TY - JOUR A1 - Schotte, Merlind A1 - Chaumel, Júlia A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae JF - MethodsX N2 - A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach. Y1 - 2020 U6 - https://doi.org/10.1016/j.mex.2020.100905 VL - 7 SP - 100905 ER - TY - GEN A1 - Schotte, Merlind A1 - Chaumel, Júlia A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae N2 - A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach. T3 - ZIB-Report - 20-12 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78237 SN - 1438-0064 ER - TY - JOUR A1 - Willsch, Maraike A1 - Friedrich, Frank A1 - Baum, Daniel A1 - Jurisch, Ivo A1 - Ohl, Michael T1 - A comparative description of the mesosomal musculature in Sphecidae and Ampulicidae (Hymenoptera, Apoidea) using 3D techniques JF - Deutsche Entomologische Zeitschrift N2 - Conflicting hypotheses about the relationships among the major lineages of aculeate Hymenoptera clearly show the necessity of detailed comparative morphological studies. Using micro-computed tomography and 3D reconstructions, the skeletal musculature of the meso- and metathorax and the first and second abdominal segment in Apoidea are described. Females of Sceliphron destillatorium, Sphex (Fernaldina) lucae (both Sphecidae), and Ampulex compressa (Ampulicidae) were examined. The morphological terminology provided by the Hymenoptera Anatomy Ontology is used. Up to 42 muscles were found. The three species differ in certain numerical and structural aspects. Ampulicidae differs significantly from Sphecidae in the metathorax and the anterior abdomen. The metapleural apodeme and paracoxal ridge are weakly developed in Ampulicidae, which affect some muscular structures. Furthermore, the muscles that insert on the coxae and trochanters are broader and longer in Ampulicidae. A conspicuous characteristic of Sphecidae is the absence of the metaphragma. Overall, we identified four hitherto unrecognized muscles. Our work suggests additional investigations on structures discussed in this paper. Y1 - 2020 U6 - https://doi.org/10.3897/dez.67.49493 VL - 67 IS - 1 SP - 51 EP - 67 ER - TY - JOUR A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Lindow, Norbert A1 - Powers, James A. A1 - Cota, Vanessa A1 - Quintanilla, Luis J. A1 - Brugués, Jan A1 - Prohaska, Steffen A1 - Chu, Diana S. A1 - Müller-Reichert, Thomas T1 - Sperm-specific meiotic chromosome segregation in C. elegans JF - eLife Y1 - 2020 U6 - https://doi.org/10.7554/eLife.50988 VL - 9 SP - e50988 ER - TY - JOUR A1 - Ege, Yannic A1 - Foth, Christian A1 - Baum, Daniel A1 - Wirkner, Christian S. A1 - Richter, Stefan T1 - Making spherical-harmonics-based Geometric Morphometrics (SPHARM) approachable for 3D images containing large cavity openings using Ambient Occlusion - a study using hermit crab claw shape variability JF - Zoomorphology N2 - An advantageous property of mesh-based geometric morphometrics (GM) towards landmark-based approaches, is the possibility of precisely examining highly irregular shapes and highly topographic surfaces. In case of spherical-harmonics-based GM the main requirement is a completely closed mesh surface, which often is not given, especially when dealing with natural objects. Here we present a methodological workflow to prepare 3D segmentations containing large cavity openings for the conduction of spherical-harmonics-based GM. This will be exemplified with a case study on claws of hermit crabs (Paguroidea, Decapoda, Crustacea), whereby joint openings – between manus and “movable finger” – typify the large-cavity-opening problem. We found a methodology including an ambient-occlusion-based segmentation algorithm leading to results precise and suitable to study the inter- and intraspecific differences in shape of hermit crab claws. Statistical analyses showed a significant separation between all examined diogenid and pagurid claws, whereas the separation between all left and right claws did not show significance. Additionally, the procedure offers other benefits. It is easy to reproduce and creates sparse variance in the data, closures integrate smoothly into the total structures and the algorithm saves a significant amount of time. Y1 - 2020 U6 - https://doi.org/10.1007/s00435-020-00488-z VL - 139 SP - 421 EP - 432 ER - TY - JOUR A1 - Scholtz, Gerhard A1 - Knötel, David A1 - Baum, Daniel T1 - D’Arcy W. Thompson’s Cartesian transformations: a critical evaluation JF - Zoomorphology N2 - The images of D’Arcy Wentworth Thompson’s book “On Growth and Form” got an iconic status and became influential for biometrics and other mathematical approaches to organismic form. In particular, this is true for those of the chapter on the theory of transformation, which even has an impact on art and humanities. Based on his approach, Thompson formulated far-reaching conclusions with a partly anti-Darwinian stance. Here, we use the example of Thompson’s transformation of crab carapaces to test to what degree the transformation of grids, landmarks, and shapes result in congruent images. For comparison, we applied the same series of tests to digitized carapaces of real crabs. Both approaches show similar results. Only the simple transformations show a reasonable form of congruence. In particular, the transformations to majoid spider crabs reveal a complicated transformation of grids with partly crossing lines. By contrast, the carapace of the lithodid species is relatively easily created despite the fact that it is no brachyuran, but evolved a spider crab-like shape convergently from a hermit crab ancestor. Y1 - 2020 U6 - https://doi.org/10.1007/s00435-020-00494-1 VL - 139 SP - 293 EP - 308 ER - TY - JOUR A1 - Lindow, Norbert A1 - Brünig, Florian A1 - Dercksen, Vincent J. A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Redemann, Stefanie A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen A1 - Baum, Daniel T1 - Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography JF - bioRxiv N2 - We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite the problems related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets. Y1 - 2020 U6 - https://doi.org/10.1101/2020.05.28.120899 ER - TY - JOUR A1 - Soares, Ana Prates A1 - Baum, Daniel A1 - Hesse, Bernhard A1 - Kupsch, Andreas A1 - Müller, Bernd A1 - Zaslansky, Paul T1 - Scattering and phase-contrast X-ray methods reveal damage to glass fibers in endodontic posts following dental bur trimming JF - Dental Materials Y1 - 2020 U6 - https://doi.org/10.1016/j.dental.2020.10.018 VL - 37 IS - 2 SP - 201 EP - 211 ER - TY - GEN A1 - Baum, Daniel A1 - Herter, Felix A1 - Lepper, Verena T1 - Jerash Silver Scroll: Virtually Unfolded Volume T2 - figshare N2 - A new virtual unfolding technique was applied to a silver scroll excavated in Jerash, Jordan, in 2014. As result of the unfolding, 17 lines of writing are clearly visible in the unfolded volumetric data that is published here. Y1 - 2020 U6 - https://doi.org/10.6084/m9.figshare.12145236 ER - TY - JOUR A1 - Titschack, Jürgen A1 - Baum, Daniel A1 - Matsuyama, Kei A1 - Boos, Karin A1 - Färber, Claudia A1 - Kahl, Wolf-Achim A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Soriano, Carmen A1 - Stock, Stuart R. T1 - Ambient occlusion – a powerful algorithm to segment shell and skeletal intrapores in computed tomography data JF - Computers and Geosciences N2 - During the last decades, X-ray (micro-)computed tomography has gained increasing attention for the description of porous skeletal and shell structures of various organism groups. However, their quantitative analysis is often hampered by the difficulty to discriminate cavities and pores within the object from the surrounding region. Herein, we test the ambient occlusion (AO) algorithm and newly implemented optimisations for the segmentation of cavities (implemented in the software Amira). The segmentation accuracy is evaluated as a function of (i) changes in the ray length input variable, and (ii) the usage of AO (scalar) field and other AO-derived (scalar) fields. The results clearly indicate that the AO field itself outperforms all other AO-derived fields in terms of segmentation accuracy and robustness against variations in the ray length input variable. The newly implemented optimisations improved the AO field-based segmentation only slightly, while the segmentations based on the AO-derived fields improved considerably. Additionally, we evaluated the potential of the AO field and AO-derived fields for the separation and classification of cavities as well as skeletal structures by comparing them with commonly used distance-map-based segmentations. For this, we tested the zooid separation within a bryozoan colony, the stereom classification of an ophiuroid tooth, the separation of bioerosion traces within a marble block and the calice (central cavity)-pore separation within a dendrophyllid coral. The obtained results clearly indicate that the ideal input field depends on the three-dimensional morphology of the object of interest. The segmentations based on the AO-derived fields often provided cavity separations and skeleton classifications that were superior to or impossible to obtain with commonly used distance- map-based segmentations. The combined usage of various AO-derived fields by supervised or unsupervised segmentation algorithms might provide a promising target for future research to further improve the results for this kind of high-end data segmentation and classification. Furthermore, the application of the developed segmentation algorithm is not restricted to X-ray (micro-)computed tomographic data but may potentially be useful for the segmentation of 3D volume data from other sources. Y1 - 2018 U6 - https://doi.org/10.1016/j.cageo.2018.03.007 VL - 115 SP - 75 EP - 87 ER - TY - GEN A1 - Titschack, Jürgen A1 - Baum, Daniel A1 - Matsuyama, Kei A1 - Boos, Karin A1 - Färber, Claudia A1 - Kahl, Wolf-Achim A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Soriano, Carmen A1 - Stock, Stuart R. T1 - Ambient occlusion – a powerful algorithm to segment shell and skeletal intrapores in computed tomography data N2 - During the last decades, X-ray (micro-)computed tomography has gained increasing attention for the description of porous skeletal and shell structures of various organism groups. However, their quantitative analysis is often hampered by the difficulty to discriminate cavities and pores within the object from the surrounding region. Herein, we test the ambient occlusion (AO) algorithm and newly implemented optimisations for the segmentation of cavities (implemented in the software Amira). The segmentation accuracy is evaluated as a function of (i) changes in the ray length input variable, and (ii) the usage of AO (scalar) field and other AO-derived (scalar) fields. The results clearly indicate that the AO field itself outperforms all other AO-derived fields in terms of segmentation accuracy and robustness against variations in the ray length input variable. The newly implemented optimisations improved the AO field-based segmentation only slightly, while the segmentations based on the AO-derived fields improved considerably. Additionally, we evaluated the potential of the AO field and AO-derived fields for the separation and classification of cavities as well as skeletal structures by comparing them with commonly used distance-map-based segmentations. For this, we tested the zooid separation within a bryozoan colony, the stereom classification of an ophiuroid tooth, the separation of bioerosion traces within a marble block and the calice (central cavity)-pore separation within a dendrophyllid coral. The obtained results clearly indicate that the ideal input field depends on the three-dimensional morphology of the object of interest. The segmentations based on the AO-derived fields often provided cavity separations and skeleton classifications that were superior to or impossible to obtain with commonly used distance- map-based segmentations. The combined usage of various AO-derived fields by supervised or unsupervised segmentation algorithms might provide a promising target for future research to further improve the results for this kind of high-end data segmentation and classification. Furthermore, the application of the developed segmentation algorithm is not restricted to X-ray (micro-)computed tomographic data but may potentially be useful for the segmentation of 3D volume data from other sources. T3 - ZIB-Report - 18-14 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67982 SN - 1438-0064 ER - TY - GEN A1 - Knötel, David A1 - Seidel, Ronald A1 - Zaslansky, Paul A1 - Prohaska, Steffen A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage (Supplementary Material) N2 - Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. In particular, sections from hyomandibulae harvested from specimens of round stingray Urobatis halleri, donated from another study (DOI: 10.1002/etc.2564). Specimens were from sub-adults/adults collected by beach seine from collection sites in San Diego and Seal Beach, California, USA. The hyomandibulae were mounted in clay, sealed in ethanol-humidified plastic tubes and scanned with a Skyscan 1172 desktop μCT scanner (Bruker μCT, Kontich, Belgium) in association with another study (DOI: 10.1111/joa.12508). Scans for all samples were performed with voxel sizes of 4.89 μm at 59 kV source voltage and 167 μA source current, over 360◦ sample 120 rotation. For our segmentations, the datasets were resampled to a voxel size of 9.78 μm to reduce the size of the images and speed up processing. In addition, the processed data that was generated with the visualization software Amira with techniques described in the related publication based on the mentioned specimens. Y1 - 2017 U6 - https://doi.org/10.12752/4.DKN.1.0 N1 - Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. ER - TY - JOUR A1 - Baum, Daniel A1 - Weaver, James C. A1 - Zlotnikov, Igor A1 - Knötel, David A1 - Tomholt, Lara A1 - Dean, Mason N. T1 - High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms JF - Integrative And Comparative Biology N2 - Various 3D imaging techniques are routinely used to examine biological materials, the results of which are usually a stack of grayscale images. In order to quantify structural aspects of the biological materials, however, they must first be extracted from the dataset in a process called segmentation. If the individual structures to be extracted are in contact or very close to each other, distance-based segmentation methods utilizing the Euclidean distance transform are commonly employed. Major disadvantages of the Euclidean distance transform, however, are its susceptibility to noise (very common in biological data), which often leads to incorrect segmentations (i.e. poor separation of objects of interest), and its limitation of being only effective for roundish objects. In the present work, we propose an alternative distance transform method, the random-walk distance transform, and demonstrate its effectiveness in high-throughput segmentation of three microCT datasets of biological tilings (i.e. structures composed of a large number of similar repeating units). In contrast to the Euclidean distance transform, this random-walk approach represents the global, rather than the local, geometric character of the objects to be segmented and, thus, is less susceptible to noise. In addition, it is directly applicable to structures with anisotropic shape characteristics. Using three case studies—stingray tessellated cartilage, starfish dermal endoskeleton, and the prismatic layer of bivalve mollusc shell—we provide a typical workflow for the segmentation of tiled structures, describe core image processing concepts that are underused in biological research, and show that for each study system, large amounts of biologically-relevant data can be rapidly segmented, visualized and analyzed. Y1 - 2019 U6 - https://doi.org/10.1093/icb/icz117 ER - TY - JOUR A1 - Mahnke, Heinz-Eberhard A1 - Arlt, Tobias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Herter, Felix A1 - Lindow, Norbert A1 - Manke, Ingo A1 - Siopi, Tzulia A1 - Menei, Eve A1 - Etienne, Marc A1 - Lepper, Verena T1 - Virtual unfolding of folded papyri JF - Journal of Cultural Heritage N2 - 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 Musée 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”. Y1 - 2020 U6 - https://doi.org/10.1016/j.culher.2019.07.007 VL - 41 SP - 264 EP - 269 PB - Elsevier ER - TY - GEN A1 - Baum, Daniel A1 - Weaver, James C. A1 - Zlotnikov, Igor A1 - Knötel, David A1 - Tomholt, Lara A1 - Dean, Mason N. T1 - High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms N2 - Various 3D imaging techniques are routinely used to examine biological materials, the results of which are usually a stack of grayscale images. In order to quantify structural aspects of the biological materials, however, they must first be extracted from the dataset in a process called segmentation. If the individual structures to be extracted are in contact or very close to each other, distance-based segmentation methods utilizing the Euclidean distance transform are commonly employed. Major disadvantages of the Euclidean distance transform, however, are its susceptibility to noise (very common in biological data), which often leads to incorrect segmentations (i.e. poor separation of objects of interest), and its limitation of being only effective for roundish objects. In the present work, we propose an alternative distance transform method, the random-walk distance transform, and demonstrate its effectiveness in high-throughput segmentation of three microCT datasets of biological tilings (i.e. structures composed of a large number of similar repeating units). In contrast to the Euclidean distance transform, this random-walk approach represents the global, rather than the local, geometric character of the objects to be segmented and, thus, is less susceptible to noise. In addition, it is directly applicable to structures with anisotropic shape characteristics. Using three case studies—stingray tessellated cartilage, starfish dermal endoskeleton, and the prismatic layer of bivalve mollusc shell—we provide a typical workflow for the segmentation of tiled structures, describe core image processing concepts that are underused in biological research, and show that for each study system, large amounts of biologically-relevant data can be rapidly segmented, visualized and analyzed. T3 - ZIB-Report - 19-33 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73841 SN - 1438-0064 ER - TY - JOUR A1 - Pöthkow, Kai A1 - Petz, Christoph A1 - Hege, Hans-Christian T1 - Approximate Level-Crossing Probabilities for Interactive Visualization of Uncertain Isocontours JF - International Journal for Uncertainty Quantification Y1 - 2013 U6 - https://doi.org/10.1615/Int.J.UncertaintyQuantification.2012003958 VL - 3 IS - 2 SP - 101 EP - 117 ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Wiebel, Alexander A1 - Prohaska, Steffen A1 - Hege, Hans-Christian ED - Bremer, Peer-Timo ED - Hotz, Ingrid ED - Pascucci, Valerio ED - Peikert, Ronald T1 - Definition, Extraction, and Validation of Pore Structures in Porous Materials BT - Theory, Algorithms, and Applications T2 - Topological Methods in Data Analysis and Visualization III Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-04099-8_15 SP - 235 EP - 248 PB - Springer ER - TY - CHAP A1 - Klindt, Marco A1 - Prohaska, Steffen A1 - Baum, Daniel A1 - Hege, Hans-Christian ED - Arnold, David ED - Kaminski, Jaime ED - Niccolucci, Franco ED - Stork, Andre T1 - Conveying Archaeological Contexts to Museum Visitors: Case Study Pergamon Exhibition T2 - VAST12: The 13th International Symposium on Virtual Reality, Archaeology and Intelligent Cultural Heritage - Short Papers Y1 - 2012 UR - http://diglib.eg.org/EG/DL/PE/VAST/VAST12S/025-028.pdf U6 - https://doi.org/10.2312/PE/VAST/VAST12S/025-028 SP - 25 EP - 28 PB - Eurographics Association CY - Brighton, UK ER - TY - CHAP A1 - Klindt, Marco A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - iCon.text – a customizable iPad app for kiosk applications in museum exhibitions T2 - EVA 2012 Berlin Y1 - 2012 SP - 150 EP - 155 PB - Gesellschaft zur Förderung angewandter Informatik e.V. CY - Volmerstraße 3, 12489 Berlin ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Bondar, Ana-Nicoleta A1 - Hege, Hans-Christian T1 - Exploring cavity dynamics in biomolecular systems JF - BMC Bioinformatics Y1 - 2013 U6 - https://doi.org/10.1186/1471-2105-14-S19-S5 VL - 14 ET - (Suppl 19):S5 ER - TY - JOUR A1 - Kratz, Andrea A1 - Baum, Daniel A1 - Hotz, Ingrid T1 - Anisotropic Sampling of Planar and Two-Manifold Domains for Texture Generation and Glyph Distribution JF - Transactions on Visualization and Computer Graphics (TVCG) Y1 - 2013 U6 - https://doi.org/10.1109/TVCG.2013.83 VL - 19 SP - 1782 EP - 1794 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Voronoi-Based Extraction and Visualization of Molecular Paths JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2011 U6 - https://doi.org/10.1109/TVCG.2011.259 VL - 17 IS - 12 SP - 2025 EP - 2034 ER - TY - JOUR A1 - Kleinfeld, David A1 - Bharioke, Arjun A1 - Blinder, Pablo A1 - Bock, David A1 - Briggman, Kevin A1 - Chklovskii, Dmitri A1 - Denk, Winfried A1 - Helmstaedter, Moritz A1 - Kaufhold, John A1 - Lee, Wei-Chung A1 - Meyer, Hanno A1 - Micheva, Kristina A1 - Oberlaender, Marcel A1 - Prohaska, Steffen A1 - Reid, R. A1 - Smith, Stephen A1 - Takemura, Shinya A1 - Tsai, Philbert A1 - Sakmann, Bert T1 - Large-scale automated histology in the pursuit of connectomes JF - Journal of Neuroscience Y1 - 2011 UR - http://www.zib.de/prohaska/docs/Kleinfeld_JNS_Connectomes_2011.pdf U6 - https://doi.org/10.1523/JNEUROSCI.4077-11.2011 VL - 31 IS - 45 SP - 16125 EP - 16138 ER - TY - JOUR A1 - Rigort, Alexander A1 - Günther, David A1 - Hegerl, Reiner A1 - Baum, Daniel A1 - Weber, Britta A1 - Prohaska, Steffen A1 - Medalia, Ohad A1 - Baumeister, Wolfgang A1 - Hege, Hans-Christian T1 - Automated segmentation of electron tomograms for a quantitative description of actin filament networks JF - Journal of Structural Biology Y1 - 2012 U6 - https://doi.org/10.1016/j.jsb.2011.08.012 VL - 177 SP - 135 EP - 144 ER - TY - JOUR A1 - Petz, Christoph A1 - Oberleithner, Kilian A1 - Sieber, Moritz A1 - Nayeri, Christian A1 - Paschereit, Oliver A1 - Wygnanski, Israel A1 - Noack, Bernd A1 - Hege, Hans-Christian T1 - Global Modes in a Swirling Jet Undergoing Vortex Breakdown JF - Physics of Fluids Y1 - 2011 U6 - https://doi.org/10.1063/1.3640007 VL - 23 SP - 091102 PB - Awarded Visualization; First Prize at 28th Annual Gallery of Fluid Motion exhibit, held at the 63th Annual Meeting of the American Physical Society, Division of Fluid Dynamics (Long Beach, CA, USA, November 21-23, 2010). ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Interactive Rendering of Materials and Biological Structures on Atomic and Nanoscopic Scale JF - Computer Graphics Forum Y1 - 2012 U6 - https://doi.org/10.1111/j.1467-8659.2012.03128.x target VL - 31 IS - 3 SP - 1325 EP - 1334 ER - TY - JOUR A1 - Petz, Christoph A1 - Pöthkow, Kai A1 - Hege, Hans-Christian T1 - Probabilistic Local Features in Uncertain Vector Fields with Spatial Correlation JF - Computer Graphics Forum Y1 - 2012 VL - 31 IS - 3 SP - 1045 EP - 1054 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Schaller, Jens A1 - Kertzscher, Ulrich A1 - van den Bruck, Nils A1 - Pöthkow, Kai A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Spuler, Andreas T1 - Statistical wall shear stress maps of ruptured and unruptured middle cerebral artery aneurysms JF - J. R. Soc. Interface Y1 - 2012 U6 - https://doi.org/10.1098/rsif.2011.0490 VL - 9 IS - 69 SP - 677 EP - 688 ER - TY - CHAP A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Kalbe, Ute A1 - Witt, Karl Josef T1 - Automatic Extraction and Analysis of Realistic Pore Structures from µCT Data for Pore Space Characterization of Graded Soil T2 - Proceedings of the 6th International Conference on Scour and Erosion (ICSE-6) Y1 - 2012 SP - 345 EP - 352 ER - TY - JOUR A1 - Weber, Britta A1 - Greenan, Garrett A1 - Prohaska, Steffen A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Müller-Reichert, Thomas A1 - Hyman, Anthony A1 - Verbavatz, Jean-Marc T1 - Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos JF - Journal of Structural Biology Y1 - 2012 UR - http://www.sciencedirect.com/science/article/pii/S1047847711003509 U6 - https://doi.org/10.1016/j.jsb.2011.12.004 VL - 178 IS - 2 SP - 129 EP - 138 ER - TY - JOUR A1 - Torsney-Weir, Thomas A1 - Saad, Ahmed A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - Weber, Britta A1 - Verbavatz, Jean-Marc T1 - Tuner: Principled Parameter Finding for Image Segmentation Algorithms Using Visual Response Surface Exploration JF - IEEE Trans. Vis. Comput. Graph. Y1 - 2011 VL - 17 IS - 12 SP - 1892 EP - 1901 ER - TY - CHAP A1 - Ehrig, Karsten A1 - Goebbels, Jürgen A1 - Meinel, Dietmar A1 - Paetsch, Olaf A1 - Prohaska, Steffen A1 - Zobel, Valentin T1 - Comparison of Crack Detection Methods for Analyzing Damage Processes in Concrete with Computed Tomography T2 - International Symposium on Digital Industrial Radiology and Computed Tomography Y1 - 2011 ER - TY - JOUR A1 - Oberleithner, Kilian A1 - Sieber, Moritz A1 - Nayeri, Christian A1 - Paschereit, Christian A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Wygnanski, Israel T1 - Self Excited Oscillations in Swirling Jets: Stability Analysis and Empirical Mode Construction JF - Bulletin of the American Physical Society Y1 - 2010 UR - http://meetings.aps.org/link/BAPS.2010.DFD.GE.8 N1 - 63rd Annual Meeting of the APS Division of Fluid Dynamics, November 21-23, 2010, Long Beach, CA VL - 55 IS - 16 SP - GE.00008 ER - TY - CHAP A1 - Binner, Richard A1 - Homberg, Ulrike A1 - Prohaska, Steffen A1 - Kalbe, Ute A1 - Witt, Karl Josef T1 - Identification of Descriptive Parameters of the Soil Pore Structure using Experiments and CT Data T2 - Proceedings of the 5th International Conference on Scour and Erosion (ICSE-5) Y1 - 2010 SP - 397 EP - 407 PB - American Society of Civil Engineers (ASCE) ER - TY - CHAP A1 - Günther, David A1 - McGuire, Patrick C. A1 - Walter, Sebastian A1 - Weinkauf, Tino A1 - Hege, Hans-Christian T1 - Extraction of Valley Networks in Mars Elevation Maps T2 - Proc. European Planetary Science Congress Y1 - 2010 VL - 5 SP - EPSC2010 EP - 216 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Accelerated Visualization of Dynamic Molecular Surfaces JF - Comput. Graph. Forum Y1 - 2010 U6 - https://doi.org/10.1111/j.1467-8659.2009.01693.x VL - 29 SP - 943 EP - 952 ER - TY - CHAP A1 - Reininghaus, Jan A1 - Günther, David A1 - Hotz, Ingrid A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - TADD: A Computational Framework for Data Analysis Using Discrete Morse Theory T2 - Mathematical Software - ICMS 2010 Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-15582-6_35 VL - 6327 SP - 198 EP - 208 PB - Springer ER - TY - JOUR A1 - Kuß, Anja A1 - Gensel, Maria A1 - Meyer, Björn A1 - Dercksen, Vincent J. A1 - Prohaska, Steffen T1 - Effective Techniques to Visualize Filament-Surface Relationships JF - Comput. Graph. Forum Y1 - 2010 VL - 29 SP - 1003 EP - 1012 ER - TY - JOUR A1 - Pöthkow, Kai A1 - Weber, Britta A1 - Hege, Hans-Christian T1 - Probabilistic Marching Cubes JF - Computer Graphics Forum Y1 - 2011 U6 - https://doi.org/10.1111/j.1467-8659.2011.01942.x VL - 30 IS - 3 SP - 931 EP - 940 ER - TY - JOUR A1 - Oberleithner, Kilian A1 - Sieber, Moritz A1 - Nayeri, Christian A1 - Paschereit, Christian A1 - Petz, Christoph A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - J. Wygnanski, Israel T1 - Three-dimensional Coherent Structures of the Swirling Jet Undergoing Vortex breakdown: Stability Analysis and Empirical Mode Construction JF - J. Fluid Mech. Y1 - 2011 U6 - https://doi.org/10.1017/jfm.2011.141 VL - 679 SP - 383 EP - 414 ER - TY - GEN A1 - Günther, David A1 - Reininghaus, Jan A1 - Prohaska, Steffen A1 - Weinkauf, Tino A1 - Hege, Hans-Christian ED - Peikert, Ronny ED - Hauser, Helwig ED - Carr, Hamish T1 - Efficient Computation of a Hierarchy of Discrete 3D Gradient Vector Fields T2 - Topological Methods in Data Analysis and Visualization II Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-23175-9_2 SP - 15 EP - 29 PB - Springer ER - TY - CHAP A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen ED - Mücklich, Frank ED - Slussallek, Philipp ED - Schladitz, Katja T1 - Describing and Analyzing the Dual Structures of Porous Media T2 - Proc. 3D-Microstructure Meeting Y1 - 2011 SP - 24 EP - 25 ER - TY - CHAP A1 - Weber, Britta A1 - Möller, Marit A1 - Verbavatz, Jean-Marc A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Prohaska, Steffen T1 - Fast Tracing of Microtubule Centerlines in Electron Tomograms T2 - BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization Y1 - 2011 ER - TY - CHAP A1 - Clasen, Malte A1 - Prohaska, Steffen T1 - Image-Error-Based Level of Detail for Landscape Visualization T2 - Proc. VMV 2010 Y1 - 2010 SP - 267 EP - 274 ER - TY - JOUR A1 - Kasten, Jens A1 - Petz, Christoph A1 - Hotz, Ingrid A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Tadmor, Gilead T1 - Lagrangian Feature Extraction of the Cylinder Wake JF - Physics of Fluids Y1 - 2010 U6 - https://doi.org/10.1063/1.3483220 VL - 22 IS - 9 SP - 091108 ER - TY - JOUR A1 - Ziegler, Alexander A1 - Ogurreck, Malte A1 - Steinke, Thomas A1 - Beckmann, Felix A1 - Prohaska, Steffen A1 - Ziegler, Andreas T1 - Opportunities and challenges for digital morphology JF - Biology Direct Y1 - 2010 U6 - https://doi.org/10.1186/1745-6150-5-45 VL - 5 IS - 1 SP - 45 ER - TY - CHAP A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Bondar, Ana-Nicoleta A1 - Hege, Hans-Christian T1 - Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization T2 - Proceedings of IEEE Symposium on Biological Data Visualization (biovis’12) Y1 - 2012 U6 - https://doi.org/10.1109/BioVis.2012.6378599 SP - 99 EP - 106 ER - TY - CHAP A1 - Pöthkow, Kai A1 - Hege, Hans-Christian ED - Laidlaw, David ED - Vilanova, Anna T1 - Uncertainty Propagation in DT-MRI Anisotropy Isosurface Extraction T2 - New Developments in the Visualization and Processing of Tensor Fields Y1 - 2012 SP - 209 EP - 225 PB - Springer CY - Berlin ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Perceptually Linear Parameter Variations JF - Computer Graphics Forum Y1 - 2012 U6 - https://doi.org/10.1111/j.1467-8659.2012.03054.x target VL - 31 IS - 2 SP - 535 EP - 544 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Weber, Sarah A1 - Petz, Christoph A1 - Spuler, Andreas A1 - Pöthke, Jens A1 - Berthe, André A1 - Hege, Hans-Christian T1 - Wall-PIV as a Near Wall Flow Validation Tool for CFD JF - Journal of Visualization Y1 - 2009 VL - 12 IS - 3 SP - 241 EP - 250 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Wellnhofer, Ernst A1 - Kertzscher, Ulrich A1 - Affeld, Klaus A1 - Petz, Christoph A1 - Hege, Hans-Christian T1 - Coronary Artery WSS Profiling Using a Geometry Reconstruction Based on Biplane Angiography JF - Annals of Biomedical Engineering Y1 - 2009 U6 - https://doi.org/s10439-009-9656-7 VL - 37 IS - 4 SP - 682 EP - 691 PB - Springer ER -