@misc{RosanwoPetzProhaskaetal.2008, author = {Rosanwo, Olufemi and Petz, Christoph and Prohaska, Steffen and Hotz, Ingrid and Hege, Hans-Christian}, title = {Dual Streamline Seeding - Method and Implementation}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11032}, number = {08-49}, year = {2008}, abstract = {This work introduces a novel streamline seeding technique based on dual streamlines that are orthogonal to the vector field, instead of tangential. The greedy algorithm presented here produces a net of orthogonal streamlines that is iteratively refined resulting in good domain coverage and a high degree of continuity and uniformity. The algorithm is easy to implement and efficient, and it naturally extends to curved surfaces.}, language = {en} } @misc{GuentherLameckerWeiser2011, author = {G{\"u}nther, Andreas and Lamecker, Hans and Weiser, Martin}, title = {Direct LDDMM of Discrete Currents with Adaptive Finite Elements}, doi = {10.1007/s11263-012-0599-3}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-13090}, number = {11-22}, year = {2011}, abstract = {We consider Large Deformation Diffeomorphic Metric Mapping of general \$m\$-currents. After stating an optimization algorithm in the function space of admissable morph generating velocity fields, two innovative aspects in this framework are presented and numerically investigated: First, we spatially discretize the velocity field with conforming adaptive finite elements and discuss advantages of this new approach. Second, we directly compute the temporal evolution of discrete \$m\$-current attributes.}, language = {en} } @misc{KratzMeyerHotz2010, author = {Kratz, Andrea and Meyer, Bj{\"o}rn and Hotz, Ingrid}, title = {A Visual Approach to Analysis of Stress Tensor Fields}, doi = {/10.4230/DFU.Vol2.SciViz.2011.188}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11915}, number = {10-26}, year = {2010}, abstract = {We present a visual approach for the exploration of stress tensor fields. Therefore, we introduce the idea of multiple linked views to tensor visualization. In contrast to common tensor visualization methods that only provide a single view to the tensor field, we pursue the idea of providing various perspectives onto the data in attribute and object space. Especially in the context of stress tensors, advanced tensor visualization methods have a young tradition. Thus, we propose a combination of visualization techniques domain experts are used to with statistical views of tensor attributes. The application of this concept to tensor fields was achieved by extending the notion of shape space. It provides an intuitive way of finding tensor invariants that represent relevant physical properties. Using brushing techniques, the user can select features in attribute space, which are mapped to displayable entities in a three-dimensional hybrid visualization in object space. Volume rendering serves as context, while glyphs encode the whole tensor information in focus regions. Tensorlines can be included to emphasize directionally coherent features in the tensor field. We show that the benefit of such a multi-perspective approach is manifold. Foremost, it provides easy access to the complexity of tensor data. Moreover, including wellknown analysis tools, such as Mohr diagrams, users can familiarize themselves gradually with novel visualization methods. Finally, by employing a focus-driven hybrid rendering, we significantly reduce clutter, which was a major problem of other three-dimensional tensor visualization methods.}, language = {en} } @misc{ReininghausKastenWeinkaufetal.2011, author = {Reininghaus, Jan and Kasten, Jens and Weinkauf, Tino and Hotz, Ingrid}, title = {Combinatorial Feature Flow Fields: Tracking Critical Points in Discrete Scalar Fields}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-12151}, number = {11-02}, year = {2011}, abstract = {We propose a combinatorial algorithm to track critical points of 2D time-dependent scalar fields. Existing tracking algorithms such as Feature Flow Fields apply numerical schemes utilizing derivatives of the data, which makes them prone to noise and involve a large number of computational parameters. In contrast, our method is robust against noise since it does not require derivatives, interpolation, and numerical integration. Furthermore, we propose an importance measure that combines the spatial persistence of a critical point with its temporal evolution. This leads to a time-aware feature hierarchy, which allows us to discriminate important from spurious features. Our method requires only a single, easy-to-tune computational parameter and is naturally formulated in an out-of-core fashion, which enables the analysis of large data sets. We apply our method to a number of data sets and compare it to the stabilized continuous Feature Flow Field tracking algorithm.}, language = {en} } @misc{KratzReininghausHadwigeretal.2011, author = {Kratz, Andrea and Reininghaus, Jan and Hadwiger, Markus and Hotz, Ingrid}, title = {Adaptive Screen-Space Sampling for Volume Ray-Casting}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-12446}, number = {11-04}, year = {2011}, abstract = {This work is concerned with adaptive screen-space sampling for volume ray-casting. The goal is to reduce the number of rays being cast into the scene and, thus, the overall number of sampling points. We guarantee reliable images through explicit error control using an error estimator that is founded in the field of finite element methods (FEM). FEM theory further provides a well-founded theory to prove the efficiency of the presented algorithm via convergence analysis. We, therefore, compare the convergence behavior of our method against uniform subdivisions and a refinement scheme that was presented in the context of CPU volume ray-casting. Minimizing the number of sampling points is of interest for rendering large datasets where each evaluation might need an expensive decompression. Furthermore, with increasing screen resolutions high-resolution images are created more efficiently with our method.}, language = {en} } @misc{ClasenPaarProhaska2011, author = {Clasen, Malte and Paar, Philip and Prohaska, Steffen}, title = {Level of Detail for Trees Using Clustered Ellipsoids}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-14251}, number = {11-41}, year = {2011}, abstract = {We present a level of detail method for trees based on ellipsoids and lines. We leverage the Expectation Maximization algorithm with a Gaussian Mixture Model to create a hierarchy of high-quality leaf clusterings, while the branches are simplified using agglomerative bottom-up clustering to preserve the connectivity. The simplification runs in a preprocessing step and requires no human interaction. For a fly by over and through a scene of 10k trees, our method renders on average at 40 ms/frame, up to 6 times faster than billboard clouds with comparable artifacts.}, language = {en} } @misc{WiebelVosHege2011, author = {Wiebel, Alexander and Vos, Frans M. and Hege, Hans-Christian}, title = {Perception-Oriented Picking of Structures in Direct Volumetric Renderings}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-14343}, number = {11-45}, year = {2011}, abstract = {Radiologists from all application areas are trained to read slice-based visualizations of 3D medical image data. Despite the numerous examples of sophisticated three-dimensional renderings, especially all variants of direct volume rendering, such methods are often considered not very useful by radiologists who prefer slice-based visualization. Just recently there have been attempts to bridge this gap between 2D and 3D renderings. These attempts include specialized techniques for volume picking that result in repositioning slices. In this paper, we present a new volume picking technique that, in contrast to previous work, does not require pre-segmented data or metadata. The positions picked by our method are solely based on the data itself, the transfer function and, most importantly, on the way the volumetric rendering is perceived by viewers. To demonstrate the usefulness of the proposed method we apply it for automatically repositioning slices in an abdominal MRI scan, a data set from a flow simulation and a number of other volumetric scalar fields. Furthermore we discuss how the method can be implemented in combination with various different volumetric rendering techniques.}, language = {en} } @misc{ZilskeLameckerZachow2007, author = {Zilske, Michael and Lamecker, Hans and Zachow, Stefan}, title = {Adaptive Remeshing of Non-Manifold Surfaces}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9445}, number = {07-01}, year = {2007}, abstract = {We present a unified approach for consistent remeshing of arbitrary non-manifold triangle meshes with additional user-defined feature lines, which together form a feature skeleton. Our method is based on local operations only and produces meshes of high regularity and triangle quality while preserving the geometry as well as topology of the feature skeleton and the input mesh.}, 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{EhlkeRammLameckeretal.2013, author = {Ehlke, Moritz and Ramm, Heiko and Lamecker, Hans and Hege, Hans-Christian and Zachow, Stefan}, title = {Fast Generation of Virtual X-ray Images from Deformable Tetrahedral Meshes}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41896}, year = {2013}, abstract = {We propose a novel GPU-based approach to render virtual X-ray projections of deformable tetrahedral meshes. These meshes represent the shape and the internal density distribution of a particular anatomical structure and are derived from statistical shape and intensity models (SSIMs). We apply our method to improve the geometric reconstruction of 3D anatomy (e.g.\ pelvic bone) from 2D X-ray images. For that purpose, shape and density of a tetrahedral mesh are varied and virtual X-ray projections are generated within an optimization process until the similarity between the computed virtual X-ray and the respective anatomy depicted in a given clinical X-ray is maximized. The OpenGL implementation presented in this work deforms and projects tetrahedral meshes of high resolution (200.000+ tetrahedra) at interactive rates. It generates virtual X-rays that accurately depict the density distribution of an anatomy of interest. Compared to existing methods that accumulate X-ray attenuation in deformable meshes, our novel approach significantly boosts the deformation/projection performance. The proposed projection algorithm scales better with respect to mesh resolution and complexity of the density distribution, and the combined deformation and projection on the GPU scales better with respect to the number of deformation parameters. The gain in performance allows for a larger number of cycles in the optimization process. Consequently, it reduces the risk of being stuck in a local optimum. We believe that our approach contributes in orthopedic surgery, where 3D anatomy information needs to be extracted from 2D X-rays to support surgeons in better planning joint replacements.}, language = {en} } @misc{EhlkeRammLameckeretal.2012, author = {Ehlke, Moritz and Ramm, Heiko and Lamecker, Hans and Zachow, Stefan}, title = {Efficient projection and deformation of volumetric intensity models for accurate simulation of X-ray images}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-16580}, year = {2012}, abstract = {We present an efficient GPU-based method to generate virtual X-ray images from tetrahedral meshes which are associated with attenuation values. In addition, a novel approach is proposed that performs the model deformation on the GPU. The tetrahedral grids are derived from volumetric statistical shape and intensity models (SSIMs) and describe anatomical structures. Our research targets at reconstructing 3D anatomical shapes by comparing virtual X-ray images generated using our novel approach with clinical data while varying the shape and density of the SSIM in an optimization process. We assume that a deformed SSIM adequately represents an anatomy of interest when the similarity between the virtual and the clinical X-ray image is maximized. The OpenGL implementation presented here generates accurate (virtual) X-ray images at interactive rates, thus qualifying it for its use in the reconstruction process.}, language = {en} } @misc{RammMorilloVictoriaTodtetal.2013, author = {Ramm, Heiko and Morillo Victoria, Oscar Salvador and Todt, Ingo and Schirmacher, Hartmut and Ernst, Arneborg and Zachow, Stefan and Lamecker, Hans}, title = {Visual Support for Positioning Hearing Implants}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42495}, year = {2013}, abstract = {We present a software planning tool that provides intuitive visual feedback for finding suitable positions of hearing implants in the human temporal bone. After an automatic reconstruction of the temporal bone anatomy the tool pre-positions the implant and allows the user to adjust its position interactively with simple 2D dragging and rotation operations on the bone's surface. During this procedure, visual elements like warning labels on the implant or color encoded bone density information on the bone geometry provide guidance for the determination of a suitable fit.}, 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{KuhnEngelkeRoessletal.2013, author = {Kuhn, Alexander and Engelke, Wito and R{\"o}ssl, Christian and Hadwiger, Markus and Theisel, Holger}, title = {Time Line Cell Tracking for the Approximation of Lagrangian Coherent Structures with Subgrid Accuracy}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-43050}, year = {2013}, abstract = {Lagrangian Coherent Structures (LCS) have become a widespread and powerful method to describe dynamic motion patterns in time-dependent flow fields. The standard way to extract LCS is to compute height ridges in the Finite Time Lyapunov Exponent (FTLE) field. In this work, we present an alternative method to approximate Lagrangian features for 2D unsteady flow fields that achieves subgrid accuracy without additional particle sampling. We obtain this by a geometric reconstruction of the flow map using additional material constraints for the available samples. In comparison to the standard method, this allows for a more accurate global approximation of LCS on sparse grids and for long integration intervals. The proposed algorithm works directly on a set of given particle trajectories and without additional flow map derivatives. We demonstrate its application for a set of computational fluid dynamic examples, as well as trajectories acquired by Lagrangian methods, and discuss its benefits and limitations.}, language = {en} } @misc{DercksenHegeOberlaender2013, author = {Dercksen, Vincent J. and Hege, Hans-Christian and Oberlaender, Marcel}, title = {The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology}, issn = {1438-0064}, doi = {10.1007/s12021-013-9213-2}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-43157}, year = {2013}, abstract = {Neuroanatomical analysis, such as classification of cell types, depends on reliable reconstruction of large numbers of complete 3D dendrite and axon morphologies. At present, the majority of neuron reconstructions are obtained from preparations in a single tissue slice in vitro, thus suffering from cut off dendrites and, more dramatically, cut off axons. In general, axons can innervate volumes of several cubic millimeters and may reach path lengths of tens of centimeters. Thus, their complete reconstruction requires in vivo labeling, histological sectioning and imaging of large fields of view. Unfortunately, anisotropic background conditions across such large tissue volumes, as well as faintly labeled thin neurites, result in incomplete or erroneous automated tracings and even lead experts to make annotation errors during manual reconstructions. Consequently, tracing reliability renders the major bottleneck for reconstructing complete 3D neuron morphologies. Here, we present a novel set of tools, integrated into a software environment named 'Filament Editor', for creating reliable neuron tracings from sparsely labeled in vivo datasets. The Filament Editor allows for simultaneous visualization of complex neuronal tracings and image data in a 3D viewer, proof-editing of neuronal tracings, alignment and interconnection across sections, and morphometric analysis in relation to 3D anatomical reference structures. We illustrate the functionality of the Filament Editor on the example of in vivo labeled axons and demonstrate that for the exemplary dataset the final tracing results after proof-editing are independent of the expertise of the human operator.}, language = {en} } @misc{AmbellanLameckervonTycowiczetal.2019, author = {Ambellan, Felix and Lamecker, Hans and von Tycowicz, Christoph and Zachow, Stefan}, title = {Statistical Shape Models - Understanding and Mastering Variation in Anatomy}, issn = {1438-0064}, doi = {10.1007/978-3-030-19385-0_5}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-72699}, year = {2019}, abstract = {In our chapter we are describing how to reconstruct three-dimensional anatomy from medical image data and how to build Statistical 3D Shape Models out of many such reconstructions yielding a new kind of anatomy that not only allows quantitative analysis of anatomical variation but also a visual exploration and educational visualization. Future digital anatomy atlases will not only show a static (average) anatomy but also its normal or pathological variation in three or even four dimensions, hence, illustrating growth and/or disease progression. Statistical Shape Models (SSMs) are geometric models that describe a collection of semantically similar objects in a very compact way. SSMs represent an average shape of many three-dimensional objects as well as their variation in shape. The creation of SSMs requires a correspondence mapping, which can be achieved e.g. by parameterization with a respective sampling. If a corresponding parameterization over all shapes can be established, variation between individual shape characteristics can be mathematically investigated. We will explain what Statistical Shape Models are and how they are constructed. Extensions of Statistical Shape Models will be motivated for articulated coupled structures. In addition to shape also the appearance of objects will be integrated into the concept. Appearance is a visual feature independent of shape that depends on observers or imaging techniques. Typical appearances are for instance the color and intensity of a visual surface of an object under particular lighting conditions, or measurements of material properties with computed tomography (CT) or magnetic resonance imaging (MRI). A combination of (articulated) statistical shape models with statistical models of appearance lead to articulated Statistical Shape and Appearance Models (a-SSAMs).After giving various examples of SSMs for human organs, skeletal structures, faces, and bodies, we will shortly describe clinical applications where such models have been successfully employed. Statistical Shape Models are the foundation for the analysis of anatomical cohort data, where characteristic shapes are correlated to demographic or epidemiologic data. SSMs consisting of several thousands of objects offer, in combination with statistical methods ormachine learning techniques, the possibility to identify characteristic clusters, thus being the foundation for advanced diagnostic disease scoring.}, language = {en} } @misc{AmbellanTackEhlkeetal.2019, author = {Ambellan, Felix and Tack, Alexander and Ehlke, Moritz and Zachow, Stefan}, title = {Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-72704}, year = {2019}, abstract = {We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging (MRI) that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs).The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures.The shape models and neural networks employed are trained using data from the Osteoarthritis Initiative (OAI) and the MICCAI grand challenge "Segmentation of Knee Images 2010" (SKI10), respectively. We evaluate our method on 40 validation and 50 submission datasets from the SKI10 challenge.For the first time, an accuracy equivalent to the inter-observer variability of human readers is achieved in this challenge.Moreover, the quality of the proposed method is thoroughly assessed using various measures for data from the OAI, i.e. 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy for both OAI datasets. We make the 507 manual segmentations as well as our experimental setup publicly available to further aid research in the field of medical image segmentation.In conclusion, combining localized classification via CNNs with statistical anatomical knowledge via SSMs results in a state-of-the-art segmentation method for knee bones and cartilage from MRI data.}, 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{SakuraiOnoCarretal.2019, author = {Sakurai, Daisuke and Ono, Kenji and Carr, Hamish and Nonaka, Jorji and Kawanabe, Tomohiro}, title = {Flexible Fiber Surfaces: A Reeb-Free Approach}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-72599}, year = {2019}, abstract = {The fiber surface generalizes the popular isosurface to multi-fields, so that pre-images can be visualized as surfaces. As with the isosurface, however, the fiber surface suffers from visual occlusion. We propose to avoid such occlusion by restricting the components to only the relevant ones with a new component-wise flexing algorithm. The approach, flexible fiber surface, generalizes the manipulation idea found in the flexible isosurface for the fiber surface. The flexible isosurface in the original form, however, relies on the contour tree. For the fiber surface, this corresponds to the Reeb space, which is challenging for both the computation and user interaction. We thus take a Reeb-free approach, in which one does not compute the Reeb space. Under this constraint, we generalize a few selected interactions in the flexible isosurface and discuss the implication of the restriction.}, language = {en} } @misc{SakuraiHegeKuhnetal.2017, author = {Sakurai, Daisuke and Hege, Hans-Christian and Kuhn, Alexander and Rust, Henning and Kern, Bastian and Breitkopf, Tom-Lukas}, title = {An Application-Oriented Framework for Feature Tracking in Atmospheric Sciences}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-72617}, year = {2017}, abstract = {In atmospheric sciences, sizes of data sets grow continuously due to increasing resolutions. A central task is the comparison of spatiotemporal fields, to assess different simulations and to compare simulations with observations. A significant information reduction is possible by focusing on geometric-topological features of the fields or on derived meteorological objects. Due to the huge size of the data sets, spatial features have to be extracted in time slices and traced over time. Fields with chaotic component, i.e. without 1:1 spatiotemporal correspondences, can be compared by looking upon statistics of feature properties. Feature extraction, however, requires a clear mathematical definition of the features - which many meteorological objects still lack. Traditionally, object extractions are often heuristic, defined only by implemented algorithms, and thus are not comparable. This work surveys our framework designed for efficient development of feature tracking methods and for testing new feature definitions. The framework supports well-established visualization practices and is being used by atmospheric researchers to diagnose and compare data.}, language = {en} } @misc{BuchmannKaplanPowelletal.2019, author = {Buchmann, Jens and Kaplan, Bernhard and Powell, Samuel and Prohaska, Steffen and Laufer, Jan}, title = {3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent}, issn = {1438-0064}, doi = {10.1117/1.JBO.24.6.066001}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-72995}, year = {2019}, abstract = {Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Gr{\"u}neisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori.}, 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{AgudoJacomeHegePaetschetal.2018, author = {Agudo J{\´a}come, Leonardo and Hege, Hans-Christian and Paetsch, Olaf and P{\"o}thkow, Kai}, title = {Three-Dimensional Reconstruction and Quantification of Dislocation Substructures from Transmission Electron Microscopy Stereo-Pairs}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-70339}, year = {2018}, abstract = {A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo-pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo-pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (> 300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo-pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3 \% and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed.}, language = {en} } @misc{TackZachow2019, author = {Tack, Alexander and Zachow, Stefan}, title = {Accurate Automated Volumetry of Cartilage of the Knee using Convolutional Neural Networks: Data from the Osteoarthritis Initiative}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-71439}, year = {2019}, abstract = {Volumetry of the cartilage of the knee, as needed for the assessment of knee osteoarthritis (KOA), is typically performed in a tedious and subjective process. We present an automated segmentation-based method for the quantification of cartilage volume by employing 3D Convolutional Neural Networks (CNNs). CNNs were trained in a supervised manner using magnetic resonance imaging data as well as cartilage volumetry readings given by clinical experts for 1378 subjects. It was shown that 3D CNNs can be employed for cartilage volumetry with an accuracy similar to expert volumetry readings. In future, accurate automated cartilage volumetry might support both, diagnosis of KOA as well as assessment of KOA progression via longitudinal analysis.}, language = {en} } @misc{WiebelPreisVosetal.2013, author = {Wiebel, Alexander and Preis, Philipp and Vos, Frans M. and Hege, Hans-Christian}, title = {Computation and Application of 3D Strokes on Visible Structures in Direct Volume Rendering}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-18070}, year = {2013}, abstract = {In this paper we describe VisiTrace, a novel technique to draw 3D lines in 3D volume rendered images. It allows to draw strokes in the 2D space of the screen to produce 3D lines that run on top or in the center of structures actually visible in the volume rendering. It can handle structures that only shortly occlude the structure that has been visible at the starting point of the stroke and is able to ignore such structures. For this purpose a shortest path algorithm finding the optimal curve in a specially designed graph data structure is employed. We demonstrate the usefulness of the technique by applying it to MRI data from medicine and engineering, and show how the method can be used to mark or analyze structures in the example data sets, and to automatically obtain good views toward the selected structures.}, language = {en} } @misc{TycowiczAmbellanMukhopadhyayetal.2016, author = {Tycowicz, Christoph von and Ambellan, Felix and Mukhopadhyay, Anirban and Zachow, Stefan}, title = {A Riemannian Statistical Shape Model using Differential Coordinates}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-61175}, year = {2016}, abstract = {We propose a novel Riemannian framework for statistical analysis of shapes that is able to account for the nonlinearity in shape variation. By adopting a physical perspective, we introduce a differential representation that puts the local geometric variability into focus. We model these differential coordinates as elements of a Lie group thereby endowing our shape space with a non-Euclidian structure. A key advantage of our framework is that statistics in a manifold shape space become numerically tractable improving performance by several orders of magnitude over state-of-the-art. We show that our Riemannian model is well suited for the identification of intra-population variability as well as inter-population differences. In particular, we demonstrate the superiority of the proposed model in experiments on specificity and generalization ability. We further derive a statistical shape descriptor that outperforms the standard Euclidian approach in terms of shape-based classification of morphological disorders.}, 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{VincensWittHomberg2014, author = {Vincens, Eric and Witt, Karl Josef and Homberg, Ulrike}, title = {Approaches to Determine the Constriction Size Distribution for Understanding Filtration Phenomena in Granular Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-43960}, year = {2014}, abstract = {Granular filters in hydraulically loaded earth structures constitute the ultimate barrier for the blockage of small particles moving through the structure regularly or along concentrated leaks. If filters are inefficient to block small particles several types of internal erosion may be initiated. A corresponding phenomenon appears during suffusion in a wide graded hydraulically loaded fill, when fine particles, embedded in the pore structure of a soil skeleton, are washed out. The cumulative constriction size distribution (CSD) is physically the key property that qualifies the soils retention capability as like a spatial acting sieve. Constrictions are defined as the narrowest sections of channels between larger volumes (pores) within the pore network of granular material and they are the main obstacles for a small particle to overcome when flowing along pathways. At least three different approaches are available to determine and compute the CSD, i.e. experimental, numerical and analytical methods. The purpose of this review is to present and discuss these methods pointing out their limits, advantages and significance related to internal erosion phenomena.}, 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{BrandtTycowiczHildebrandt2016, author = {Brandt, Christopher and Tycowicz, Christoph von and Hildebrandt, Klaus}, title = {Geometric Flows of Curves in Shape Space for Processing Motion of Deformable Objects}, issn = {1438-0064}, doi = {10.1111/cgf.12832}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59504}, year = {2016}, abstract = {We introduce techniques for the processing of motion and animations of non-rigid shapes. The idea is to regard animations of deformable objects as curves in shape space. Then, we use the geometric structure on shape space to transfer concepts from curve processing in R^n to the processing of motion of non-rigid shapes. Following this principle, we introduce a discrete geometric flow for curves in shape space. The flow iteratively replaces every shape with a weighted average shape of a local neighborhood and thereby globally decreases an energy whose minimizers are discrete geodesics in shape space. Based on the flow, we devise a novel smoothing filter for motions and animations of deformable shapes. By shortening the length in shape space of an animation, it systematically regularizes the deformations between consecutive frames of the animation. The scheme can be used for smoothing and noise removal, e.g., for reducing jittering artifacts in motion capture data. We introduce a reduced-order method for the computation of the flow. In addition to being efficient for the smoothing of curves, it is a novel scheme for computing geodesics in shape space. We use the scheme to construct non-linear "B{\´e}zier curves" by executing de Casteljau's algorithm in shape space.}, language = {en} } @misc{CostaMantonOstrovskyetal.2016, author = {Costa, Marta and Manton, James D. and Ostrovsky, Aaron D. and Prohaska, Steffen and Jefferis, Gregory S.X.E.}, title = {NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases}, issn = {1438-0064}, doi = {10.1016/j.neuron.2016.06.012}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59672}, year = {2016}, abstract = {Neural circuit mapping is generating datasets of 10,000s of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types including searching neurons against transgene expression patterns. Finally we show that NBLAST is effective with data from other invertebrates and zebrafish.}, language = {en} } @misc{GuentherKuhnHegeetal.2016, author = {G{\"u}nther, Tobias and Kuhn, Alexander and Hege, Hans-Christian and Theisel, Holger}, title = {MCFTLE: Monte Carlo Rendering of Finite-Time Lyapunov Exponent Fields}, issn = {1438-0064}, doi = {10.1111/cgf.12914}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59054}, year = {2016}, abstract = {Traditionally, Lagrangian fields such as finite-time Lyapunov exponents (FTLE) are precomputed on a discrete grid and are ray casted afterwards. This, however, introduces both grid discretization errors and sampling errors during ray marching. In this work, we apply a progressive, view-dependent Monte Carlo-based approach for the visualization of such Lagrangian fields in time-dependent flows. Our ap- proach avoids grid discretization and ray marching errors completely, is consistent, and has a low memory consumption. The system provides noisy previews that con- verge over time to an accurate high-quality visualization. Compared to traditional approaches, the proposed system avoids explicitly predefined fieldline seeding structures, and uses a Monte Carlo sampling strategy named Woodcock tracking to distribute samples along the view ray. An acceleration of this sampling strategy requires local upper bounds for the FTLE values, which we progressively acquire during the rendering. Our approach is tailored for high-quality visualizations of complex FTLE fields and is guaranteed to faithfully represent detailed ridge surface structures as indicators for Lagrangian coherent structures (LCS). We demonstrate the effectiveness of our approach by using a set of analytic test cases and real-world numerical simulations.}, 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{NavaYazdaniHegevonTycowiczetal.2018, author = {Nava-Yazdani, Esfandiar and Hege, Hans-Christian and von Tycowicz, Christoph and Sullivan, T. J.}, title = {A Shape Trajectories Approach to Longitudinal Statistical Analysis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-69759}, year = {2018}, abstract = {For Kendall's shape space we determine analytically Jacobi fields and parallel transport, and compute geodesic regression. Using the derived expressions, we can fully leverage the geometry via Riemannian optimization and reduce the computational expense by several orders of magnitude. The methodology is demonstrated by performing a longitudinal statistical analysis of epidemiological shape data. As application example we have chosen 3D shapes of knee bones, reconstructed from image data of the Osteoarthritis Initiative. Comparing subject groups with incident and developing osteoarthritis versus normal controls, we find clear differences in the temporal development of femur shapes. This paves the way for early prediction of incident knee osteoarthritis, using geometry data only.}, language = {en} } @misc{RedemannLantzschLindowetal.2018, author = {Redemann, Stefanie and Lantzsch, Ina and Lindow, Norbert and Prohaska, Steffen and Srayko, Martin and M{\"u}ller-Reichert, Thomas}, title = {A switch in microtubule orientation during C. elegans meiosis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-69855}, year = {2018}, abstract = {In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [1-5]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter- chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter- chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [6, 7]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [8, 9]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here we applied large-scale electron tomography [10] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes.}, 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{PapazovHege2017, author = {Papazov, Chavdar and Hege, Hans-Christian}, title = {Blue-noise Optimized Point Sets Based on Procrustes Analysis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65356}, year = {2017}, abstract = {In this paper, we propose a new method for optimizing the blue noise characteristics of point sets. It is based on Procrustes analysis, a technique for adjusting shapes to each other by applying optimal elements of an appropriate transformation group. We adapt this technique to the problem at hand and introduce a very simple, efficient and provably convergent point set optimizer.}, language = {en} } @misc{AmbellanTackWilsonetal.2017, author = {Ambellan, Felix and Tack, Alexander and Wilson, Dave and Anglin, Carolyn and Lamecker, Hans and Zachow, Stefan}, title = {Evaluating two methods for Geometry Reconstruction from Sparse Surgical Navigation Data}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66052}, year = {2017}, abstract = {In this study we investigate methods for fitting a Statistical Shape Model (SSM) to intraoperatively acquired point cloud data from a surgical navigation system. We validate the fitted models against the pre-operatively acquired Magnetic Resonance Imaging (MRI) data from the same patients. We consider a cohort of 10 patients who underwent navigated total knee arthroplasty. As part of the surgical protocol the patients' distal femurs were partially digitized. All patients had an MRI scan two months pre-operatively. The MRI data were manually segmented and the reconstructed bone surfaces used as ground truth against which the fit was compared. Two methods were used to fit the SSM to the data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). For both approaches, the difference between model fit and ground truth surface averaged less than 1.7 mm and excellent correspondence with the distal femoral morphology can be demonstrated.}, language = {en} } @misc{SeblanyHombergVincensetal.2018, author = {Seblany, Feda and Homberg, Ulrike and Vincens, Eric and Winkler, Paul and Witt, Karl Josef}, title = {Merging criteria for defining pores and constrictions in numerical packing of spheres}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-69158}, year = {2018}, abstract = {The void space of granular materials is generally divided into larger local volumes denoted as pores and throats connecting pores. The smallest section in a throat is usually denoted as constriction. A correct description of pores and constrictions may help to understand the processes related to the transport of fluid or fine particles through granular materials, or to build models of imbibition for unsaturated granular media. In the case of numerical granular materials involving packings of spheres, different methods can be used to compute the pore space properties. However, these methods generally induce an over-segmentation of the pore network and a merging step is usually applied to mitigate such undesirable artifacts even if a precise delineation of a pore is somewhat subjective. This study provides a comparison between different merging criteria for pores in packing of spheres and a discussion about their implication on both the pore size distribution and the constriction size distribution of the material. A correspondence between these merging techniques is eventually proposed as a guide for the user.}, language = {en} } @misc{BuchmannKaplanPowelletal.2019, author = {Buchmann, Jens and Kaplan, Bernhard and Powell, Samuel and Prohaska, Steffen and Laufer, Jan}, title = {Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms}, issn = {1438-0064}, doi = {10.1016/j.pacs.2019.100157}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-75416}, year = {2019}, abstract = {Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies.}, 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{GreweLeRouxPilzetal.2018, author = {Grewe, Carl Martin and Le Roux, Gabriel and Pilz, Sven-Kristofer and Zachow, Stefan}, title = {Spotting the Details: The Various Facets of Facial Expressions}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-67696}, year = {2018}, abstract = {3D Morphable Models (MM) are a popular tool for analysis and synthesis of facial expressions. They represent plausible variations in facial shape and appearance within a low-dimensional parameter space. Fitted to a face scan, the model's parameters compactly encode its expression patterns. This expression code can be used, for instance, as a feature in automatic facial expression recognition. For accurate classification, an MM that can adequately represent the various characteristic facets and variants of each expression is necessary. Currently available MMs are limited in the diversity of expression patterns. We present a novel high-quality Facial Expression Morphable Model built from a large-scale face database as a tool for expression analysis and synthesis. Establishment of accurate dense correspondence, up to finest skin features, enables a detailed statistical analysis of facial expressions. Various characteristic shape patterns are identified for each expression. The results of our analysis give rise to a new facial expression code. We demonstrate the advantages of such a code for the automatic recognition of expressions, and compare the accuracy of our classifier to state-of-the-art.}, 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{TackMukhopadhyayZachow2018, author = {Tack, Alexander and Mukhopadhyay, Anirban and Zachow, Stefan}, title = {Knee Menisci Segmentation using Convolutional Neural Networks: Data from the Osteoarthritis Initiative}, volume = {26}, number = {5}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-68038}, pages = {680 -- 688}, year = {2018}, abstract = {Abstract: Objective: To present a novel method for automated segmentation of knee menisci from MRIs. To evaluate quantitative meniscal biomarkers for osteoarthritis (OA) estimated thereof. Method: A segmentation method employing convolutional neural networks in combination with statistical shape models was developed. Accuracy was evaluated on 88 manual segmentations. Meniscal volume, tibial coverage, and meniscal extrusion were computed and tested for differences between groups of OA, joint space narrowing (JSN), and WOMAC pain. Correlation between computed meniscal extrusion and MOAKS experts' readings was evaluated for 600 subjects. Suitability of biomarkers for predicting incident radiographic OA from baseline to 24 months was tested on a group of 552 patients (184 incident OA, 386 controls) by performing conditional logistic regression. Results: Segmentation accuracy measured as Dice Similarity Coefficient was 83.8\% for medial menisci (MM) and 88.9\% for lateral menisci (LM) at baseline, and 83.1\% and 88.3\% at 12-month follow-up. Medial tibial coverage was significantly lower for arthritic cases compared to non-arthritic ones. Medial meniscal extrusion was significantly higher for arthritic knees. A moderate correlation between automatically computed medial meniscal extrusion and experts' readings was found (ρ=0.44). Mean medial meniscal extrusion was significantly greater for incident OA cases compared to controls (1.16±0.93 mm vs. 0.83±0.92 mm; p<0.05). Conclusion: Especially for medial menisci an excellent segmentation accuracy was achieved. Our meniscal biomarkers were validated by comparison to experts' readings as well as analysis of differences w.r.t groups of OA, JSN, and WOMAC pain. It was confirmed that medial meniscal extrusion is a predictor for incident OA.}, language = {en} } @misc{LindowRedemannFabigetal.2018, author = {Lindow, Norbert and Redemann, Stefanie and Fabig, Gunar and M{\"u}ller-Reichert, Thomas and Prohaska, Steffen}, title = {Quantification of Three-Dimensional Spindle Architecture}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66562}, year = {2018}, abstract = {Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. Three-dimensional reconstruction of microtubules, however, is only the first step towards biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms.}, language = {en} } @misc{SeblanyHombergVincensetal.2018, author = {Seblany, Feda and Homberg, Ulrike and Vincens, Eric and Winkler, Paul and Witt, Karl Josef}, title = {Merging criteria for the definition of a local pore and the CSD computation of granular materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-67069}, year = {2018}, 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{OezelKulkarniHasanetal.2019, author = {{\"O}zel, M. Neset and Kulkarni, Abhishek and Hasan, Amr and Brummer, Josephine and Moldenhauer, Marian and Daumann, Ilsa-Maria and Wolfenberg, Heike and Dercksen, Vincent J. and Kiral, F. Ridvan and Weiser, Martin and Prohaska, Steffen and von Kleist, Max and Hiesinger, Peter Robin}, title = {Serial synapse formation through filopodial competition for synaptic seeding factors}, issn = {1438-0064}, doi = {10.1016/j.devcel.2019.06.014}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74397}, year = {2019}, abstract = {Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.}, language = {en} }