}, number = {1}, doi = {10.3390/met10010103}, pages = {103}, year = {2020}, language = {en} }