@misc{Baum2004, author = {Baum, Daniel}, title = {Multiple Semi-flexible 3D Superposition of Drug-sized Molecules}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-8278}, number = {04-52}, year = {2004}, abstract = {In this paper we describe a new algorithm for multiple semi-flexible superpositioning of drug-sized molecules. The algorithm identifies structural similarities of two or more molecules. When comparing a set of molecules on the basis of their three-dimensional structures, one is faced with two main problems. (1) Molecular structures are not fixed but flexible, i.e., a molecule adopts different forms. To address this problem, we consider a set of conformers per molecule. As conformers we use representatives of conformational ensembles, generated by the program ZIBMol. (2) The degree of similarity may vary considerably among the molecules. This problem is addressed by searching for similar substructures present in arbitrary subsets of the given set of molecules. The algorithm requires to preselect a reference molecule. All molecules are compared to this reference molecule. For this pairwise comparison we use a two-step approach. Clique detection on the correspondence graph of the molecular structures is used to generate start transformations, which are then iteratively improved to compute large common substructures. The results of the pairwise comparisons are efficiently merged using binary matching trees. All common substructures that were found, whether they are common to all or only a few molecules, are ranked according to different criteria, such as number of molecules containing the substructure, size of substructure, and geometric fit. For evaluating the geometric fit, we extend a known scoring function by introducing weights which allow to favor potential pharmacophore points. Despite considering the full atomic information for identifying multiple structural similarities, our algorithm is quite fast. Thus it is well suited as an interactive tool for the exploration of structural similarities of drug-sized molecules.}, language = {en} } @misc{Baum2004, author = {Baum, Daniel}, title = {Finding All Maximal Cliques of a Family of Induced Subgraphs}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7758}, number = {03-53}, year = {2004}, abstract = {Many real world problems can be mapped onto graphs and solved with well-established efficient algorithms studied in graph theory. One such problem is to find large sets of points satisfying some mutual relationship. This problem can be transformed to the problem of finding all cliques of an undirected graph by mapping each point onto a vertex of the graph and connecting any two vertices by an edge whose corresponding points satisfy our desired relationship. Clique detection has been widely studied and there exist efficient algorithms. In this paper we study a related problem, where all points have a set of binary attributes, each of which is either 0 or 1. This is only a small limitation, since all discrete properties can be mapped onto binary attributes. In our case, we want to find large sets of points not only satisfying some mutual relationship; but, in addition, all points of a set also need to have at least one common attribute with value 1. The problem we described can be mapped onto a set of induced subgraphs, where each subgraph represents a single attribute. For attribute \$i\$, its associated subgraph contains those vertices corresponding to the points with attribute \$i\$ set to 1. We introduce the notion of a maximal clique of a family, \$\mathcal{G}\$, of induced subgraphs of an undirected graph, and show that determining all maximal cliques of \$\mathcal{G}\$ solves our problem. Furthermore, we present an efficient algorithm to compute all maximal cliques of \$\mathcal{G}\$. The algorithm we propose is an extension of the widely used Bron-Kerbosch algorithm.}, language = {en} } @misc{KlindtBaumProhaskaetal.2013, 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}, year = {2013}, 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} } @misc{HombergBaumWiebeletal.2013, 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}, year = {2013}, 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} } @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} } @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} } @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} } @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} } @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} } @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} } @misc{ChaumelSchotteBizzarroetal.2020, author = {Chaumel, J{\´u}lia and Schotte, Merlind and Bizzarro, Joseph J. and Zaslansky, Paul and Fratzl, Peter and Baum, Daniel and Dean, Mason N.}, title = {Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-77087}, year = {2020}, abstract = {In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone.}, language = {en} } @misc{SchotteChaumelDeanetal.2020, author = {Schotte, Merlind and Chaumel, J{\´u}lia and Dean, Mason N. and Baum, Daniel}, title = {Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-78237}, year = {2020}, abstract = {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.}, language = {en} } @misc{EgeFothBaumetal.2020, author = {Ege, Yannic and Foth, Christian and Baum, Daniel and Wirkner, Christian S. and Richter, Stefan}, title = {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}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-77744}, year = {2020}, abstract = {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.}, language = {en} } @misc{TitschackBaumMatsuyamaetal.2018, author = {Titschack, J{\"u}rgen and Baum, Daniel and Matsuyama, Kei and Boos, Karin and F{\"a}rber, Claudia and Kahl, Wolf-Achim and Ehrig, Karsten and Meinel, Dietmar and Soriano, Carmen and Stock, Stuart R.}, title = {Ambient occlusion - a powerful algorithm to segment shell and skeletal intrapores in computed tomography data}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-67982}, year = {2018}, abstract = {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.}, language = {en} } @misc{Baum2019, author = {Baum, Daniel}, title = {An Evaluation of Color Maps for Visual Data Exploration}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74259}, year = {2019}, language = {en} } @misc{MahnkeArltBaumetal.2019, 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}, year = {2019}, 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{BaumWeaverZlotnikovetal.2019, author = {Baum, Daniel and Weaver, James C. and Zlotnikov, Igor and Kn{\"o}tel, David and Tomholt, Lara and Dean, Mason N.}, title = {High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-73841}, year = {2019}, abstract = {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.}, language = {en} } @misc{BaumGiliardHasleretal.2019, author = {Baum, Daniel and Giliard, Nicole and Hasler, Tim and Peters-Kottig, Wolfgang}, title = {Leitlinien zum Umgang mit Forschungsdaten am Zuse-Institut Berlin}, address = {Berlin}, doi = {10.12752/7378}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-73781}, year = {2019}, abstract = {Die nachhaltige Sicherung und Bereitstellung von Forschungsdaten dienen nicht nur der Reproduzierbarkeit fr{\"u}herer Ergebnisse, sondern in hohem Maße auch der Erzielung k{\"u}nftiger Ergebnisse mit dem Ziel, die Qualit{\"a}t, Produktivit{\"a}t und Wettbewerbsf{\"a}higkeit der Wissenschaft zu f{\"o}rdern. Die folgenden Grunds{\"a}tze gelten als Leitlinien zur Handhabung von Forschungsdaten im ZIB.}, language = {de} } @misc{LindowBaumHege2014, 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}, 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{HoerthBaumKnoeteletal.2015, 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}, year = {2015}, 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} }