@article{FroehlerElberfeldMoelleretal., author = {Fr{\"o}hler, Bernhard and Elberfeld, Tim and M{\"o}ller, Torsten and Hege, Hans-Christian and De Beenhouwer, Jan and Sijbers, Jan and Kastner, Johann and Heinzl, Christoph}, title = {Analysis and comparison of algorithms for the tomographic reconstruction of curved fibres}, series = {Nondestructive Testing and Evaluation}, volume = {35}, journal = {Nondestructive Testing and Evaluation}, number = {3}, doi = {10.1080/10589759.2020.1774583}, pages = {328 -- 341}, abstract = {We present visual methods for the analysis and comparison of the results of curved fibre reconstruction algorithms, i.e., of algorithms extracting characteristics of curved fibres from X-ray computed tomography scans. In this work, we extend previous methods for the analysis and comparison of results of different fibre reconstruction algorithms or parametrisations to the analysis of curved fibres. We propose fibre dissimilarity measures for such curved fibres and apply these to compare multiple results to a specified reference. We further propose visualisation methods to analyse differences between multiple results quantitatively and qualitatively. In two case studies, we show that the presented methods provide valuable insights for advancing and parametrising fibre reconstruction algorithms, and support in improving their results in characterising curved fibres.}, language = {en} } @article{BanyassadyBarbaMulzer, author = {Banyassady, Bahareh and Barba, Luis and Mulzer, Wolfgang}, title = {Time-Space Trade-Offs for Computing Euclidean Minimum Spanning Trees}, series = {Journal of Computational Geometry (JoCG)}, volume = {11(1)}, journal = {Journal of Computational Geometry (JoCG)}, url = {http://nbn-resolving.de/https://jocg.org/index.php/jocg/article/view/473}, pages = {525 -- 547}, abstract = {We present time-space trade-offs for computing the Euclidean minimum spanning tree of a set S of n point-sites in the plane. More precisely, we assume that S resides in a random-access memory that can only be read. The edges of the Euclidean minimum spanning tree EMST(S) have to be reported sequentially, and they cannot be accessed or modified afterwards. There is a parameter s in {1, ..., n} so that the algorithm may use O(s) cells of read-write memory (called the workspace) for its computations. Our goal is to find an algorithm that has the best possible running time for any given s between 1 and n. We show how to compute EMST(S) in O(((n^3)/(s^2)) log s) time with O(s) cells of workspace, giving a smooth trade-off between the two best-known bounds O(n^3) for s = 1 and O(n log n) for s = n. For this, we run Kruskal's algorithm on the "relative neighborhood graph" (RNG) of S. It is a classic fact that the minimum spanning tree of RNG(S) is exactly EMST(S). To implement Kruskal's algorithm with O(s) cells of workspace, we define s-nets, a compact representation of planar graphs. This allows us to efficiently maintain and update the components of the current minimum spanning forest as the edges are being inserted.}, language = {en} } @article{BanyassadyChiuKormanetal., author = {Banyassady, Bahareh and Chiu, Man-Kwun and Korman, Matias and Mulzer, Wolfgang and van Renssen, Andr{\´e} and Roeloffzen, Marcel and Seiferth, Paul and Stein, Yannik and Vogtenhuber, Birgit and Willert, Max}, title = {Routing in polygonal domains}, series = {Computational Geometry, Theory and Applications}, volume = {87}, journal = {Computational Geometry, Theory and Applications}, publisher = {Elsevier}, doi = {10.1016/j.comgeo.2019.101593}, abstract = {We consider the problem of routing a data packet through the visibility graph of a polygonal domain P with n vertices and h holes. We may preprocess P to obtain a "label" and a "routing table" for each vertex of P. Then, we must be able to route a data packet between any two vertices p and q of P, where each step must use only the label of the target node q and the routing table of the current node. For any fixed epsilon > 0, we present a routing scheme that always achieves a routing path whose length exceeds the shortest path by a factor of at most 1 + epsilon. The labels have O(log n) bits, and the routing tables are of size O(((epsilon^-1)+h)log n). The preprocessing time is O((n^2)log n). It can be improved to O(n^2) for simple polygons.}, language = {en} } @article{FroehlerElberfeldMoelleretal., author = {Fr{\"o}hler, Bernhard and Elberfeld, Tim and M{\"o}ller, Torsten and Hege, Hans-Christian and Weissenb{\"o}ck, Johannes and De Beenhouwer, Jan and Sijbers, Jan and Kastner, Johann and Heinzl, Christoph}, title = {A Visual Tool for the Analysis of Algorithms for Tomographic Fiber Reconstruction in Materials Science}, series = {Computer Graphics Forum}, volume = {38}, journal = {Computer Graphics Forum}, number = {3}, doi = {10.1111/cgf.13688}, pages = {273 -- 283}, abstract = {We present visual analysis methods for the evaluation of tomographic fiber reconstruction algorithms by means of analysis, visual debugging and comparison of reconstructed fibers in materials science. The methods are integrated in a tool (FIAKER) that supports the entire workflow. It enables the analysis of various fiber reconstruction algorithms, of differently parameterized fiber reconstruction algorithms and of individual steps in iterative fiber reconstruction algorithms. Insight into the performance of fiber reconstruction algorithms is obtained by a list-based ranking interface. A 3D view offers interactive visualization techniques to gain deeper insight, e.g., into the aggregated quality of the examined fiber reconstruction algorithms and parameterizations. The tool was designed in close collaboration with researchers who work with fiber-reinforced polymers on a daily basis and develop algorithms for tomographic reconstruction and characterization of such materials. We evaluate the tool using synthetic datasets as well as tomograms of real materials. Five case studies certify the usefulness of the tool, showing that it significantly accelerates the analysis and provides valuable insights that make it possible to improve the fiber reconstruction algorithms. The main contribution of the paper is the well-considered combination of methods and their seamless integration into a visual tool that supports the entire workflow. Further findings result from the analysis of (dis-)similarity measures for fibers as well as from the discussion of design decisions. It is also shown that the generality of the analytical methods allows a wider range of applications, such as the application in pore space analysis.}, language = {en} } @article{GoubergritsHellmeierBrueningetal., author = {Goubergrits, Leonid and Hellmeier, Florian and Bruening, Jan Joris and Spuler, Andreas and Hege, Hans-Christian and Voss, Samuel and Janiga, G{\´a}bor and Saalfeld, Sylvia and Beuing, Oliver and Berg, Philipp}, title = {Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH): Uncertainty Quantification of Geometric Rupture Risk Parameters}, series = {BioMedical Engineering OnLine}, volume = {18}, journal = {BioMedical Engineering OnLine}, number = {35}, doi = {10.1186/s12938-019-0657-y}, abstract = {Background Geometric parameters have been proposed for prediction of cerebral aneurysm rupture risk. Predicting the rupture risk for incidentally detected unruptured aneurysms could help clinicians in their treatment decision. However, assessment of geometric parameters depends on several factors, including the spatial resolution of the imaging modality used and the chosen reconstruction procedure. The aim of this study was to investigate the uncertainty of a variety of previously proposed geometric parameters for rupture risk assessment, caused by variability of reconstruction procedures. Materials 26 research groups provided segmentations and surface reconstructions of five cerebral aneurysms as part of the Multiple Aneurysms AnaTomy CHallenge (MATCH) 2018. 40 dimensional and non-dimensional geometric parameters, describing aneurysm size, neck size, and irregularity of aneurysm shape, were computed. The medians as well as the absolute and relative uncertainties of the parameters were calculated. Additionally, linear regression analysis was performed on the absolute uncertainties and the median parameter values. Results A large variability of relative uncertainties in the range between 3.9 and 179.8\% was found. Linear regression analysis indicates that some parameters capture similar geometric aspects. The lowest uncertainties < 6\% were found for the non-dimensional parameters isoperimetric ratio, convexity ratio, and ellipticity index. Uncertainty of 2D and 3D size parameters was significantly higher than uncertainty of 1D parameters. The most extreme uncertainties > 80\% were found for some curvature parameters. Conclusions Uncertainty analysis is essential on the road to clinical translation and use of rupture risk prediction models. Uncertainty quantification of geometric rupture risk parameters provided by this study may help support development of future rupture risk prediction models.}, language = {en} } @article{MahnkeArltBaumetal., 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}, series = {Journal of Cultural Heritage}, volume = {41}, journal = {Journal of Cultural Heritage}, publisher = {Elsevier}, doi = {10.1016/j.culher.2019.07.007}, pages = {264 -- 269}, 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} } @inproceedings{FroehlerdaCunhaMeloWeissenboecketal., author = {Fr{\"o}hler, Bernhard and da Cunha Melo, Lucas and Weissenb{\"o}ck, Johannes and Kastner, Johann and M{\"o}ller, Torsten and Hege, Hans-Christian and Gr{\"o}ller, Eduard M. and Sanctorum, Jonathan and De Beenhouwer, Jan and Sijbers, Jan and Heinzl, Christoph}, title = {Tools for the analysis of datasets from X-ray computed tomography based on Talbot-Lau grating interferometry}, series = {Proceedings of iCT 2019, (9th Conference on Industrial Computed Tomography, Padova, Italy - iCT 2019, February 13-15, 2019)}, booktitle = {Proceedings of iCT 2019, (9th Conference on Industrial Computed Tomography, Padova, Italy - iCT 2019, February 13-15, 2019)}, number = {paper 52}, pages = {8}, abstract = {This work introduces methods for analyzing the three imaging modalities delivered by Talbot-Lau grating interferometry X-ray computed tomography (TLGI-XCT). The first problem we address is providing a quick way to show a fusion of all three modal- ities. For this purpose the tri-modal transfer function widget is introduced. The widget controls a mixing function that uses the output of the transfer functions of all three modalities, allowing the user to create one customized fused image. A second problem prevalent in processing TLGI-XCT data is a lack of tools for analyzing the segmentation process of such multimodal data. We address this by providing methods for computing three types of uncertainty: From probabilistic segmentation algorithms, from the voxel neighborhoods as well as from a collection of results. We furthermore introduce a linked views interface to explore this data. The techniques are evaluated on a TLGI-XCT scan of a carbon-fiber reinforced dataset with impact damage. We show that the transfer function widget accelerates and facilitates the exploration of this dataset, while the uncertainty analysis methods give insights into how to tweak and improve segmentation algorithms for more suitable results.}, language = {en} } @article{BorongCannistraciConrad, author = {Borong, Shao and Cannistraci, Carlo and Conrad, Tim}, title = {Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data}, series = {Genomics and Computational Biology}, volume = {3}, journal = {Genomics and Computational Biology}, number = {3}, doi = {http://dx.doi.org/10.18547/gcb.2017.vol3.iss3.e57}, pages = {1 -- 13}, abstract = {Epithelial mesenchymal transition (EMT) process has been shown as highly relevant to cancer prognosis. However, although different biological network-based biomarker identification methods have been proposed to predict cancer prognosis, EMT network has not been directly used for this purpose. In this study, we constructed an EMT regulatory network consisting of 87 molecules and tried to select features that are useful for prognosis prediction in Lung Adenocarcinoma (LUAD). To incorporate multiple molecular profiles, we obtained four types of molecular data including mRNA-Seq, copy number alteration (CNA), DNA methylation, and miRNA-Seq data from The Cancer Genome Atlas. The data were mapped to the EMT network in three alternative ways: mRNA-Seq and miRNA-Seq, DNA methylation, and CNA and miRNA-Seq. Each mapping was employed to extract five different sets of features using discretization and network-based biomarker identification methods. Each feature set was then used to predict prognosis with SVM and logistic regression classifiers. We measured the prediction accuracy with AUC and AUPR values using 10 times 10-fold cross validation. For a more comprehensive evaluation, we also measured the prediction accuracies of clinical features, EMT plus clinical features, randomly picked 87 molecules from each data mapping, and using all molecules from each data type. Counter-intuitively, EMT features do not always outperform randomly selected features and the prediction accuracies of the five feature sets are mostly not significantly different. Clinical features are shown to give the highest prediction accuracies. In addition, the prediction accuracies of both EMT features and random features are comparable as using all features (more than 17,000) from each data type.}, language = {en} } @article{AgudoJacomeHegePaetschetal., 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}, series = {Ultramicroscopy}, volume = {195}, journal = {Ultramicroscopy}, doi = {10.1016/j.ultramic.2018.08.015}, pages = {157 -- 170}, 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} } @inproceedings{UllmerPaarCoconuetal.2018, author = {Ullmer, Brygg and Paar, Philip and Coconu, Liviu and Liu, Jing and Konkel, Miriam and Hege, Hans-Christian}, title = {An 1834 mediterranean garden in Berlin - engaged from 2004, 2018, 2032, and 2202}, series = {PerDis '18 - 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018}, booktitle = {PerDis '18 - 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018}, publisher = {ACM}, address = {New York, NY, USA}, doi = {10.1145/3205873.3205894}, pages = {no. 12}, year = {2018}, abstract = {In 2004, a team of researchers realized a semi-immersive interactive gallery installation, visualizing an 1834 Mediterranean garden, introduced as "italienisches Kunstst{\"u}ck" (Italian legerdemain) by Peter Joseph Lenn{\´e}. The park was originally realized on the grounds of Schloss Sanssouci in Potsdam, Germany. The installation centered on highly detailed renderings of hundreds of plants projected upon a panoramic display. Interactivity was expressed with a tangible interface which (while presently dated) we believe remains without near-precedent then or since. We present the installation (experienced by roughly 20,000 visitors), focusing on the interaction aspects. We introduce new book and table/door-format mockups. Drawing upon a heuristic of the scientist-philosopher Freeman Dyson, we consider grounded future prospect variations in the contexts of 2018, 2032, and 2202. We see this exercise as prospectively generalizing to a variety of similar and widely diverse application domains.}, language = {en} }