@misc{ZoecklerReinBrandtetal., author = {Z{\"o}ckler, Malte and Rein, Karlheinz and Brandt, Robert and Stalling, Detlev and Hege, Hans-Christian}, title = {Creating Virtual Insect Brains with Amira}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6589}, number = {01-32}, abstract = {By combining techniques of preparation, histology, confocal microscopy, data visualization and data processing, we have created and recently published a standard brain model for drosophila and honey bee brains. This report describes the algorithms and implementation of the corresponding software modules. At the same time it serves as a user's guide for scientist who want to reproduce the results for differerent species or mutants.}, language = {en} } @misc{StallingSeebassZoeckleretal., author = {Stalling, Detlev and Seebass, Martin and Z{\"o}ckler, Malte and Hege, Hans-Christian}, title = {Hyperthermia Treatment Planning with HyperPlan - User's Manual}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-5957}, number = {00-27}, abstract = {HyperPlan is a software system for performing 3D-simulations and treatment planning in regional hyperthermia. It allows the user to understand the complex effects of electromagnetic wave propagation and heat transport inside a patient's body. Optimized power amplitudes and phase settings can be calculated for the BSD radiowave applicators Sigma 60 and Sigma 2000 (eye-applicator). HyperPlan is built on top of the modular, object-oriented visualization system Amira. This system already contains powerful algorithms for image processing, geometric modelling and 3D graphics display. HyperPlan provides a number of hyperthermia-specific modules, allowing the user to create 3D tetrahedral patient models suitable for treatment planning. In addition, all numerical simulation modules required for hyperthermia simulation are part of HyperPlan. This guide provides a step-by-step introduction to hyperthermia planning using HyperPlan. It also describes the usage of the underlying visualization system Amira.}, language = {en} } @misc{DeuflhardHege, author = {Deuflhard, Peter and Hege, Hans-Christian}, title = {Die Vision einer individuellen quantitativen Medizin}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-8805}, number = {05-47}, abstract = {Die Autoren schreiben dieses Papier aus der eingeschr{\"a}nkten Sicht der Mathematik und der Informationstechnik. Um den speziellen Beitrag dieser Disziplinen {\"u}berhaupt diskutieren zu k{\"o}nnen, sehen wir uns jedoch gezwungen, einen Rahmen abzustecken, den wir f{\"u}r das Jahr 2020 vorhersehen -- nach Wahrscheinlichkeit und aus unserem engeren fachlichen Blickwinkel. Vorab bitten wir schon einmal bei den medizinischen Fachleuten um Nachsicht, wenn wir uns in ihrem Revier allzu dillettantisch bewegen. Vielleicht f{\"o}rdert aber auch unser eingeschr{\"a}nkter Blickwinkel ansonsten unbedachte Aspekte zutage -- das hoffen wir zumindest.}, language = {de} } @misc{HoerthBaumKnoeteletal., author = {Hoerth, Rebecca M. and Baum, Daniel and Kn{\"o}tel, David and Prohaska, Steffen and Willie, Bettina M. and Duda, Georg and Hege, Hans-Christian and Fratzl, Peter and Wagermaier, Wolfgang}, title = {Registering 2D and 3D Imaging Data of Bone during Healing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53426}, abstract = {Purpose/Aims of the Study: Bone's hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro computed tomography (μCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. Materials and Methods: We investigated bone during healing by means of μCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue's calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. Results: We present an approach for the registration of 2D data in a 3D μCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into μCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. Conclusions: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.}, language = {en} } @misc{VohraHarthIsoeetal., author = {Vohra, Sumit Kumar and Harth, Philipp and Isoe, Yasuko and Bahl, Armin and Fotowat, Haleh and Engert, Florian and Hege, Hans-Christian and Baum, Daniel}, title = {A Visual Interface for Exploring Hypotheses about Neural Circuits}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-89932}, abstract = {One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa.}, language = {en} } @misc{NavaYazdaniHegevonTycowicz, author = {Nava-Yazdani, Esfandiar and Hege, Hans-Christian and von Tycowicz, Christoph}, title = {A Hierarchical Geodesic Model for Longitudinal Analysis on Manifolds}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-85187}, abstract = {In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and employ the approach for longitudinal analysis of 2D rat skulls shapes as well as 3D shapes derived from an imaging study on osteoarthritis. Particularly, we perform hypothesis test and estimate the mean trends.}, language = {en} }