@article{HarthUdvaryBoeltsetal.2024, author = {Harth, Philipp and Udvary, Daniel and Boelts, Jan and Baum, Daniel and Macke, Jakob H. and Hege, Hans-Christian and Oberlaender, Marcel}, title = {Dissecting origins of wiring specificity in dense cortical connectomes}, journal = {bioRxiv}, doi = {10.1101/2024.12.14.628490}, year = {2024}, abstract = {Wiring specificity in the cortex is observed across scales from the subcellular to the network level. It describes the deviations of connectivity patterns from those expected in randomly connected networks. Understanding the origins of wiring specificity in neural networks remains difficult as a variety of generative mechanisms could have contributed to the observed connectome. To take a step forward, we propose a generative modeling framework that operates directly on dense connectome data as provided by saturated reconstructions of neural tissue. The computational framework allows testing different assumptions of synaptic specificity while accounting for anatomical constraints posed by neuron morphology, which is a known confounding source of wiring specificity. We evaluated the framework on dense reconstructions of the mouse visual and the human temporal cortex. Our template model incorporates assumptions of synaptic specificity based on cell type, single-cell identity, and subcellular compartment. Combinations of these assumptions were sufficient to model various connectivity patterns that are indicative of wiring specificity. Moreover, the identified synaptic specificity parameters showed interesting similarities between both datasets, motivating further analysis of wiring specificity across species.}, language = {en} } @article{BoeltsHarthGaoetal.2023, author = {Boelts, Jan and Harth, Philipp and Gao, Richard and Udvary, Daniel and Yanez, Felipe and Baum, Daniel and Hege, Hans-Christian and Oberlaender, Marcel and Macke, Jakob H.}, title = {Simulation-based inference for efficient identification of generative models in computational connectomics}, volume = {19}, journal = {PLOS Computational Biology}, number = {9}, doi = {10.1371/journal.pcbi.1011406}, year = {2023}, abstract = {Recent advances in connectomics research enable the acquisition of increasing amounts of data about the connectivity patterns of neurons. How can we use this wealth of data to efficiently derive and test hypotheses about the principles underlying these patterns? A common approach is to simulate neuronal networks using a hypothesized wiring rule in a generative model and to compare the resulting synthetic data with empirical data. However, most wiring rules have at least some free parameters, and identifying parameters that reproduce empirical data can be challenging as it often requires manual parameter tuning. Here, we propose to use simulation-based Bayesian inference (SBI) to address this challenge. Rather than optimizing a fixed wiring rule to fit the empirical data, SBI considers many parametrizations of a rule and performs Bayesian inference to identify the parameters that are compatible with the data. It uses simulated data from multiple candidate wiring rule parameters and relies on machine learning methods to estimate a probability distribution (the 'posterior distribution over parameters conditioned on the data') that characterizes all data-compatible parameters. We demonstrate how to apply SBI in computational connectomics by inferring the parameters of wiring rules in an in silico model of the rat barrel cortex, given in vivo connectivity measurements. SBI identifies a wide range of wiring rule parameters that reproduce the measurements. We show how access to the posterior distribution over all data-compatible parameters allows us to analyze their relationship, revealing biologically plausible parameter interactions and enabling experimentally testable predictions. We further show how SBI can be applied to wiring rules at different spatial scales to quantitatively rule out invalid wiring hypotheses. Our approach is applicable to a wide range of generative models used in connectomics, providing a quantitative and efficient way to constrain model parameters with empirical connectivity data.}, language = {en} } @article{OkaforntaFarhadifarFabigetal.2025, author = {Okafornta, Chukwuebuka William and Farhadifar, Reza and Fabig, Gunar and Wu, Hai-Yin and K{\"o}ckert, Maria and Vogel, Martin and Baum, Daniel and Haase, Robert and Shelley, Michael J. and Needleman, Daniel J. and M{\"u}ller-Reichert, Thomas}, title = {Cell size reduction scales spindle elongation but not chromosome segregation in C. elegans}, journal = {bioRxiv}, doi = {10.1101/2025.10.13.681585}, year = {2025}, abstract = {How embryos adapt their internal cellular machinery to reductions in cell size during development remains a fundamental question in cell biology. Here, we use high-resolution lattice light-sheet fluorescence microscopy and automated image analysis to quantify lineage-resolved mitotic spindle and chromosome segregation dynamics from the 2- to 64-cell stages in Caenorhabditis elegans embryos. While spindle length scales with cell size across both wild-type and size-perturbed embryos, chromosome segregation dynamics remain largely invariant, suggesting that distinct mechanisms govern these mitotic processes. Combining femtosecond laser ablation with large-scale electron tomography, we find that central spindle microtubules mediate chromosome segregation dynamics and remain uncoupled from cell size across all stages of early development. In contrast, spindle elongation is driven by cortically anchored motor proteins and astral microtubules, rendering it sensitive to cell size. Incorporating these experimental results into an extended stoichiometric model for both the spindle and chromosomes, we find that allowing only cell size and microtubule catastrophe rates to vary reproduces elongation dynamics across development. The same model also accounts for centrosome separation and pronuclear positioning in the one-cell C. elegans embryo, spindle-length scaling across nematode species spanning ~100 million years of divergence, and spindle rotation in human cells. Thus, a unified stoichiometric framework provides a predictive, mechanistic account of spindle and nuclear dynamics across scales and species.}, language = {en} } @article{BoeltsHarthGaoetal.2023, author = {Boelts, Jan and Harth, Philipp and Gao, Richard and Udvary, Daniel and Yanez, Felipe and Baum, Daniel and Hege, Hans-Christian and Oberlaender, Marcel and Macke, Jakob H}, title = {Simulation-based inference for efficient identification of generative models in connectomics}, journal = {bioRxiv}, doi = {10.1101/2023.01.31.526269}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-89890}, year = {2023}, abstract = {Recent advances in connectomics research enable the acquisition of increasing amounts of data about the connectivity patterns of neurons. How can we use this wealth of data to efficiently derive and test hypotheses about the principles underlying these patterns? A common approach is to simulate neural networks using a hypothesized wiring rule in a generative model and to compare the resulting synthetic data with empirical data. However, most wiring rules have at least some free parameters and identifying parameters that reproduce empirical data can be challenging as it often requires manual parameter tuning. Here, we propose to use simulation-based Bayesian inference (SBI) to address this challenge. Rather than optimizing a single rule to fit the empirical data, SBI considers many parametrizations of a wiring rule and performs Bayesian inference to identify the parameters that are compatible with the data. It uses simulated data from multiple candidate wiring rules and relies on machine learning methods to estimate a probability distribution (the `posterior distribution over rule parameters conditioned on the data') that characterizes all data-compatible rules. We demonstrate how to apply SBI in connectomics by inferring the parameters of wiring rules in an in silico model of the rat barrel cortex, given in vivo connectivity measurements. SBI identifies a wide range of wiring rule parameters that reproduce the measurements. We show how access to the posterior distribution over all data-compatible parameters allows us to analyze their relationship, revealing biologically plausible parameter interactions and enabling experimentally testable predictions. We further show how SBI can be applied to wiring rules at different spatial scales to quantitatively rule out invalid wiring hypotheses. Our approach is applicable to a wide range of generative models used in connectomics, providing a quantitative and efficient way to constrain model parameters with empirical connectivity data.}, language = {en} } @article{KiewiszFabigConwayetal.2022, author = {Kiewisz, Robert and Fabig, Gunar and Conway, William and Baum, Daniel and Needleman, Daniel and M{\"u}ller-Reichert, Thomas}, title = {Three-dimensional structure of kinetochore-fibers in human mitotic spindles}, volume = {11}, journal = {eLife}, doi = {10.7554/eLife.75459}, pages = {e75459}, year = {2022}, abstract = {During cell division, kinetochore microtubules (KMTs) provide a physical linkage between the chromosomes and the rest of the spindle. KMTs in mammalian cells are organized into bundles, so-called kinetochore-fibers (k-fibers), but the ultrastructure of these fibers is currently not well characterized. Here we show by large-scale electron tomography that each k-fiber in HeLa cells in metaphase is composed of approximately nine KMTs, only half of which reach the spindle pole. Our comprehensive reconstructions allowed us to analyze the three-dimensional (3D) morphology of k-fibers and their surrounding MTs in detail. We found that k-fibers exhibit remarkable variation in circumference and KMT density along their length, with the pole-proximal side showing a broadening. Extending our structural analysis then to other MTs in the spindle, we further observed that the association of KMTs with non-KMTs predominantly occurs in the spindle pole regions. Our 3D reconstructions have implications for KMT growth and k-fiber self-organization models as covered in a parallel publication applying complementary live-cell imaging in combination with biophysical modeling (Conway et al., 2022). Finally, we also introduce a new visualization tool allowing an interactive display of our 3D spindle data that will serve as a resource for further structural studies on mitosis in human cells.}, language = {en} } @article{EigenBaumDeanetal.2022, author = {Eigen, Lennart and Baum, Daniel and Dean, Mason N. and Werner, Daniel and W{\"o}lfer, Jan and Nyakatura, John A.}, title = {Ontogeny of a tessellated surface: carapace growth of the longhorn cowfish Lactoria cornuta}, volume = {241}, journal = {Journal of Anatomy}, number = {3}, publisher = {Wiley}, doi = {10.1111/joa.13692}, pages = {565 -- 580}, year = {2022}, abstract = {Biological armors derive their mechanical integrity in part from their geometric architectures, often involving tessellations: individual structural elements tiled together to form surface shells. The carapace of boxfish, for example, is comprised of mineralized polygonal plates, called scutes, arranged in a complex geometric pattern and nearly completely encasing the body. In contrast to artificial armors, the boxfish exoskeleton grows with the fish; the relationship between the tessellation and the gross structure of the armor is therefore critical to sustained protection throughout growth. To clarify whether or how the boxfish tessellation is maintained or altered with age, we quantify architectural aspects of the tessellated carapace of the longhorn cowfish Lactoria cornuta through ontogeny (across nearly an order of magnitude in standard length) and in a high-throughput fashion, using high-resolution microCT data and segmentation algorithms to characterize the hundreds of scutes that cover each individual. We show that carapace growth is canalized with little variability across individuals: rather than continually adding scutes to enlarge the carapace surface, the number of scutes is surprisingly constant, with scutes increasing in volume, thickness, and especially width with age. As cowfish and their scutes grow, scutes become comparatively thinner, with the scutes at the edges (weak points in a boxy architecture) being some of the thickest and most reinforced in younger animals and thinning most slowly across ontogeny. In contrast, smaller scutes with more variable curvature were found in the limited areas of more complex topology (e.g. around fin insertions, mouth, and anus). Measurements of Gaussian and mean curvature illustrate that cowfish are essentially tessellated boxes throughout life: predominantly zero curvature surfaces comprised of mostly flat scutes, and with scutes with sharp bends used sparingly to form box edges. Since growth of a curved, tiled surface with a fixed number of tiles would require tile restructuring to accommodate the surface's changing radius of curvature, our results therefore illustrate a previously unappreciated advantage of the odd boxfish morphology: by having predominantly flat surfaces, it is the box-like body form that in fact permits a relatively straightforward growth system of this tessellated architecture (i.e. where material is added to scute edges). Our characterization of the ontogeny and maintenance of the carapace tessellation provides insights into the potentially conflicting mechanical, geometric and developmental constraints of this species, but also perspectives into natural strategies for constructing mutable tiled architectures.}, language = {en} } @inproceedings{HarthVohraUdvaryetal.2022, author = {Harth, Philipp and Vohra, Sumit and Udvary, Daniel and Oberlaender, Marcel and Hege, Hans-Christian and Baum, Daniel}, title = {A Stratification Matrix Viewer for Analysis of Neural Network Data}, booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)}, address = {Vienna, Austria}, doi = {10.2312/vcbm.20221194}, year = {2022}, abstract = {The analysis of brain networks is central to neurobiological research. In this context the following tasks often arise: (1) understand the cellular composition of a reconstructed neural tissue volume to determine the nodes of the brain network; (2) quantify connectivity features statistically; and (3) compare these to predictions of mathematical models. We present a framework for interactive, visually supported accomplishment of these tasks. Its central component, the stratification matrix viewer, allows users to visualize the distribution of cellular and/or connectional properties of neurons at different levels of aggregation. We demonstrate its use in four case studies analyzing neural network data from the rat barrel cortex and human temporal cortex.}, language = {en} } @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} } @article{SchmidtEhrenbergBaumHege2001, author = {Schmidt-Ehrenberg, Johannes and Baum, Daniel and Hege, Hans-Christian}, title = {Visually stunning - Molecular conformations}, volume = {23}, journal = {The Biochemist}, number = {5}, pages = {22 -- 26}, year = {2001}, language = {en} } @inproceedings{SchmidtEhrenbergBaumHege2002, author = {Schmidt-Ehrenberg, Johannes and Baum, Daniel and Hege, Hans-Christian}, title = {Visualizing Dynamic Molecular Conformations}, booktitle = {Proceedings of IEEE Visualization 2002}, editor = {J. Moorhead, Robert and Gross, Markus and I. Joy, Kenneth}, publisher = {IEEE Computer Society Press}, address = {Boston MA, USA}, doi = {10.1109/VISUAL.2002.1183780}, pages = {235 -- 242}, year = {2002}, language = {en} } @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} } @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} }