TY - CHAP A1 - Reininghaus, Jan A1 - Günther, David A1 - Hotz, Ingrid A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - TADD: A Computational Framework for Data Analysis Using Discrete Morse Theory T2 - Mathematical Software - ICMS 2010 Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-15582-6_35 VL - 6327 SP - 198 EP - 208 PB - Springer ER - TY - JOUR A1 - Kuß, Anja A1 - Gensel, Maria A1 - Meyer, Björn A1 - Dercksen, Vincent J. A1 - Prohaska, Steffen T1 - Effective Techniques to Visualize Filament-Surface Relationships JF - Comput. Graph. Forum Y1 - 2010 VL - 29 SP - 1003 EP - 1012 ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Wiebel, Alexander A1 - Prohaska, Steffen A1 - Hege, Hans-Christian ED - Bremer, Peer-Timo ED - Hotz, Ingrid ED - Pascucci, Valerio ED - Peikert, Ronald T1 - Definition, Extraction, and Validation of Pore Structures in Porous Materials BT - Theory, Algorithms, and Applications T2 - Topological Methods in Data Analysis and Visualization III Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-04099-8_15 SP - 235 EP - 248 PB - Springer ER - TY - CHAP A1 - Rosanwo, Olufemi A1 - Petz, Christoph A1 - Prohaska, Steffen A1 - Hotz, Ingrid A1 - Hege, Hans-Christian ED - Eades, Peter ED - Ertl, Thomas ED - Shen, Han-Wei T1 - Dual Streamline Seeding T2 - Proceedings of the IEEE Pacific Visualization Symposium Y1 - 2009 SP - 9 EP - 16 CY - Beijing, China ER - TY - CHAP A1 - Homberg, Ulrike A1 - Binner, Richard A1 - Prohaska, Steffen A1 - Dercksen, Vincent J. A1 - Kuß, Anja A1 - Kalbe, Ute T1 - Determining Geometric Grain Structure from X-Ray Micro-Tomograms of Gradated Soil T2 - Workshop Internal Erosion Y1 - 2009 VL - 21 SP - 37 EP - 52 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Ebell, Gino T1 - 3D Corrosion Detection in Time-dependent CT Images of Concrete T2 - DIR-2015 Proceedings N2 - In civil engineering, the corrosion of steel reinforcements in structural elements of concrete bares a risk of stability-reduction, mainly caused by the exposure to chlorides. 3D computed tomography (CT) reveals the inner structure of concrete and allows one to investigate the corrosion with non-destructive testing methods. To carry out such investigations, specimens with a large artificial crack and an embedded steel rebar have been manufactured. 3D CT images of those specimens were acquired in the original state. Subsequently three cycles of electrochemical pre-damaging together with CT imaging were applied. These time series have been evaluated by means of image processing algorithms to segment and quantify the corrosion products. Visualization of the results supports the understanding of how corrosion propagates into cracks and pores. Furthermore, pitting of structural elements can be seen without dismantling. In this work, several image processing and visualization techniques are presented that have turned out to be particularly effective for the visualization and segmentation of corrosion products. Their combination to a workflow for corrosion analysis is the main contribution of this work. Y1 - 2015 UR - http://www.ndt.net/events/DIR2015/app/content/Paper/36_Paetsch.pdf ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Wiebel, Alexander A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Definition, Extraction, and Validation of Pore Structures in Porous Materials N2 - 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. T3 - ZIB-Report - 13-56 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42510 SN - 1438-0064 ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Günster, Jens A1 - Krauß-Schüler, Stefanie T1 - Adapting trabecular structures for 3D printing: an image processing approach based on µCT data N2 - Materials with a trabecular structure notably combine advantages such as lightweight, reasonable strength, and permeability for fluids. This combination of advantages is especially interesting for tissue engineering in trauma surgery and orthopedics. Bone-substituting scaffolds for instance are designed with a trabecular structure in order to allow cell migration for bone ingrowth and vascularization. An emerging and recently very popular technology to produce such complex, porous structures is 3D printing. However, several technological aspects regarding the scaffold architecture, the printable resolution, and the feature size have to be considered when fabricating scaffolds for bone tissue replacement and regeneration. Here, we present a strategy to assess and prepare realistic trabecular structures for 3D printing using image analysis with the aim of preserving the structural elements. We discuss critical conditions of the printing system and present a 3-stage approach to adapt a trabecular structure from $\mu$CT data while incorporating knowledge about the printing system. In the first stage, an image-based extraction of solid and void structures is performed, which results in voxel- and graph-based representations of the extracted structures. These representations not only allow us to quantify geometrical properties such as pore size or strut geometry and length. But, since the graph represents the geometry and the topology of the initial structure, it can be used in the second stage to modify and adjust feature size, volume and sample size in an easy and consistent way. In the final reconstruction stage, the graph is then converted into a voxel representation preserving the topology of the initial structure. This stage generates a model with respect to the printing conditions to ensure a stable and controlled voxel placement during the printing process. T3 - ZIB-Report - 17-26 KW - trabecular structures KW - image-based analysis KW - additive manufacturing KW - printability Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64004 SN - 1438-0064 ER - TY - JOUR A1 - Redemann, Stefanie A1 - Baumgart, Johannes A1 - Lindow, Norbert A1 - Shelley, Michael A1 - Nazockdast, Ehssan A1 - Kratz, Andrea A1 - Prohaska, Steffen A1 - Brugués, Jan A1 - Fürthauer, Sebastian A1 - Müller-Reichert, Thomas T1 - C. elegans chromosomes connect to centrosomes by anchoring into the spindle network JF - Nature Communications N2 - The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient. Y1 - 2017 U6 - https://doi.org/10.1038/ncomms15288 VL - 8 IS - 15288 ER - TY - JOUR A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Günster, Jens A1 - Krauß-Schüler, Stefanie T1 - Adapting trabecular structures for 3D printing: an image processing approach based on µCT data JF - Biomedical Physics & Engineering Express N2 - Materials with a trabecular structure notably combine advantages such as lightweight, reasonable strength, and permeability for fluids. This combination of advantages is especially interesting for tissue engineering in trauma surgery and orthopedics. Bone-substituting scaffolds for instance are designed with a trabecular structure in order to allow cell migration for bone ingrowth and vascularization. An emerging and recently very popular technology to produce such complex, porous structures is 3D printing. However, several technological aspects regarding the scaffold architecture, the printable resolution, and the feature size have to be considered when fabricating scaffolds for bone tissue replacement and regeneration. Here, we present a strategy to assess and prepare realistic trabecular structures for 3D printing using image analysis with the aim of preserving the structural elements. We discuss critical conditions of the printing system and present a 3-stage approach to adapt a trabecular structure from $\mu$CT data while incorporating knowledge about the printing system. In the first stage, an image-based extraction of solid and void structures is performed, which results in voxel- and graph-based representations of the extracted structures. These representations not only allow us to quantify geometrical properties such as pore size or strut geometry and length. But, since the graph represents the geometry and the topology of the initial structure, it can be used in the second stage to modify and adjust feature size, volume and sample size in an easy and consistent way. In the final reconstruction stage, the graph is then converted into a voxel representation preserving the topology of the initial structure. This stage generates a model with respect to the printing conditions to ensure a stable and controlled voxel placement during the printing process. Y1 - 2017 U6 - https://doi.org/10.1088/2057-1976/aa7611 VL - 3 IS - 3 PB - IOP Publishing ER - TY - GEN A1 - Zhukova, Yulia A1 - Hiepen, Christian A1 - Knaus, Petra A1 - Osterland, Marc A1 - Prohaska, Steffen A1 - Dunlop, John W. C. A1 - Fratzl, Peter A1 - Skorb, Ekaterina V. T1 - The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration N2 - Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered – mesoporous titania (TMS), and ordered – titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair. T3 - ZIB-Report - 17-06 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63053 SN - 1438-0064 ER - TY - JOUR A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Ehrig, Karsten A1 - Ebell, Gino A1 - Meinel, Dietmar A1 - Heyn, Andreas T1 - Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben JF - DGZfP-Jahrestagung 2014 Konferenzband Y1 - 2014 ER - TY - JOUR A1 - Knötel, David A1 - Seidel, Ronald A1 - Prohaska, Steffen A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage JF - PLOS ONE N2 - Introduction – Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays. Methods – Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size. Results – Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0188018 ER - TY - GEN A1 - Knötel, David A1 - Seidel, Ronald A1 - Zaslansky, Paul A1 - Prohaska, Steffen A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage (Supplementary Material) N2 - Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. In particular, sections from hyomandibulae harvested from specimens of round stingray Urobatis halleri, donated from another study (DOI: 10.1002/etc.2564). Specimens were from sub-adults/adults collected by beach seine from collection sites in San Diego and Seal Beach, California, USA. The hyomandibulae were mounted in clay, sealed in ethanol-humidified plastic tubes and scanned with a Skyscan 1172 desktop μCT scanner (Bruker μCT, Kontich, Belgium) in association with another study (DOI: 10.1111/joa.12508). Scans for all samples were performed with voxel sizes of 4.89 μm at 59 kV source voltage and 167 μA source current, over 360◦ sample 120 rotation. For our segmentations, the datasets were resampled to a voxel size of 9.78 μm to reduce the size of the images and speed up processing. In addition, the processed data that was generated with the visualization software Amira with techniques described in the related publication based on the mentioned specimens. Y1 - 2017 U6 - https://doi.org/10.12752/4.DKN.1.0 N1 - Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. ER - TY - GEN A1 - Lindow, Norbert A1 - Redemann, Stefanie A1 - Fabig, Gunar A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen T1 - Quantification of Three-Dimensional Spindle Architecture N2 - 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. T3 - ZIB-Report - 18-07 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66562 SN - 1438-0064 ER - TY - JOUR A1 - Zhukova, Yulia A1 - Hiepen, Christian A1 - Knaus, Petra A1 - Osterland, Marc A1 - Prohaska, Steffen A1 - Dunlop, John W. C. A1 - Fratzl, Peter A1 - Skorb, Ekaterina V. T1 - The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration JF - Advanced Healthcare Materials N2 - Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered – mesoporous titania (TMS), and ordered – titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair. Y1 - 2017 U6 - https://doi.org/10.1002/adhm.201601244 ER - TY - CHAP A1 - Kaplan, Bernhard A1 - Buchmann, Jens A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography T2 - Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing 2017 N2 - The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data. Y1 - 2017 U6 - https://doi.org/10.1117/12.2251945 VL - 10064 SP - 100645J EP - 100645J-13 ER - TY - CHAP A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Experimental validation of a Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography T2 - Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing N2 - Quantitative photoacoustic tomography (qPAT) aims to extract physiological parameters, such as blood oxygen saturation (sO2), from measured multi-wavelength image data sets. The challenge of this approach lies in the inherently nonlinear fluence distribution in the tissue, which has to be accounted for by using an appropriate model, and the large scale of the inverse problem. In addition, the accuracy of experimental and scanner-specific parameters, such as the wavelength dependence of the incident fluence, the acoustic detector response, the beam profile and divergence, needs to be considered. This study aims at quantitative imaging of blood sO2, as it has been shown to be a more robust parameter compared to absolute concentrations. We propose a Monte-Carlo–based inversion scheme in conjunction with a reduction in the number of variables achieved using image segmentation. The inversion scheme is experimentally validated in tissue-mimicking phantoms consisting of polymer tubes suspended in a scattering liquid. The tubes were filled with chromophore solutions at different concentration ratios. 3-D multi-spectral image data sets were acquired using a Fabry-Perot based PA scanner. A quantitative comparison of the measured data with the output of the forward model is presented. Parameter estimates of chromophore concentration ratios were found to be within 5 % of the true values. Y1 - 2017 U6 - https://doi.org/10.1117/12.2252359 VL - 10064 SP - 1006416 EP - 1006416-8 ER - TY - JOUR A1 - Costa, Marta A1 - Manton, James D. A1 - Ostrovsky, Aaron D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases JF - Neuron N2 - Neural circuit mapping is generating datasets of tens of thousands 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 1,052 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. Y1 - 2016 U6 - https://doi.org/10.1016/j.neuron.2016.06.012 VL - 91 IS - 2 SP - 293 EP - 311 ER - TY - GEN A1 - Osterland, Marc A1 - Benn, Andreas A1 - Prohaska, Steffen A1 - Schütte, Christof T1 - Single Cell Tracking in Phase-Contrast Microscopy T2 - EMBL Symposium 2015 - Seeing is Believing - Imaging the Processes of Life N2 - In this work, we developed an automatic algorithm to analyze cell migration in chemotaxis assays, based on phase-contrast time-lapse microscopy. While manual approaches are still widely used in recent publications, our algorithm is able to track hundreds of single cells per frame. The extracted paths are analysed with traditional geometrical approaches as well as diffusion-driven Markov state models (MSM). Based on these models, a detailed view on spatial and temporal effects is possible. Using our new approach on experimental data, we are able to distinguish between directed migration (e.g. towards a VEGF gradient) and random migration without favored direction. A calculation of the committor probabilities reveals that cells of the whole image area are more likely to migrate directly towards the VEGF than away from it during the first four hours. However, in absence of a chemoattractant, cells migrate more likely to their nearest image border. These conclusions are supported by the spatial mean directions. In a next step, the cell-cell interaction during migration and the migration of cell clusters will be analyzed. Furthermore, we want to observe phenotypical changes during migration based on fluorescence microscopy and machine learning. The algorithm is part of a collaborative platform which brings the experimental expertise of scientists from life sciences and the analytical knowledge of computer scientists together. This platform is built using web-based technologies with a responsive real-time user interface. All data, including raw and metadata as well as the accompanying results, will be stored in a secure and scalable compute cluster. The compute cluster provides sufficient space and computational power for modern image-based experiments and their analyses. Specific versions of data and results can be tagged to keep immutable records for archival. Y1 - 2015 ER - TY - CHAP A1 - Ritter, Zully A1 - Prohaska, Steffen A1 - Brand, R. A1 - Friedmann, A. A1 - Hege, Hans-Christian A1 - Goebbels, Jürgen A1 - Felsenberg, Dieter T1 - Osteocytes number and volume in osteoporotic and in healthy bone biopsies analysed using Synchrotron CT: a pilot study T2 - Proc. ISB 2011 Y1 - 2011 ER - TY - CHAP A1 - Streicher, Doreen A1 - Paetsch, Olaf A1 - Seiler, Robert A1 - Prohaska, Steffen A1 - Krause, Martin A1 - Boller, Christian T1 - 3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira T2 - Proc. DGZfP-Jahrestagung 2011 Y1 - 2011 ER - TY - GEN A1 - Günther, David A1 - Reininghaus, Jan A1 - Prohaska, Steffen A1 - Weinkauf, Tino A1 - Hege, Hans-Christian ED - Peikert, Ronny ED - Hauser, Helwig ED - Carr, Hamish T1 - Efficient Computation of a Hierarchy of Discrete 3D Gradient Vector Fields T2 - Topological Methods in Data Analysis and Visualization II Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-23175-9_2 SP - 15 EP - 29 PB - Springer ER - TY - CHAP A1 - Kuß, Anja A1 - Prohaska, Steffen A1 - Meyer, Björn A1 - Rybak, Jürgen A1 - Hege, Hans-Christian T1 - Ontology-Based Visualization of Hierarchical Neuroanatomical Structures T2 - Proceedings of the Eurographics Workshop on Visual Computing for Biomedicine VCBM 2008 Y1 - 2008 SP - 177 EP - 184 ER - TY - CHAP A1 - Petz, Christoph A1 - Prohaska, Steffen A1 - Goubergrits, Leonid A1 - Kertzscher, Ulrich A1 - Hege, Hans-Christian T1 - Near-Wall Flow Visualization in Flattened Surface Neighborhoods T2 - Proc. Simulation and Visualization 2008 Y1 - 2008 UR - http://www.simvis.org/Tagung2008/sv-proceedings.html SP - 93 EP - 105 CY - Magdeburg, Germany ER - TY - JOUR A1 - Sahner, Jan A1 - Weber, Britta A1 - Lamecker, Hans A1 - Prohaska, Steffen T1 - Extraction of feature Lines on surface meshes based on discrete Morse theory JF - Computer Graphics Forum Y1 - 2008 U6 - https://doi.org/10.1111/j.1467-8659.2008.01202.x VL - 27 IS - 3 SP - 735 EP - 742 CY - Eindhoven, Netherlands ER - TY - CHAP A1 - Mehlhorn, Tobias A1 - Prohaska, Steffen A1 - Homberg, Ulrike A1 - Slowik, Volker T1 - Modelling and Analysis of Particle and Pore Structures in Soils T2 - Workshop Internal Erosion Y1 - 2009 VL - 21 SP - 53 EP - 60 ER - TY - CHAP A1 - Semar, Olivier A1 - Binner, Richard A1 - Homberg, Ulrike A1 - Kalbe, Ute A1 - Mehlhorn, Tobias A1 - Prohaska, Steffen A1 - Slowik, Volker A1 - Witt, Karl Josef T1 - Conditions for Suffosive Erosion Phemomena in Soils – Concept and Approach T2 - Workshop Internal Erosion Y1 - 2009 VL - 21 SP - 29 EP - 35 ER - TY - CHAP A1 - Clasen, Malte A1 - Prohaska, Steffen T1 - Image-Error-Based Level of Detail for Landscape Visualization T2 - Proc. VMV 2010 Y1 - 2010 SP - 267 EP - 274 ER - TY - CHAP A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen ED - Mücklich, Frank ED - Slussallek, Philipp ED - Schladitz, Katja T1 - Describing and Analyzing the Dual Structures of Porous Media T2 - Proc. 3D-Microstructure Meeting Y1 - 2011 SP - 24 EP - 25 ER - TY - CHAP A1 - Weber, Britta A1 - Möller, Marit A1 - Verbavatz, Jean-Marc A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Prohaska, Steffen T1 - Fast Tracing of Microtubule Centerlines in Electron Tomograms T2 - BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization Y1 - 2011 ER - TY - CHAP A1 - Ehrig, Karsten A1 - Goebbels, Jürgen A1 - Meinel, Dietmar A1 - Paetsch, Olaf A1 - Prohaska, Steffen A1 - Zobel, Valentin T1 - Comparison of Crack Detection Methods for Analyzing Damage Processes in Concrete with Computed Tomography T2 - International Symposium on Digital Industrial Radiology and Computed Tomography Y1 - 2011 ER - TY - JOUR A1 - Petz, Christoph A1 - Kasten, Jens A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Hierarchical Vortex Regions in Swirling Flow JF - Computer Graphics Forum Y1 - 2009 VL - 28 IS - 3 SP - 863 EP - 870 ER - TY - CHAP A1 - Dercksen, Vincent J. A1 - Weber, Britta A1 - Günther, David A1 - Oberlaender, Marcel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Automatic alignment of stacks of filament data T2 - Proc. IEEE International Symposium on Biomedical Imaging Y1 - 2009 SP - 971 EP - 974 PB - IEEE press CY - Boston, USA ER - TY - CHAP A1 - Kuß, Anja A1 - Prohaska, Steffen A1 - Rybak, Jürgen T1 - Using Ontologies for the Visualization of Hierarchical Neuroanatomical Structures T2 - Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics Y1 - 2009 U6 - https://doi.org/10.3389/conf.neuro.11.2009.08.017 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computer-Tomographie T2 - Tagungsband der DACH Jahrestagung 2012 Y1 - 2012 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Breßler, David A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - 3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben T2 - Tagungsband der DGZfP Jahrestagung 2013 Y1 - 2013 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography T2 - Proceedings of Conference on Industrial Computed Tomography Y1 - 2012 SP - 321 EP - 330 ER - TY - JOUR A1 - Ziegler, Alexander A1 - Ogurreck, Malte A1 - Steinke, Thomas A1 - Beckmann, Felix A1 - Prohaska, Steffen A1 - Ziegler, Andreas T1 - Opportunities and challenges for digital morphology JF - Biology Direct Y1 - 2010 U6 - https://doi.org/10.1186/1745-6150-5-45 VL - 5 IS - 1 SP - 45 ER - TY - CHAP A1 - Binner, Richard A1 - Homberg, Ulrike A1 - Prohaska, Steffen A1 - Kalbe, Ute A1 - Witt, Karl Josef T1 - Identification of Descriptive Parameters of the Soil Pore Structure using Experiments and CT Data T2 - Proceedings of the 5th International Conference on Scour and Erosion (ICSE-5) Y1 - 2010 SP - 397 EP - 407 PB - American Society of Civil Engineers (ASCE) ER - TY - JOUR A1 - Hutanu, Andrei A1 - Allen, Gabrielle A1 - Beck, Stephen A1 - Holub, Petr A1 - Kaiser, Hartmut A1 - Kulshrestha, Archit A1 - Liska, Milos A1 - MacLaren, Jon A1 - Matyska, Ludek A1 - Paruchuri, Ravi A1 - Prohaska, Steffen A1 - Seidel, Edward A1 - Ullmer, Brygg A1 - Venkataraman, Shalini T1 - Distributed and collaborative visualization of large data sets using high-speed networks JF - Future Generation Comp. Syst Y1 - 2006 U6 - https://doi.org/10.1016/j.future.2006.03.026 VL - 22(8) SP - 1004 EP - 1010 ER - TY - CHAP A1 - Prohaska, Steffen T1 - Interaktive Visualisierung und Datenanalyse: Herausforderungen durch wachsende Datenmengen T2 - Kartographische Schriften Y1 - 2006 VL - 10 SP - 103 EP - 110 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Weinkauf, Tino A1 - Prohaska, Steffen A1 - Hutanu, Andrei T1 - Towards distributed visualization and analysis of large flow data JF - JSME International Journal, Series B Y1 - 2005 VL - 48 (2) SP - 241 EP - 246 ER - TY - CHAP A1 - Dercksen, Vincent J. A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Fast cross-sectional display of large data sets T2 - IAPR Conference on Machine Vision Applications Y1 - 2005 SP - 336 EP - 339 CY - Tsukuba, Japan ER - TY - CHAP A1 - Kähler, Ralf A1 - Prohaska, Steffen A1 - Hutanu, Andrei A1 - Hege, Hans-Christian T1 - Visualization of time-dependent remote adaptive mesh refinement data T2 - Proc. IEEE Visualization 2005 Y1 - 2005 U6 - https://doi.org/10.1109/VISUAL.2005.1532793 SP - 175 EP - 182 CY - Minneapolis, USA ER - TY - JOUR A1 - Thomsen, Jesper A1 - Laib, Andreas A1 - Koller, Bruno A1 - Prohaska, Steffen A1 - Mosekilde, L. A1 - Gowin, Wolfgang T1 - Stereological measures of trabecular bone structure: Comparison of 3D micro computed tomography with 2D histological sections in human proximal tibial bone biopsies JF - Journal of Microscopy Y1 - 2005 VL - 218 SP - 171 EP - 179 ER - TY - JOUR A1 - Cassot, Francis A1 - Lauwers, Frederic A1 - Fouard, Céline A1 - Prohaska, Steffen A1 - Lauwer-Cances, Valerie T1 - A novel three-dimensional computer assisted method for a quantitative study of microvascular networks of the human cerebral cortex JF - Microcirculation Y1 - 2006 VL - 13 SP - 15 EP - 32 ER - TY - JOUR A1 - Fouard, Céline A1 - Malandain, Grégoire A1 - Prohaska, Steffen A1 - Westerhoff, Malte T1 - Blockwise processing applied to brain micro-vascular network study JF - IEEE Transactions on Medical Imaging Y1 - 2006 U6 - https://doi.org/10.1109/TMI.2006.880670 VL - 25 IS - 10 SP - 1319 EP - 1328 ER - TY - JOUR A1 - Zaikin, Alexei A1 - Saparin, Peter A1 - Kurths, Jürgen A1 - Prohaska, Steffen A1 - Gowin, Wolfgang T1 - Modeling resorption in 2D-CT and 3D μ-CT bone images JF - Int. J. of Bif. and Chaos Y1 - 2005 VL - 15(9) SP - 2995 EP - 3009 ER - TY - CHAP A1 - Prohaska, Steffen A1 - Hutanu, Andrei T1 - Remote data access for interactive visualization T2 - 13th Annual Mardi Gras Conference: Frontiers of Grid Applications and Technologies Y1 - 2005 SP - 17 EP - 22 ER -