@article{ConradYou2016, author = {Conrad, Tim and You, Xintian}, title = {Acfs: accurate circRNA identification and quantification from NGS data}, volume = {6}, journal = {Nature Scientific Reports}, doi = {10.1038/srep38820}, year = {2016}, abstract = {Circular RNAs (circRNAs) are a group of single-stranded RNAs in closed circular form. They are splicing-generated, widely expressed in various tissues and have functional implications in development and diseases. To facilitate genome-wide characterization of circRNAs using RNA-Seq data, we present a freely available software package named acfs. Acfs allows de novo, accurate and fast identification and abundance quantification of circRNAs from single- and paired-ended RNA-Seq data. On simulated datasets, acfs achieved the highest F1 accuracy and lowest false discovery rate among current state-of-the-art tools. On real-world datasets, acfs efficiently identified more bona fide circRNAs. Furthermore, we demonstrated the power of circRNA analysis on two leukemia datasets. We identified a set of circRNAs that are differentially expressed between AML and APL samples, which might shed light on the potential molecular classification of complex diseases using circRNA profiles. Moreover, chromosomal translocation, as manifested in numerous diseases, could produce not only fusion transcripts but also fusion circRNAs of clinical relevance. Featured with high accuracy, low FDR and the ability to identify fusion circRNAs, we believe that acfs is well suited for a wide spectrum of applications in characterizing the landscape of circRNAs from non-model organisms to cancer biology.}, language = {en} } @article{MirelesConrad2016, author = {Mireles, Victor and Conrad, Tim}, title = {Decomposing biological systems into reusable modules reveals characteristic module size distributions}, year = {2016}, abstract = {One of the widely recognized features of biological systems is their modularity. The modules that comprise biological systems are said to be redeployed and combined across several conditions. In this work, we analyze to what extent are these modules indeed reusable as compared to randomized versions of a system. We develop a notion of modular decompositions of systems that allows for modules to overlap while maximizing the number of times a module is reused across several conditions. Different biological systems present modules whose reusability ranges from the condition specific to the constitutive, although their average reusability is not always higher than random equivalents of the system. These decompositions reveal a distinct distribution of module sizes in real biological systems. This distribution stems, in part, from the peculiar usage pattern of the elements of biological systems, and constitutes a new angle to study the evolution of modularity.}, language = {en} } @article{HoppeObermeierMehlhansetal.2016, author = {Hoppe, Christian and Obermeier, Patrick and Mehlhans, S. and Alchikh, Maren and Seeber, L. and Tief, Franziska and Karsch, K. and Chen, X. and Boettcher, Sindy and Diedrich, S. and Conrad, Tim}, title = {Innovative Digital Tools and Surveillance Systems for the Timely Detection of Adverse Events at the Point of Care: A Proof-of-Concept Study}, volume = {39}, journal = {Drug Safety}, number = {10}, doi = {10.1007/s40264-016-0437-6}, pages = {977 -- 988}, year = {2016}, abstract = {Regulatory authorities often receive poorly structured safety reports requiring considerable effort to investigate potential adverse events post hoc. Automated question-and-answer systems may help to improve the overall quality of safety information transmitted to pharmacovigilance agencies. This paper explores the use of the VACC-Tool (ViVI Automated Case Classification Tool) 2.0, a mobile application enabling physicians to classify clinical cases according to 14 pre-defined case definitions for neuroinflammatory adverse events (NIAE) and in full compliance with data standards issued by the Clinical Data Interchange Standards Consortium. METHODS: The validation of the VACC-Tool 2.0 (beta-version) was conducted in the context of a unique quality management program for children with suspected NIAE in collaboration with the Robert Koch Institute in Berlin, Germany. The VACC-Tool was used for instant case classification and for longitudinal follow-up throughout the course of hospitalization. Results were compared to International Classification of Diseases , Tenth Revision (ICD-10) codes assigned in the emergency department (ED). RESULTS: From 07/2013 to 10/2014, a total of 34,368 patients were seen in the ED, and 5243 patients were hospitalized; 243 of these were admitted for suspected NIAE (mean age: 8.5 years), thus participating in the quality management program. Using the VACC-Tool in the ED, 209 cases were classified successfully, 69 \\% of which had been missed or miscoded in the ED reports. Longitudinal follow-up with the VACC-Tool identified additional NIAE. CONCLUSION: Mobile applications are taking data standards to the point of care, enabling clinicians to ascertain potential adverse events in the ED setting and during inpatient follow-up. Compliance with Clinical Data Interchange Standards Consortium (CDISC) data standards facilitates data interoperability according to regulatory requirements.}, language = {en} } @inproceedings{ShaoConrad2016, author = {Shao, Borong and Conrad, Tim}, title = {Epithelial Mesenchymal Transition Regulatory Network-based Feature Selection in Lung Cancer Prognosis Prediction}, volume = {9656}, booktitle = {Lecture Notes in Computer Science (LNCS)}, doi = {10.1007/978-3-319-31744-1_13}, pages = {1235 -- 146}, year = {2016}, abstract = {Feature selection technique is often applied in identifying cancer prognosis biomarkers. However, many feature selection methods are prone to over-fitting or poor biological interpretation when applied on biological high-dimensional data. Network-based feature selection and data integration approaches are proposed to identify more robust biomarkers. We conducted experiments to investigate the advantages of the two approaches using epithelial mesenchymal transition regulatory network, which is demonstrated as highly relevant to cancer prognosis. We obtained data from The Cancer Genome Atlas. Prognosis prediction was made using Support Vector Machine. Under our experimental settings, the results showed that network-based features gave significantly more accurate predictions than individual molecular features, and features selected from integrated data (RNA-Seq and micro-RNA data) gave significantly more accurate predictions than features selected from single source data (RNA-Seq data). Our study indicated that biological network-based feature transformation and data integration are two useful approaches to identify robust cancer biomarkers.}, language = {en} } @article{TiefHoppeSeeberetal.2016, author = {Tief, Franziska and Hoppe, Christian and Seeber, L. and Obermeier, Patrick and Chen, X. and Karsch, K. and Muehlhans, S. and Adamou, E. and Conrad, Tim and Schweiger, Brunhilde and Adam, T. and Rath, Barbara}, title = {An inception cohort study assessing the role of bacterial co-infections in children with influenza and ILI and a clinical decision model for stringent antibiotic use}, volume = {21}, journal = {Antiviral Therapy}, doi = {10.3851/IMP3034}, pages = {413 -- 424}, year = {2016}, abstract = {BACKGROUND: Influenza-like illness (ILI) is a common reason for paediatric consultations. Viral causes predominate, but antibiotics are used frequently. With regard to influenza, pneumococcal coinfections are considered major contributors to morbidity/mortality. METHODS: In the context of a perennial quality management (QM) programme at the Charit{\'e} Departments of Paediatrics and Microbiology in collaboration with the Robert Koch Institute, children aged 0-18 years presenting with signs and symptoms of ILI were followed from the time of initial presentation until hospital discharge (Charit{\'e} Influenza-Like Disease = ChILD Cohort). An independent QM team performed highly standardized clinical assessments using a disease severity score based on World Health Organization criteria for uncomplicated and complicated/progressive disease. Nasopharyngeal and pharyngeal samples were collected for viral reverse transcription polymerase chain reaction and bacterial culture/sensitivity and MaldiTOF analyses. The term 'detection' was used to denote any evidence of viral or bacterial pathogens in the (naso)pharyngeal cavity. With the ChILD Cohort data collected, a standard operating procedure (SOP) was created as a model system to reduce the inappropriate use of antibiotics in children with ILI. Monte Carlo simulations were performed to assess cost-effectiveness. RESULTS: Among 2,569 ChILD Cohort patients enrolled from 12/2010 to 04/2013 (55\\% male, mean age 3.2 years, range 0-18, 19\\% {\ensuremath{>}}5 years), 411 patients showed laboratory-confirmed influenza, with bacterial co-detection in 35\\%. Influenza and pneumococcus were detected simultaneously in 12/2,569 patients, with disease severity clearly below average. Pneumococcal vaccination rates were close to 90\\%. Nonetheless, every fifth patient was already on antibiotics upon presentation; new antibiotic prescriptions were issued in an additional 20\\%. Simulation of the model SOP in the same dataset revealed that the proposed decision model could have reduced the inappropriate use of antibiotics significantly (P{\ensuremath{<}}0.01) with an incremental cost-effectiveness ratio of -99.55?. CONCLUSIONS: Physicians should be made aware that in times of pneumococcal vaccination the prevalence and severity of influenza infections complicated by pneumococci may decline. Microbiological testing in combination with standardized disease severity assessments and review of vaccination records could be cost-effective, as well as promoting stringent use of antibiotics and a personalized approach to managing children with ILI.}, language = {en} } @article{ObermeierMuehlhansHoppeetal.2016, author = {Obermeier, Patrick and Muehlhans, S. and Hoppe, Christian and Karsch, K. and Tief, Franziska and Seeber, L. and Chen, X. and Conrad, Tim and Boettcher, Sindy and Diedrich, S. and Rath, Barbara}, title = {Enabling Precision Medicine With Digital Case Classification at the Point-of-Care}, volume = {4}, journal = {EBioMedicine}, doi = {10.1016/j.ebiom.2016.01.008}, pages = {191 -- 196}, year = {2016}, abstract = {Infectious and inflammatory diseases of the central nervous system are difficult to identify early. Case definitions for aseptic meningitis, encephalitis, myelitis, and acute disseminated encephalomyelitis (ADEM) are available, but rarely put to use. The VACC-Tool (Vienna Vaccine Safety Initiative Automated Case Classification-Tool) is a mobile application enabling immediate case ascertainment based on consensus criteria at the point-of-care. The VACC-Tool was validated in a quality management program in collaboration with the Robert-Koch-Institute. Results were compared to ICD-10 coding and retrospective analysis of electronic health records using the same case criteria. Of 68,921 patients attending the emergency room in 10/2010-06/2013, 11,575 were hospitalized, with 521 eligible patients (mean age: 7.6 years) entering the quality management program. Using the VACC-Tool at the point-of-care, 180/521 cases were classified successfully and 194/521 ruled out with certainty. Of the 180 confirmed cases, 116 had been missed by ICD-10 coding, 38 misclassified. By retrospective application of the same case criteria, 33 cases were missed. Encephalitis and ADEM cases were most likely missed or misclassified. The VACC-Tool enables physicians to ask the right questions at the right time, thereby classifying cases consistently and accurately, facilitating translational research. Future applications will alert physicians when additional diagnostic procedures are required.}, language = {en} } @article{ConradBrucknerKayser2013, author = {Conrad, Tim and Bruckner, Sharon and Kayser, Bastian}, title = {Finding Modules in Networks with Non-modular Regions}, volume = {7933}, journal = {Lecture Notes in Computer Science (Proceedings of SEA 2013)}, doi = {10.1007/978-3-642-38527-8_18}, pages = {188 -- 199}, year = {2013}, abstract = {Most network clustering methods share the assumption that the network can be completely decomposed into modules, that is, every node belongs to (usually exactly one) module. Forcing this constraint can lead to misidentification of modules where none exist, while the true modules are drowned out in the noise, as has been observed e.g. for protein interaction networks. We thus propose a clustering model where networks contain both a modular region consisting of nodes that can be partitioned into modules, and a transition region containing nodes that lie between or outside modules. We propose two scores based on spectral properties to determine how well a network fits this model. We then evaluate three (partially adapted) clustering algorithms from the literature on random networks that fit our model, based on the scores and comparison to the ground truth. This allows to pinpoint the types of networks for which the different algorithms perform well.}, language = {en} } @article{ConradRathTiefetal.2013, author = {Conrad, Tim and Rath, Barbara and Tief, Franziska and Karsch, K. and Muehlhans, S. and Obermeier, Patrick and Adamou, E. and Chen, X. and Seeber, L. and Peiser, Ch. and Hoppe, Christian and von Kleist, Max and Schweiger, Brunhilde}, title = {Towards a personalized approach to managing of influenza infections in infants and children - food for thought and a note on oseltamivir}, volume = {13}, journal = {Infectious Disorders - Drug Targets}, number = {1}, pages = {25 -- 33}, year = {2013}, language = {en} } @article{ConradLeichtleNuofferetal.2012, author = {Conrad, Tim and Leichtle, Alexander Benedikt and Nuoffer, Jean-Marc and Ceglarek, Uta and Kase, Julia and Witzigmann, Helmut and Thiery, Joachim and Fiedler, Georg Martin}, title = {Serum amino acid profiles and their alterations in colorectal cancer}, journal = {Metabolomics}, doi = {10.1007/s11306-011-0357-5}, year = {2012}, abstract = {Mass spectrometry-based serum metabolic profiling is a promising tool to analyse complex cancer associated metabolic alterations, which may broaden our pathophysiological understanding of the disease and may function as a source of new cancer-associated biomarkers. Highly standardized serum samples of patients suffering from colon cancer (n = 59) and controls (n = 58) were collected at the University Hospital Leipzig. We based our investigations on amino acid screening profiles using electrospray tandem-mass spectrometry. Metabolic profiles were evaluated using the Analyst 1.4.2 software. General, comparative and equivalence statistics were performed by R 2.12.2. 11 out of 26 serum amino acid concentrations were significantly different between colorectal cancer patients and healthy controls. We found a model including CEA, glycine, and tyrosine as best discriminating and superior to CEA alone with an AUROC of 0.878 (95\\% CI 0.815?0.941). Our serum metabolic profiling in colon cancer revealed multiple significant disease-associated alterations in the amino acid profile with promising diagnostic power. Further large-scale studies are necessary to elucidate the potential of our model also to discriminate between cancer and potential differential diagnoses. In conclusion, serum glycine and tyrosine in combination with CEA are superior to CEA for the discrimination between colorectal cancer patients and controls.}, language = {en} } @article{GuptaConradSpoetteretal.2012, author = {Gupta, Pooja and Conrad, Tim and Sp{\"o}tter, Andreas and Reinsch, Norbert and Bienefeld, Kaspar}, title = {Simulating a base population in honey bee for molecular genetic studies}, journal = {Genetics Selection Evolution}, doi = {10.1186/1297-9686-44-14}, year = {2012}, abstract = {Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding values estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has distinct genetic and reproductive biology characteristics. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee.  Results: Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) ?2 statistics for Hardy- Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r2 values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. Conclusion: We developed a software program that takes into account the genetic and reproductive biology characteristics specific to the honey bee and that can be used to constitute a genomic dataset compatible with the simulation studies necessary to optimize breeding programs. The source code together with an instruction file is freely accessible at http://msproteomics.org/Research/Misc/honeybeepopulationsimulator.html}, language = {en} } @article{Conrad2004, author = {Conrad, Tim}, title = {New Appraches for Visualizing and Analyzing Metabolic Pathways}, journal = {Proceedings of the Second Australian Undergraduate Students? Computing Conference}, year = {2004}, abstract = {Visualizing of metabolic pathways (or networks) has been done by many differentapproaches. In this work, we implemented and tested existing graph layout algorithms, and present a new approach to lay-out medium size metabolic pathways (500-20,000 vertices) by implementing and combining three well known graph lay-out algorithms (high dimension embedding, spring-embedder preprocessing, spring-embedder), through 3D space density analysis facilitated by the Octree technique. For the analysis of the results of metabolic pathways simulations we present two new techniques: rstly, a powerful technique to visualize pathways simulation data was created to unveil and understand concentration ows through metabolic pathways. This was achieved by mapping the color encoded concentration value of every substance from each time step of the simulation to its graphical representation in the layout. By combining all resulting images (from each time step) and displaying them as a movie, many characteristics such as subnetworks, alternative routes through the network, and differences between a modied pathway and its unmodied version can be revealed. Secondly, a new method to detect co-regulated substances in metabolic pathways and to recognize differences between two versions of a pathway, was established. To do this, we transformed the simulation data into a row-based representation, color-coded these rows, and reordered them with respect to similarity by using a Genetic Algorithm variant. From the arising discrete 2-dimensional matrix consisting of concentration values, a continuous 2-dimensional fourier row function was computed. This function can be used to measure properties, such as similarities in a pathway between time steps, or substances, or to detect and evaluate differences between modied versions of the same pathway.}, language = {en} } @phdthesis{Conrad2004, author = {Conrad, Tim}, title = {Metabolic Pathways}, year = {2004}, language = {en} } @article{KozlikovaKroneFalketal.2016, author = {Kozl{\´i}kov{\´a}, Barbora and Krone, Michael and Falk, Martin and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian}, title = {Visualization of Biomolecular Structures: State of the Art Revisited}, volume = {36}, journal = {Computer Graphics Forum}, number = {8}, doi = {10.1111/cgf.13072}, pages = {178 -- 204}, year = {2016}, abstract = {Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.}, language = {en} } @misc{GuentherKuhnHegeetal.2016, author = {G{\"u}nther, Tobias and Kuhn, Alexander and Hege, Hans-Christian and Gross, Markus and Theisel, Holger}, title = {Progressive Monte-Carlo Rendering of Atmospheric Flow Features Across Scales}, journal = {69th Annual Meeting of the APS Division of Fluid Dynamics, Gallery of Fluid Motion, Nov 20-22, 2016, Portland, OR, USA.}, doi = {10.1103/APS.DFD.2016.GFM.P0030}, year = {2016}, abstract = {To improve existing weather prediction and reanalysis capabilities, high-resolution and multi-modal climate data becomes an increasingly important topic. The advent of increasingly dense numerical simulation of atmospheric phenomena, provides new means to better understand dynamic processes and to visualize structural flow patterns that remain hidden otherwise. In the presented illustrations we demonstrate an advanced technique to visualize multiple scales of dense flow fields and Lagrangian patterns therein, simulated by state-of-the-art simulation models for each scale. They provide a deeper insight into the structural differences and patterns that occur on each scale and highlight the complexity of flow phenomena in our atmosphere.}, language = {en} } @inproceedings{ArltLindowBaumetal.2016, author = {Arlt, Tobias and Lindow, Norbert and Baum, Daniel and Hilger, Andre and Mahnke, Ingo and Hege, Hans-Christian and Lepper, Verena and Siopi, Tzulia and Mahnke, Heinz.Eberhard}, title = {Virtual Access to Hidden Texts - Study of Ancient Papyri}, booktitle = {Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany}, year = {2016}, abstract = {When physical unfolding/unrolling of papyri is not possible or too dangerous for preserving the precious object, tomographic approaches may be the ap- propriate alternative. Requirements are the resolution and the contrast to distinguish writing and substrate. The steps to be performed are the following: (1) Select the object of interest (archaeological arguments, cultural back- ground of the object, etc.). (2) Find the proper physical procedure, especially with respect to contrast, take the tomographic data, e.g. by absorption x-ray tomography. (3) Apply mathematical unfolding transformations to the tomographic data, in order to obtain a 2d-planar reconstruction of text.}, language = {en} } @inproceedings{KuhnHege2017, author = {Kuhn, Alexander and Hege, Hans-Christian}, title = {Object-based visualization and evaluation of cloud-resolving simulations}, booktitle = {Book of Abstracts, SCCS 2017 - Scaling Cascades in Complex Systems, Mar 27-29, 2017, Berlin, Germany}, year = {2017}, abstract = {Recent advances in high-resolution, cloud resolving simulation models pose several challenges towards respective analysis methodologies. To enable efficient comparison and validation of such models efficient, scalable, and informative diagnostic procedures are mandatory. In this talk, an object-based evaluation scheme based on the notion of scalar field topology will be presented. The presentation will cover the application of topological clustering procedures for object identification, tracking, and the retrieval of object-based statistics. The pro-posed methodology is shown to enable an advanced in-depth evaluation and visualization of high cloud-resolving models. Using a newly developed large-scale high-resolution model (i.e., HD(CP)2 ICON), it will be demonstrated that the presented procedures are applicable to assess the model performance compared to measurements (e.g., radar, satellite) and standard operational models (COSMO) at different domains and spatial scales.}, language = {en} } @misc{ZhukovaHiepenKnausetal.2017, author = {Zhukova, Yulia and Hiepen, Christian and Knaus, Petra and Osterland, Marc and Prohaska, Steffen and Dunlop, John W. C. and Fratzl, Peter and Skorb, Ekaterina V.}, title = {The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration}, issn = {1438-0064}, doi = {10.1002/adhm.201601244}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63053}, year = {2017}, abstract = {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.}, language = {en} } @article{AboulhassanSicatBaumetal.2017, author = {Aboulhassan, Amal and Sicat, Ronell and Baum, Daniel and Wodo, Olga and Hadwiger, Markus}, title = {Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies}, volume = {36}, journal = {Computer Graphics Forum}, number = {3}, publisher = {Wiley}, doi = {10.1111/cgf.13191}, pages = {329 -- 339}, year = {2017}, abstract = {The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths.}, language = {en} } @article{SeidelBlumerZaslanskyetal.2017, author = {Seidel, Ronald and Blumer, Michael and Zaslansky, Paul and Kn{\"o}tel, David and Huber, Daniel R. and Weaver, James C. and Fratzl, Peter and Omelon, Sidney and Bertinetti, Luca and Dean, Mason N.}, title = {Ultrastructural, material and crystallographic description of endophytic masses - a possible damage response in shark and ray tessellated calcified cartilage}, journal = {Journal of Structural Biology}, doi = {10.1016/j.jsb.2017.03.004}, year = {2017}, abstract = {The cartilaginous endoskeletons of Elasmobranchs (sharks and rays) are reinforced superficially by minute, mineralized tiles, called tesserae. Unlike the bony skeletons of other vertebrates, elasmobranch skeletons have limited healing capability and their tissues' mechanisms for avoiding damage or managing it when it does occur are largely unknown. Here we describe an aberrant type of mineralized elasmobranch skeletal tissue called endophytic masses (EPMs), which grow into the uncalcified cartilage of the skeleton, but exhibit a strikingly different morphology compared to tesserae and other elasmobranch calcified tissues. We use biological and materials characterization techniques, including computed tomography, electron and light microscopy, x-ray and Raman spectroscopy and histology to characterize the morphology, ultrastructure and chemical composition of tesserae-associated EPMs in different elasmobranch species. EPMs appear to develop between and in intimate association with tesserae, but lack the lines of periodic growth and varying mineral density characteristic of tesserae. EPMs are mineral-dominated (high mineral and low organic content), comprised of birefringent bundles of large monetite or brushite crystals aligned end to end in long strings. Both Unusual skeletal mineralization in elasmobranchs tesserae and EPMs appear to develop in a type-2 collagen-based matrix, but in contrast to tesserae, all chondrocytes embedded or in contact with EPMs are dead and mineralized. The differences outlined between EPMs and tesserae demonstrate them to be distinct tissues. We discuss several possible reasons for EPM development, including tissue reinforcement, repair, and disruptions of mineralization processes, within the context of elasmobranch skeletal biology as well as descriptions of damage responses of other vertebrate mineralized tissues.}, language = {en} } @misc{Pilz2016, type = {Master Thesis}, author = {Pilz, Sven-Kristofer}, title = {Multi-View Reconstruction based on Mesh Photo-Consistency Optimization}, pages = {41}, year = {2016}, language = {en} } @masterthesis{Auch2016, type = {Bachelor Thesis}, author = {Auch, Sim{\´o}n}, title = {Realtime Action Unit detection}, pages = {38}, year = {2016}, language = {en} } @article{SuinesiaputraAlbinAlbaetal.2017, author = {Suinesiaputra, Avan and Albin, Pierre and Alba, Xenia and Alessandrini, Martino and Allen, Jack and Bai, Wenjia and Cimen, Serkan and Claes, Peter and Cowan, Brett and D'hooge, Jan and Duchateau, Nicolas and Ehrhardt, Jan and Frangi, Alejandro and Gooya, Ali and Grau, Vicente and Lekadir, Karim and Lu, Allen and Mukhopadhyay, Anirban and Oksuz, Ilkay and Parajuli, Nripesh and Pennec, Xavier and Pereanez, Marco and Pinto, Catarina and Piras, Paolo and Rohe, Marc-Michael and Rueckert, Daniel and Saring, Dennis and Sermesant, Maxime and Siddiqi, Kaleem and Tabassian, Mahdi and Teresi, Lusiano and Tsaftaris, Sotirios and Wilms, Matthias and Young, Alistair and Zhang, Xingyu and Medrano-Gracia, Pau}, title = {Statistical shape modeling of the left ventricle: myocardial infarct classification challenge}, journal = {IEEE Journal of Biomedical and Health Informatics}, number = {99}, doi = {10.1109/JBHI.2017.2652449}, year = {2017}, abstract = {Statistical shape modeling is a powerful tool for visualizing and quantifying geometric and functional patterns of the heart. After myocardial infarction (MI), the left ventricle typically remodels in response to physiological challenges. Several methods have been proposed in the literature to describe statistical shape changes. Which method best characterizes left ventricular remodeling after MI is an open research question. A better descriptor of remodeling is expected to provide a more accurate evaluation of disease status in MI patients. We therefore designed a challenge to test shape characterization in MI given a set of three-dimensional left ventricular surface points. The training set comprised 100 MI patients, and 100 asymptomatic volunteers (AV). The challenge was initiated in 2015 at the Statistical Atlases and Computational Models of the Heart workshop, in conjunction with the MICCAI conference. The training set with labels was provided to participants, who were asked to submit the likelihood of MI from a different (validation) set of 200 cases (100 AV and 100 MI). Sensitivity, specificity, accuracy and area under the receiver operating characteristic curve were used as the outcome measures. The goals of this challenge were to (1) establish a common dataset for evaluating statistical shape modeling algorithms in MI, and (2) test whether statistical shape modeling provides additional information characterizing MI patients over standard clinical measures. Eleven groups with a wide variety of classification and feature extraction approaches participated in this challenge. All methods achieved excellent classification results with accuracy ranges from 0.83 to 0.98. The areas under the receiver operating characteristic curves were all above 0.90. Four methods showed significantly higher performance than standard clinical measures. The dataset and software for evaluation are available from the Cardiac Atlas Project website1.}, language = {en} } @article{VegaSchuetteConrad2016, author = {Vega, Iliusi and Sch{\"u}tte, Christof and Conrad, Tim}, title = {Finding metastable states in real-world time series with recurrence networks}, volume = {445}, journal = {Physica A: Statistical Mechanics and its Applications}, doi = {10.1016/j.physa.2015.10.041}, pages = {1 -- 17}, year = {2016}, abstract = {In the framework of time series analysis with recurrence networks, we introduce a self-adaptive method that determines the elusive recurrence threshold and identifies metastable states in complex real-world time series. As initial step, we introduce a way to set the embedding parameters used to reconstruct the state space from the time series. We set them as the ones giving the maximum Shannon entropy of the diagonal line length distribution for the first simultaneous minima of recurrence rate and Shannon entropy. To identify metastable states, as well as the transitions between them, we use a soft partitioning algorithm for module finding which is specifically developed for the case in which a system shows metastability. We illustrate our method with a complex time series example. Finally, we show the robustness of our method for identifying metastable states. Our results suggest that our method is robust for identifying metastable states in complex time series, even when introducing considerable levels of noise and missing data points.}, language = {en} } @article{ConradGenzelCvetkovicetal.2017, author = {Conrad, Tim and Genzel, Martin and Cvetkovic, Nada and Wulkow, Niklas and Leichtle, Alexander Benedikt and Vybiral, Jan and Kytyniok, Gitta and Sch{\"u}tte, Christof}, title = {Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data}, volume = {18}, journal = {BMC Bioinfomatics}, number = {160}, doi = {10.1186/s12859-017-1565-4}, year = {2017}, abstract = {Background: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust against noise and outliers, while the identified feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA),based on thet heory of compressed sensing that allows us to identify a minimal discriminating set of features from mass spectrometry data-sets. We show (1) how our method performs on artificial and real-world data-sets, (2) that its performance is competitive with standard (and widely used) algorithms for analyzing proteomics data, and (3) that it is robust against random and systematic noise. We further demonstrate the applicability of our algorithm to two previously published clinical data-sets.}, language = {en} } @article{HombergBaumProhaskaetal.2017, author = {Homberg, Ulrike and Baum, Daniel and Prohaska, Steffen and G{\"u}nster, Jens and Krauß-Sch{\"u}ler, Stefanie}, title = {Adapting trabecular structures for 3D printing: an image processing approach based on µCT data}, volume = {3}, journal = {Biomedical Physics \& Engineering Express}, number = {3}, publisher = {IOP Publishing}, doi = {10.1088/2057-1976/aa7611}, year = {2017}, abstract = {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.}, language = {en} } @inproceedings{KuhnEngelkeFlatkenetal.2017, author = {Kuhn, Alexander and Engelke, Wito and Flatken, Markus and Hege, Hans-Christian and Hotz, Ingrid}, title = {Topology-based Analysis for Multimodal Atmospheric Data of Volcano Eruptions}, booktitle = {Topological Methods in Data Analysis and Visualization IV}, publisher = {Springer}, address = {Cham, Schweiz}, doi = {10.1007/978-3-319-44684-4_2}, pages = {35 -- 50}, year = {2017}, language = {en} } @article{WilsonAnglinAmbellanetal.2017, author = {Wilson, David and Anglin, Carolyn and Ambellan, Felix and Grewe, Carl Martin and Tack, Alexander and Lamecker, Hans and Dunbar, Michael and Zachow, Stefan}, title = {Validation of three-dimensional models of the distal femur created from surgical navigation point cloud data for intraoperative and postoperative analysis of total knee arthroplasty}, volume = {12}, journal = {International Journal of Computer Assisted Radiology and Surgery}, number = {12}, publisher = {Springer}, doi = {10.1007/s11548-017-1630-5}, pages = {2097 -- 2105}, year = {2017}, abstract = {Purpose: Despite the success of total knee arthroplasty there continues to be a significant proportion of patients who are dissatisfied. One explanation may be a shape mismatch between pre and post-operative distal femurs. The purpose of this study was to investigate a method to match a statistical shape model (SSM) to intra-operatively acquired point cloud data from a surgical navigation system, and to validate it against the pre-operative magnetic resonance imaging (MRI) data from the same patients. Methods: A total of 10 patients who underwent navigated total knee arthroplasty also had an MRI scan less than 2 months pre-operatively. The standard surgical protocol was followed which included partial digitization of the distal femur. Two different methods were employed to fit the SSM to the digitized point cloud data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). The available MRI data were manually segmented and the reconstructed three-dimensional surfaces used as ground truth against which the statistical shape model fit was compared. Results: For both approaches, the difference between the statistical shape model-generated femur and the surface generated from MRI segmentation averaged less than 1.7 mm, with maximum errors occurring in less clinically important areas. Conclusion: The results demonstrated good correspondence with the distal femoral morphology even in cases of sparse data sets. Application of this technique will allow for measurement of mismatch between pre and post-operative femurs retrospectively on any case done using the surgical navigation system and could be integrated into the surgical navigation unit to provide real-time feedback.}, language = {en} } @article{HoffmannLemanisFalkenbergetal.2017, author = {Hoffmann, Ren{\´e} and Lemanis, Robert and Falkenberg, Janina and Schneider, Steffen and Wesendonk, Hendrik and Zachow, Stefan}, title = {Integrating 2D and 3D shell morphology to disentangle the palaeobiology of ammonoids: A virtual approach}, volume = {61}, journal = {Palaeontology}, number = {1}, doi = {10.1111/pala.12328}, pages = {89 -- 104}, year = {2017}, abstract = {We demonstrate, based on data derived from computed tomography, that integrating 2D and 3D morphological data of ammonoid shells represent an important new approach to disentangle the palaeobiology of ammonoids. Characterization of ammonite morphology has long been constrained to 2D data and only a few studies collect ontogenetic data in 180° steps. We combine this traditional approach with 3D data collected from high-resolution nano-computed tomography. For this approach, ontogenetic morphological data of the hollow shell of a juvenile ammonite Kosmoceras (Jurassic, Callovian) is collected. 2D data is collected in 10° steps and show significant changes in shell morphology. Preserved hollow spines show multiple mineralized membranes never reported before, representing temporal changes of the ammonoid mantle tissue. 3D data show that chamber volumes do not always increase exponentially, as was generally assumed, but may represent a proxy for life events, e.g. stress phases. Furthermore, chamber volume cannot be simply derived from septal spacing in forms comparable to Kosmoceras. Vogel numbers, a 3D parameter for chamber shape, of Kosmoceras are similar to other ammonoids (Arnsbergites, Amauroceras) and modern cephalopods (Nautilus, Spirula). Two methods to virtually document the suture line ontogeny, used to document phylogenetic relationships of larger taxonomic entities, were applied for the first time and seem a promising alternative to hand drawings. The curvature of the chamber surfaces increases during ontogeny due to increasing strength of ornamentation and septal complexity. As increasing curvature may allow for faster handling of cameral liquid, it could compensate for decreasing SA/V ratios through ontogeny.}, language = {en} } @misc{HombergBaumProhaskaetal.2017, author = {Homberg, Ulrike and Baum, Daniel and Prohaska, Steffen and G{\"u}nster, Jens and Krauß-Sch{\"u}ler, Stefanie}, title = {Adapting trabecular structures for 3D printing: an image processing approach based on µCT data}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-64004}, year = {2017}, abstract = {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.}, language = {en} } @inproceedings{BaumMahlowLameckeretal.2014, author = {Baum, Daniel and Mahlow, Kristin and Lamecker, Hans and Zachow, Stefan and M{\"u}ller, Johannes and Hege, Hans-Christian}, title = {The Potential of Surface-based Geometric Morphometrics for Evolutionary Studies: An Example using Dwarf Snakes (Eirenis)}, booktitle = {Abstract in DigitalSpecimen 2014}, year = {2014}, abstract = {Geometric morphometrics plays an important role in evolutionary studies. The state-of-the-art in this field are landmark-based methods. Since the landmarks usually need to be placed manually, only a limited number of landmarks are generally used to represent the shape of an anatomical structure. As a result, shape characteristics that cannot be properly represented by small sets of landmarks are disregarded. In this study, we present a method that is free of this limitation. The method takes into account the whole shape of an anatomical structure, which is represented as a surface, hence the term 'surface-based morphometrics'. Correspondence between two surfaces is established by defining a partitioning of the surfaces into homologous surface patches. The first step for the generation of a surface partitioning is to place landmarks on the surface. Subsequently, the landmarks are connected by curves lying on the surface. The curves, called 'surface paths', might either follow specific anatomical features or they can be geodesics, that is, shortest paths on the surface. One important requirement, however, is that the resulting surface path networks are topologically equivalent across all surfaces. Once the surface path networks have been defined, the surfaces are decomposed into patches according to the path networks. This approach has several advantages. One of them is that we can discretize the surface by as many points as desired. Thus, even fine shape details can be resolved if this is of interest for the study. Since a point discretization is used, another advantage is that well-established analysis methods for landmark-based morphometrics can be utilized. Finally, the shapes can be easily morphed into one another, thereby greatly supporting the understanding of shape changes across all considered specimens. To show the potential of the described method for evolutionary studies of biological specimens, we applied the method to the para-basisphenoid complex of the snake genus Eirenis. By using this anatomical structure as example, we present all the steps that are necessary for surface-based morphometrics, including the segmentation of the para-basisphenoid complex from micro-CT data sets. We also show some first results using statistical analysis as well as classification methods based on the presented technique.}, language = {en} } @article{RedemannBaumgartLindowetal.2017, author = {Redemann, Stefanie and Baumgart, Johannes and Lindow, Norbert and Shelley, Michael and Nazockdast, Ehssan and Kratz, Andrea and Prohaska, Steffen and Brugu{\´e}s, Jan and F{\"u}rthauer, Sebastian and M{\"u}ller-Reichert, Thomas}, title = {C. elegans chromosomes connect to centrosomes by anchoring into the spindle network}, volume = {8}, journal = {Nature Communications}, number = {15288}, doi = {10.1038/ncomms15288}, year = {2017}, abstract = {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.}, language = {en} } @misc{RohrHerrmannIlmetal.2017, author = {Rohr, Ulrich-Peter and Herrmann, Pia and Ilm, Katharina and Zhang, Hai and Lohmann, Sabine and Reiser, Astrid and Muranyi, Andrea and Smith, Janice and Burock, Susen and Osterland, Marc and Leith, Katherine and Singh, Shalini and Brunhoeber, Patrick and Bowermaster, Rebecca and Tie, Jeanne and Christie, Michael and Wong, Hui-Li and Waring, Paul and Shanmugam, Kandavel and Gibbs, Peter and Stein, Ulrike}, title = {Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies}, issn = {1438-0064}, doi = {10.1093/annonc/mdx207}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-64184}, year = {2017}, abstract = {Background We assessed the novel MACC1 gene to further stratify stage II colon cancer patients with proficient mismatch repair (pMMR). Patients and methods Four cohorts with 596 patients were analyzed: Charit{\´e} 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charit{\´e} 2 comparison cohort was used to translate MACC1 qRT- PCR analyses to FFPE samples. In the BIOGRID 1 training cohort MACC1 mRNA levels were related to MACC1 protein levels from immunohistochemistry in FFPE sections; also analyzed for MMR. Chemotherapy-na{\"i}ve pMMR patients were stratified by MACC1 mRNA and protein expression to establish risk groups based on recurrence-free survival (RFS). Risk stratification from BIOGRID 1 was confirmed in the BIOGRID 2 validation cohort. Pooled BIOGRID datasets produced a best effect-size estimate. Results In BIOGRID 1, using qRT-PCR and immunohistochemistry for MACC1 detection, pMMR/MACC1-low patients had a lower recurrence probability versus pMMR/MACC1-high patients (5-year RFS of 92\% and 67\% versus 100\% and 68\%, respectively). In BIOGRID 2, longer RFS was confirmed for pMMR/MACC1-low versus pMMR/MACC1-high patients (5-year RFS of 100\% versus 90\%, respectively). In the pooled dataset, 6.5\% of patients were pMMR/MACC1-low with no disease recurrence, resulting in a 17\% higher 5-year RFS (95\% CI (12.6-21.3\%)) versus pMMR/MACC1-high patients (P=0.037). Outcomes were similar for pMMR/MACC1-low and deficient MMR (dMMR) patients (5-year RFS of 100\% and 96\%, respectively). Conclusions MACC1 expression stratifies colon cancer patients with unfavorable pMMR status. Stage II colon cancer patients with pMMR/MACC1-low tumors have a similar favorable prognosis to those with dMMR with potential implications for the role of adjuvant therapy.}, language = {en} } @article{RohrHerrmannIlmetal.2017, author = {Rohr, Ulrich-Peter and Herrmann, Pia and Ilm, Katharina and Zhang, Hai and Lohmann, Sabine and Reiser, Astrid and Muranyi, Andrea and Smith, Janice and Burock, Susen and Osterland, Marc and Leith, Katherine and Singh, Shalini and Brunhoeber, Patrick and Bowermaster, Rebecca and Tie, Jeanne and Christie, Michael and Wong, Hui-Li and Waring, Paul and Shanmugam, Kandavel and Gibbs, Peter and Stein, Ulrike}, title = {Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies}, volume = {28}, journal = {Annals of Oncology}, number = {8}, doi = {10.1093/annonc/mdx207}, pages = {1869 -- 1875}, year = {2017}, abstract = {Background We assessed the novel MACC1 gene to further stratify stage II colon cancer patients with proficient mismatch repair (pMMR). Patients and methods Four cohorts with 596 patients were analyzed: Charit{\´e} 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charit{\´e} 2 comparison cohort was used to translate MACC1 qRT-PCR analyses to FFPE samples. In the BIOGRID 1 training cohort MACC1 mRNA levels were related to MACC1 protein levels from immunohistochemistry in FFPE sections; also analyzed for MMR. Chemotherapy-na{\"i}ve pMMR patients were stratified by MACC1 mRNA and protein expression to establish risk groups based on recurrence-free survival (RFS). Risk stratification from BIOGRID 1 was confirmed in the BIOGRID 2 validation cohort. Pooled BIOGRID datasets produced a best effect-size estimate. Results In BIOGRID 1, using qRT-PCR and immunohistochemistry for MACC1 detection, pMMR/MACC1-low patients had a lower recurrence probability versus pMMR/MACC1-high patients (5-year RFS of 92\% and 67\% versus 100\% and 68\%, respectively). In BIOGRID 2, longer RFS was confirmed for pMMR/MACC1-low versus pMMR/MACC1-high patients (5-year RFS of 100\% versus 90\%, respectively). In the pooled dataset, 6.5\% of patients were pMMR/MACC1-low with no disease recurrence, resulting in a 17\% higher 5-year RFS (95\% CI (12.6-21.3\%)) versus pMMR/MACC1-high patients (P=0.037). Outcomes were similar for pMMR/MACC1-low and deficient MMR (dMMR) patients (5-year RFS of 100\% and 96\%, respectively). Conclusions MACC1 expression stratifies colon cancer patients with unfavorable pMMR status. Stage II colon cancer patients with pMMR/MACC1-low tumors have a similar favorable prognosis to those with dMMR with potential implications for the role of adjuvant therapy.}, language = {en} } @article{BrueningGoubergritsHepptetal.2017, author = {Br{\"u}ning, Jan and Goubergrits, Leonid and Heppt, Werner and Zachow, Stefan and Hildebrandt, Thomas}, title = {Numerical Analysis of Nasal Breathing - A Pilot Study}, volume = {33}, journal = {Facial Plastic Surgery}, number = {4}, doi = {doi:10.1055/s-0037-1603789}, pages = {388 -- 395}, year = {2017}, abstract = {Background: Currently, there is no fully sufficient way to differentiate between symptomatic and normal nasal breathing. Using the nose's total resistance is disputed as a valid means to objectify nasal airflow, and the need for a more comprehensive diagnostic method is increasing. This work's aim was to test a novel approach considering intranasal wall shear stress as well as static pressure maps obtained by computational fluid dynamics (CFD). Methods: X-ray computed tomography (CT) scan data of six symptom-free subjects and seven symptomatic patients were used. Patient-specific geometries of the nasal cavity were segmented from these data sets. Inspiratory and expiratory steady airflow simulations were performed using CFD. Calculated static pressures and wall shear stresses (WSS) were mapped onto a common template of the nasal septum, allowing for comparison of these parameters between the two patient groups. Results: Significant differences in wall shear stress distributions during the inspiratory phase could be identified between the two groups, whereas no differences were found for the expiratory phase. It is assumed that one essential feature of normal nasal breathing probably consists in distinctively different intranasal flow fields for inspiration and expiration. This is in accordance with previous investigations. Conclusion: The proposed method seems to be a promising tool for developing a new kind of patient-specific assessment of nasal breathing. However, more studies and a greater case number of data with an expanded focus, would be ideal.}, language = {en} } @misc{WeiserErdmannSchenkletal.2017, author = {Weiser, Martin and Erdmann, Bodo and Schenkl, Sebastian and Muggenthaler, Holger and Hubig, Michael and Mall, Gita and Zachow, Stefan}, title = {Uncertainty in Temperature-Based Determination of Time of Death}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63818}, year = {2017}, abstract = {Temperature-based estimation of time of death (ToD) can be per- formed either with the help of simple phenomenological models of corpse cooling or with detailed mechanistic (thermodynamic) heat transfer mod- els. The latter are much more complex, but allow a higher accuracy of ToD estimation as in principle all relevant cooling mechanisms can be taken into account. The potentially higher accuracy depends on the accuracy of tissue and environmental parameters as well as on the geometric resolution. We in- vestigate the impact of parameter variations and geometry representation on the estimated ToD based on a highly detailed 3D corpse model, that has been segmented and geometrically reconstructed from a computed to- mography (CT) data set, differentiating various organs and tissue types. From that we identify the most crucial parameters to measure or estimate, and obtain a local uncertainty quantifcation for the ToD.}, language = {en} } @article{vonTycowiczAmbellanMukhopadhyayetal.2018, author = {von Tycowicz, Christoph and Ambellan, Felix and Mukhopadhyay, Anirban and Zachow, Stefan}, title = {An Efficient Riemannian Statistical Shape Model using Differential Coordinates}, volume = {43}, journal = {Medical Image Analysis}, number = {1}, doi = {10.1016/j.media.2017.09.004}, pages = {1 -- 9}, year = {2018}, 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-Euclidean structure. A key advantage of our framework is that statistics in a manifold shape space becomes 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 Euclidean approach in terms of shape-based classification of morphological disorders.}, language = {en} } @article{BennHiepenOsterlandetal.2017, author = {Benn, Andreas and Hiepen, Christian and Osterland, Marc and Sch{\"u}tte, Christof and Zwijsen, An and Knaus, Petra}, title = {Role of bone morphogenetic proteins in sprouting angiogenesis: differential BMP receptor-dependent signaling pathways balance stalk vs. tip cell competence}, volume = {31}, journal = {FASEB Journal}, number = {11}, doi = {10.1096/fj.201700193RR}, pages = {4720 -- 4733}, year = {2017}, abstract = {Before the onset of sprouting angiogenesis, the endothelium is prepatterned for the positioning of tip and stalk cells. Both cell identities are not static, as endothelial cells (ECs) constantly compete for the tip cell position in a dynamic fashion. Here, we show that both bone morphogenetic protein (BMP) 2 and BMP6 are proangiogenic in vitro and ex vivo and that the BMP type I receptors, activin receptor-like kinase (ALK)3 and ALK2, play crucial and distinct roles in this process. BMP2 activates the expression of tip cell-associated genes, such as DLL4 (delta-like ligand 4) and KDR (kinase insert domain receptor), and p38-heat shock protein 27 (HSP27)-dependent cell migration, thereby generating tip cell competence. Whereas BMP6 also triggers collective cell migration via the p38-HSP27 signaling axis, BMP6 induces in addition SMAD1/5 signaling, thereby promoting the expression of stalk cell-associated genes, such as HES1 (hairy and enhancer of split 1) and FLT1 (fms-like tyrosine kinase 1). Specifically, ALK3 is required for sprouting from HUVEC spheroids, whereas ALK2 represses sprout formation. We demonstrate that expression levels and respective complex formation of BMP type I receptors in ECs determine stalk vs. tip cell identity, thus contributing to endothelial plasticity during sprouting angiogenesis. As antiangiogenic monotherapies that target the VEGF or ALK1 pathways have not fulfilled efficacy objectives in clinical trials, the selective targeting of the ALK2/3 pathways may be an attractive new approach.}, language = {en} } @misc{VegaSchuetteConrad2014, author = {Vega, Iliusi and Sch{\"u}tte, Christof and Conrad, Tim}, title = {SAIMeR: Self-adapted method for the identification of metastable states in real-world time series}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-50130}, year = {2014}, abstract = {In the framework of time series analysis with recurrence networks, we introduce SAIMeR, a heuristic self-adapted method that determines the elusive recurrence threshold and identifies metastable states in complex time series. To identify metastable states as well as the transitions between them, we use graph theory concepts and a fuzzy partitioning clustering algorithm. We illustrate SAIMeR by applying it to three real-world time series and show that it is able to identify metastable states in real-world data with noise and missing data points. Finally, we suggest a way to choose the embedding parameters used to construct the state space in which this method is performed, based on the analysis of how the values of these parameters affect two recurrence quantitative measurements: recurrence rate and entropy.}, language = {en} } @misc{StoppelHegeWiebel2014, author = {Stoppel, Sergej and Hege, Hans-Christian and Wiebel, Alexander}, title = {Visibility-Driven Depth Determination of Surface Patches in Direct Volume Rendering}, issn = {1438-0064}, doi = {10.2312/eurovisshort.20141164}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-50266}, year = {2014}, abstract = {This paper presents an algorithm called surfseek for selecting surfaces on the most visible features in direct volume rendering (DVR). The algorithm is based on a previously published technique (WYSIWYP) for picking 3D locations in DVR. The new algorithm projects a surface patch on the DVR image, consisting of multiple rays. For each ray the algorithm uses WYSIWYP or a variant of it to find the candidates for the most visible locations along the ray. Using these candidates the algorithm constructs a graph and computes a minimum cut on this graph. The minimum cut represents a very visible but relatively smooth surface. In the last step the selected surface is displayed. We provide examples for the results in real-world dataset as well as in artificially generated datasets.}, language = {en} } @article{PaetschBaumProhaskaetal.2014, author = {Paetsch, Olaf and Baum, Daniel and Prohaska, Steffen and Ehrig, Karsten and Ebell, Gino and Meinel, Dietmar and Heyn, Andreas}, title = {Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben}, journal = {DGZfP-Jahrestagung 2014 Konferenzband}, year = {2014}, language = {de} } @misc{HoffmannSchultzSchellhornetal.2014, author = {Hoffmann, Ren{\´e} and Schultz, Julia A. and Schellhorn, Rico and Rybacki, Erik and Keupp, Helmut and Lemanis, Robert and Zachow, Stefan}, title = {Non-invasive imaging methods applied to neo- and paleo-ontological cephalopod research}, issn = {1438-0064}, doi = {10.5194/bg-11-2721-2014}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-50300}, year = {2014}, abstract = {Several non-invasive methods are common practice in natural sciences today. Here we present how they can be applied and contribute to current topics in cephalopod (paleo-) biology. Different methods will be compared in terms of time necessary to acquire the data, amount of data, accuracy/resolution, minimum/maximum size of objects that can be studied, the degree of post-processing needed and availability. The main application of the methods is seen in morphometry and volumetry of cephalopod shells. In particular we present a method for precise buoyancy calculation. Therefore, cephalopod shells were scanned together with different reference bodies, an approach developed in medical sciences. It is necessary to know the volume of the reference bodies, which should have similar absorption properties like the object of interest. Exact volumes can be obtained from surface scanning. Depending on the dimensions of the study object different computed tomography techniques were applied.}, language = {en} } @misc{PaetschBaumEbelletal.2014, author = {Paetsch, Olaf and Baum, Daniel and Ebell, Gino and Ehrig, Karsten and Heyn, Andreas and Meinel, Dietmar and Prohaska, Steffen}, title = {Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-50912}, year = {2014}, abstract = {Kurzfassung. Durch die Alkalit{\"a}t des Betons wird Betonstahl dauerhaft vor Korrosion gesch{\"u}tzt. Infolge von Chlorideintrag kann dieser Schutz nicht l{\"a}nger aufrechterhalten werden und f{\"u}hrt zu Lochkorrosion. Die zerst{\"o}rungsfreie Pr{\"u}fung von Stahlbetonproben mit 3D-CT bietet die M{\"o}glichkeit, eine Probe mehrfach gezielt vorzusch{\"a}digen und den Korrosionsfortschritt zu untersuchen. Zur Quantifizierung des Sch{\"a}digungsgrades m{\"u}ssen die bei dieser Untersuchung anfallenden großen Bilddaten mit Bildverarbeitungsmethoden ausgewertet werden. Ein wesentlicher Schritt dabei ist die Segmentierung der Bilddaten, bei der zwischen Korrosionsprodukt (Rost), Betonstahl (BSt), Beton, Rissen, Poren und Umgebung unterschieden werden muss. Diese Segmentierung bildet die Grundlage f{\"u}r statistische Untersuchungen des Sch{\"a}digungsfortschritts. Hierbei sind die {\"A}nderung der BSt-Geometrie, die Zunahme von Korrosionsprodukten und deren Ver{\"a}nderung {\"u}ber die Zeit sowie ihrer r{\"a}umlichen Verteilung in der Probe von Interesse. Aufgrund der Gr{\"o}ße der CT-Bilddaten ist eine manuelle Segmentierung nicht durchf{\"u}hrbar, so dass automatische Verfahren unabdingbar sind. Dabei ist insbesondere die Segmentierung der Korrosionsprodukte in den Bilddaten ein schwieriges Problem. Allein aufgrund der Grauwerte ist eine Zuordnung nahezu unm{\"o}glich, denn die Grauwerte von Beton und Korrosionsprodukt unterscheiden sich kaum. Eine formbasierte Suche ist nicht offensichtlich, da die Korrosionsprodukte in Beton diffuse Formen haben. Allerdings l{\"a}sst sich Vorwissen {\"u}ber die Ausbreitung der Korrosionsprodukte nutzen. Sie bilden sich in r{\"a}umlicher N{\"a}he des BSt (in Bereichen vorheriger Volumenabnahme des BSt), entlang von Rissen sowie in Porenr{\"a}umen, die direkt am BSt und in dessen Nahbereich liegen. Davon ausgehend wird vor der Korrosionsprodukterkennung zun{\"a}chst eine BSt-Volumen-, Riss- und Porenerkennung durchgef{\"u}hrt. Dieser in der Arbeit n{\"a}her beschriebene Schritt erlaubt es, halbautomatisch Startpunkte (Seed Points) f{\"u}r die Korrosionsprodukterkennung zu finden. Weiterhin werden verschiedene in der Bildverarbeitung bekannte Algorithmen auf ihre Eignung untersucht werden.}, language = {de} } @misc{SchuetteConrad2014, author = {Sch{\"u}tte, Christof and Conrad, Tim}, title = {Showcase 3: Information-based medicine}, volume = {1}, journal = {MATHEON-Mathematics for Key Technologies}, editor = {Deuflhard, Peter and Gr{\"o}tschel, Martin and H{\"o}mberg, Dietmar and Horst, Ulrich and Kramer, J{\"u}rg and Mehrmann, Volker and Polthier, Konrad and Schmidt, Frank and Skutella, Martin and Sprekels, J{\"u}rgen}, publisher = {European Mathematical Society}, pages = {66 -- 67}, year = {2014}, language = {en} } @misc{PolthierSullivanZiegleretal.2014, author = {Polthier, Konrad and Sullivan, John and Ziegler, G{\"u}nter M. and Hege, Hans-Christian}, title = {Visualization}, journal = {MATHEON - Mathematics for Key Technologies}, editor = {Deuflhard, Peter and et al.,}, publisher = {European Mathematical Society}, isbn = {978-3-03719-137-8}, doi = {10.4171/137}, pages = {335 -- 339}, year = {2014}, language = {en} } @misc{LameckerHegeTabelowetal.2014, author = {Lamecker, Hans and Hege, Hans-Christian and Tabelow, Karsten and Polzehl, J{\"o}rg}, title = {Image Processing}, journal = {MATHEON - Mathematics for Key Technologies}, editor = {Deuflhard, Peter and et al.,}, publisher = {European Mathematical Society}, doi = {10.4171/137}, pages = {359 -- 376}, year = {2014}, language = {en} } @misc{EhlkeFrenzelRammetal.2014, author = {Ehlke, Moritz and Frenzel, Thomas and Ramm, Heiko and Lamecker, Hans and Akbari Shandiz, Mohsen and Anglin, Carolyn and Zachow, Stefan}, title = {Robust Measurement of Natural Acetabular Orientation from AP Radiographs using Articulated 3D Shape and Intensity Models}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-49824}, year = {2014}, language = {en} } @inproceedings{EngelkeKuhnFlatkenetal.2014, author = {Engelke, Wito and Kuhn, Alexander and Flatken, Markus and Chen, Fang and Hege, Hans-Christian and Gerndt, Andreas and Hotz, Ingrid}, title = {Atmospheric Impact of Volcano Eruptions}, booktitle = {Proceedings IEEE SciVis 2014}, year = {2014}, abstract = {The analysis of data that captures volcanic eruptions and their atmospheric aftermath plays an important role for domain experts to gain a deeper understanding of the volcanic eruption and their consequences for atmosphere, climate and air traffic. Thereby, one major challenge is to extract and combine the essential information, which is spread over various, mostly sparse data sources. This requires a careful integration of each data set with its strength and limitations. The sparse, but more reliable measurement data is mainly used to calibrate the more dense simulation data. This work combines a collection of visualization approaches into an exploitative framework. The goal is to support the domain experts to build a complete picture of the situation. But it is also important to understand the individual data sources, the wealth of their information and the quality of the simulation results. All presented methods are designed for direct interaction with the data from different perspectives rather than the sole generation of some final images.}, language = {en} } @article{FaerberTitschackSchoenbergetal.2016, author = {F{\"a}rber, Claudia and Titschack, J{\"u}rgen and Sch{\"o}nberg, Christine H. L. and Ehrig, Karsten and Boos, Karin and Baum, Daniel and Illerhaus, Bernd and Asgaard, Ulla and Bromley, Richard G. and Freiwald, Andr{\´e} and Wisshak, Max}, title = {Long-term macrobioerosion in the Mediterranean Sea assessed by micro-computed tomography}, volume = {13}, journal = {Biogeosciences}, number = {11}, address = {http://www.biogeosciences.net/13/3461/2016/}, doi = {10.5194/bg-13-3461-2016}, pages = {3461 -- 3474}, year = {2016}, abstract = {Biological erosion is a key process for the recycling of carbonate and the formation of calcareous sediments in the oceans. Experimental studies showed that bioerosion is subject to distinct temporal variability, but previous long-term studies were restricted to tropical waters. Here, we present results from a 14-year bioerosion experiment that was carried out along the rocky limestone coast of the island of Rhodes, Greece, in the Eastern Mediterranean Sea, in order to monitor the pace at which bioerosion affects carbonate substrate and the sequence of colonisation by bioeroding organisms. Internal macrobioerosion was visualised and quantified by micro-computed tomography and computer-algorithm-based segmentation procedures. Analysis of internal macrobioerosion traces revealed a dominance of bioeroding sponges producing eight types of characteristic Entobia cavity networks, which were matched to five different clionaid sponges by spicule identification in extracted tissue. The morphology of the entobians strongly varied depending on the species of the producing sponge, its ontogenetic stage, available space, and competition by other bioeroders. An early community developed during the first 5 years of exposure with initially very low macrobioerosion rates and was followed by an intermediate stage when sponges formed large and more diverse entobians and bioerosion rates increased. After 14 years, 30 \% of the block volumes were occupied by boring sponges, yielding maximum bioerosion rates of 900 g m^-2 yr^-1. A high spatial variability in macrobioerosion prohibited clear conclusions about the onset of macrobioerosion equilibrium conditions. This highlights the necessity of even longer experimental exposures and higher replication at various factor levels in order to better understand and quantify temporal patterns of macrobioerosion in marine carbonate environments.}, language = {en} } @phdthesis{Dercksen2015, author = {Dercksen, Vincent J.}, title = {Visual computing techniques for the reconstruction and analysis of anatomically realistic neural networks}, year = {2015}, abstract = {To understand how the brain translates sensory input into behavior, one needs to identify, at the cellular level, the involved neural circuitry and the electrical signals it carries. This thesis describes methods and tools that enable neuroscientists to obtain important anatomical data, including neuron numbers and shapes, from 3D microscopy images. On this basis, tools have been developed to create and visually analyze anatomically realistic 3D models of neural networks: 1. An automatic segmentation method for determining the number and location of neuron cell bodies in 3D microscopy images. Application of this method yields a difference of merely ∼4\% between automatically and manually counted cells, which is sufficiently accurate for application in large-scale counting experiments. 2. A method for the automatic alignment of 3D section volumes containing filamentous structures. To this end, an existing point-matching-based method has been adapted such that sections containing neuron and microtubule fragments could be successfully aligned. 3. The Filament Editor, a 3D proof-editing tool for visual verification and correction of automatically traced filaments. The usefulness of the Filament Editor is demonstrated by applying it in a validated neuron reconstruction pipeline to create 3D models of long-range and complex neuronal branches. 4. The tool NeuroNet, which is used to assemble an anatomical model of a neural network representing the rat barrel cortex (or subnetworks therein, e.g. individual cortical columns), based on reconstructed anatomical data, such as neuron distributions and 3D morphologies. The tool estimates synaptic connectivity between neurons based on structural overlap between axons and dendrites. 5. A framework for the interactive visual analysis of synaptic connectivity in such networks at multiple scales. It works from the level of neuron populations down to individual synapse positions on dendritic trees. It comprises the Cortical Column Connectivity Viewer, developed to analyze synaptic connections between neuron populations within and between cortical columns. The usefulness of these methods is demonstrated by applying them to reconstruct and analyze neural networks in the rat barrel cortex. Finally, I describe several applications of these methods and tools by neuroscientists, yielding significant biological findings regarding neuron anatomy and connectivity.}, language = {en} } @misc{KozlikovaKroneFalketal.2015, author = {Kozlikova, Barbora and Krone, Michael and Falk, Martin and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian}, title = {Visualization of Biomolecular Structures: State of the Art}, issn = {1438-0064}, doi = {10.2312/eurovisstar.20151112}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57217}, year = {2015}, abstract = {Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.}, language = {en} } @article{Zachow2015, author = {Zachow, Stefan}, title = {Computational Planning in Facial Surgery}, volume = {31}, journal = {Facial Plastic Surgery}, number = {5}, doi = {10.1055/s-0035-1564717}, pages = {446 -- 462}, year = {2015}, abstract = {This article reflects the research of the last two decades in computational planning for cranio-maxillofacial surgery. Model-guided and computer-assisted surgery planning has tremendously developed due to ever increasing computational capabilities. Simulators for education, planning, and training of surgery are often compared with flight simulators, where maneuvers are also trained to reduce a possible risk of failure. Meanwhile, digital patient models can be derived from medical image data with astonishing accuracy and thus can serve for model surgery to derive a surgical template model that represents the envisaged result. Computerized surgical planning approaches, however, are often still explorative, meaning that a surgeon tries to find a therapeutic concept based on his or her expertise using computational tools that are mimicking real procedures. Future perspectives of an improved computerized planning may be that surgical objectives will be generated algorithmically by employing mathematical modeling, simulation, and optimization techniques. Planning systems thus act as intelligent decision support systems. However, surgeons can still use the existing tools to vary the proposed approach, but they mainly focus on how to transfer objectives into reality. Such a development may result in a paradigm shift for future surgery planning.}, language = {en} } @misc{LamasRodriguezEhlkeHoffmannetal.2015, author = {Lamas-Rodr{\´i}guez, Juli{\´a}n and Ehlke, Moritz and Hoffmann, Ren{\´e} and Zachow, Stefan}, title = {GPU-accelerated denoising of large tomographic data sets with low SNR}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-56339}, year = {2015}, abstract = {Enhancements in tomographic imaging techniques facilitate non-destructive methods for visualizing fossil structures. However, to penetrate dense materials such as sediments or pyrites, image acquisition is typically performed with high beam energy and very sensitive image intensifiers, leading to artifacts and noise in the acquired data. The analysis of delicate fossil structures requires the images to be captured in maximum resolution, resulting in large data sets of several giga bytes (GB) in size. Since the structural information of interest is often almost in the same spatial range as artifacts and noise, image processing and segmentation algorithms have to cope with a very low signal-to-noise ratio (SNR). Within this report we present a study on the performance of a collection of denoising algorithms applied to a very noisy fossil dataset. The study shows that a non-local means (NLM) filter, in case it is properly configured, is able to remove a considerable amount of noise while preserving most of the structural information of interest. Based on the results of this study, we developed a software tool within ZIBAmira that denoises large tomographic datasets using an adaptive, GPU-accelerated NLM filter. With the help of our implementation a user can interactively configure the filter's parameters and thus its effectiveness with respect to the data of interest, while the filtering response is instantly visualized for a preselected region of interest (ROI). Our implementation efficiently denoises even large fossil datasets in a reasonable amount of time.}, language = {en} } @inproceedings{KozlikovaKroneLindowetal.2015, author = {Kozlikova, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian}, title = {Visualization of Biomolecular Structures: State of the Art}, booktitle = {EuroVis 2015 STARS Proceedings}, doi = {10.2312/eurovisstar.20151112}, pages = {61 -- 81}, year = {2015}, abstract = {Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.}, language = {en} } @article{GreweSchreiberZachow2015, author = {Grewe, Carl Martin and Schreiber, Lisa and Zachow, Stefan}, title = {Fast and Accurate Digital Morphometry of Facial Expressions}, volume = {31}, journal = {Facial Plastic Surgery}, number = {05}, publisher = {Thieme Medical Publishers}, address = {New York}, doi = {10.1055/s-0035-1564720}, pages = {431 -- 438}, year = {2015}, language = {en} } @misc{KuhnTroemel2015, author = {Kuhn, Alexander and Tr{\"o}mel, Silke}, title = {Intercomparison Study of Cloud Feature Extraction and Tracking Algorithms}, volume = {17}, journal = {Geophysical Research Abstracts, Vol 17}, pages = {ID 14128}, year = {2015}, abstract = {Clouds and precipitation systems are fundamental features in the global climate cycle and are one focus aspect of recent high resolution, cloud resolving simulations and measurement modalities. Highly resolved data sources allow for more precise methodologies to extract and track cloud features on different scales and enable novel evaluation tasks such as life-cycle tracking, feature-based statistics, and feature-based comparison of simulation and measurements. However, their complex dynamics and highly variable shape morphology makes extraction and tracking of clouds a challenging task with respect to stable and reliable algorithms. In this work we will present our efforts on establishing an community-wide inter-comparison study to provide an overview of state-of-the-art algorithms for cloud extraction and tracking. We propose a set of 2D and 3D benchmark data sets (from simulations and measurements) that are used as a common basis for comparison. In addition we describe a joint feature-based evaluation framework and provide an in depth analysis and comparison of those algorithms. The goal is to systematically compare and assess numerical extraction and tracking techniques for cloud features in meteorological data and provide a comprehensive overview of suitable application scenarios, describe current strengths and limitations, and derive statements about their variability for feature-based analysis tasks.}, language = {en} } @misc{DeuflhardHege2015, author = {Deuflhard, Peter and Hege, Hans-Christian}, title = {Raumtiefe in Malerei und Computergrafik}, journal = {R{\"a}ume - Bilder - Kulturen}, editor = {Lepper, Verena and Deuflhard, Peter and Markschies, Christoph}, publisher = {Walter De Gruyter}, isbn = {978-3-11-035993-0}, pages = {33 -- 46}, year = {2015}, abstract = {Einf{\"u}hrung: Die Tiefenwirkung dreidimensionaler R{\"a}ume in einem zweidimensionalen Bild einzufangen, ist ein Faszinosum nahezu aller Kulturen der Menschheitsgeschichte. Der vorliegende Aufsatz folgt den Spuren dieses Faszinosums, vergleichend in der Malerei und der mathematisierten Computergrafik. Die Entdeckung der Zentralperspektive in der italienischen Renaissance zeigt bereits den engen Zusammenhang von Malerei und Mathematik. Auf der Suche nach Maltechniken, mit denen Raumtiefe bildnerisch dargestellt werden kann, beginnen wir in Kap. 2 mit einem chronologischen Gang durch verschiedene Epochen der europ{\"a}ischen Malerei. Hieraus abgeleitete Prinzipien, soweit sie im Rechner realisierbar scheinen, stellen wir in Kap. 3 am Beispiel moderner Methoden der mathematischen Visualisierung vor.}, language = {de} } @incollection{LameckerZachow2016, author = {Lamecker, Hans and Zachow, Stefan}, title = {Statistical Shape Modeling of Musculoskeletal Structures and Its Applications}, volume = {23}, booktitle = {Computational Radiology for Orthopaedic Interventions}, publisher = {Springer}, isbn = {978-3-319-23481-6}, doi = {10.1007/978-3-319-23482-3}, pages = {1 -- 23}, year = {2016}, abstract = {Statistical shape models (SSM) describe the shape variability contained in a given population. They are able to describe large populations of complex shapes with few degrees of freedom. This makes them a useful tool for a variety of tasks that arise in computer-aided madicine. In this chapter we are going to explain the basic methodology of SSMs and present a variety of examples, where SSMs have been successfully applied.}, language = {en} } @article{ZachowHeppt2015, author = {Zachow, Stefan and Heppt, Werner}, title = {The Facial Profile}, volume = {31}, journal = {Facial Plastic Surgery}, number = {5}, doi = {10.1055/s-0035-1566132}, pages = {419 -- 420}, year = {2015}, abstract = {Facial appearance in our societies is often associated with notions of attractiveness, juvenileness, beauty, success, and so forth. Hence, the role of facial plastic surgery is highly interrelated to a patient's desire to feature many of these positively connoted attributes, which of course, are subject of different cultural perceptions or social trends. To judge about somebody's facial appearance, appropriate quantitative measures as well as methods to obtain and compare individual facial features are required. This special issue on facial profile is intended to provide an overview on how facial characteristics are surgically managed in an interdisciplinary way based on experience, instrumentation, and modern technology to obtain an aesthetic facial appearance with harmonious facial proportions. The facial profile will be discussed within the context of facial aesthetics. Latest concepts for capturing facial morphology in high speed and impressive detail are presented for quantitative analysis of even subtle changes, aging effects, or facial expressions. In addition, the perception of facial profiles is evaluated based on eye tracking technology.}, language = {en} } @article{ZahnGrotjohannRammetal.2015, author = {Zahn, Robert and Grotjohann, Sarah and Ramm, Heiko and Zachow, Stefan and Putzier, Michael and Perka, Carsten and Tohtz, Stephan}, title = {Pelvic tilt compensates for increased acetabular anteversion}, volume = {40}, journal = {International Orthopaedics}, number = {8}, doi = {10.1007/s00264-015-2949-6}, pages = {1571 -- 1575}, year = {2015}, abstract = {Pelvic tilt determines functional orientation of the acetabulum. In this study, we investigated the interaction of pelvic tilt and functional acetabular anteversion (AA) in supine position.}, language = {en} } @misc{KuhnEngelkeFlatkenetal.2016, author = {Kuhn, Alexander and Engelke, Wito and Flatken, Markus and Hege, Hans-Christian and Hotz, Ingrid}, title = {Topology-based Analysis for Multimodal Atmospheric Data of Volcano Eruptions}, issn = {1438-0064}, doi = {10.1007/978-3-319-44684-4_2}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57043}, year = {2016}, abstract = {Many scientific applications deal with data from a multitude of different sources, e.g., measurements, imaging and simulations. Each source provides an additional perspective on the phenomenon of interest, but also comes with specific limitations, e.g. regarding accuracy, spatial and temporal availability. Effectively combining and analyzing such multimodal and partially incomplete data of limited accuracy in an integrated way is challenging. In this work, we outline an approach for an integrated analysis and visualization of the atmospheric impact of volcano eruptions. The data sets comprise observation and imaging data from satellites as well as results from numerical particle simulations. To analyze the clouds from the volcano eruption in the spatiotemporal domain we apply topological methods. Extremal structures reveal structures in the data that support clustering and comparison. We further discuss the robustness of those methods with respect to different properties of the data and different parameter setups. Finally we outline open challenges for the effective integrated visualization using topological methods.}, 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}, journal = {Proceedings of the Third International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability}, editor = {Pennec, X. and Joshi, S. and Nielsen, M.}, pages = {1 -- 14}, 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} } @inproceedings{MukhopadhyayOksuzBevilacquaetal.2015, author = {Mukhopadhyay, Anirban and Oksuz, Ilkay and Bevilacqua, Marco and Dharmakumar, Rohan and Tsaftaris, Sotirios}, title = {Data-Driven Feature Learning for Myocardial Segmentation of CP-BOLD MRI}, volume = {9126}, booktitle = {Functional Imaging and Modeling of the Heart}, publisher = {Springer}, doi = {10.1007/978-3-319-20309-6_22}, pages = {189 -- 197}, year = {2015}, abstract = {Cardiac Phase-resolved Blood Oxygen-Level-Dependent (CP- BOLD) MR is capable of diagnosing an ongoing ischemia by detecting changes in myocardial intensity patterns at rest without any contrast and stress agents. Visualizing and detecting these changes require significant post-processing, including myocardial segmentation for isolating the myocardium. But, changes in myocardial intensity pattern and myocardial shape due to the heart's motion challenge automated standard CINE MR myocardial segmentation techniques resulting in a significant drop of segmentation accuracy. We hypothesize that the main reason behind this phenomenon is the lack of discernible features. In this paper, a multi scale discriminative dictionary learning approach is proposed for supervised learning and sparse representation of the myocardium, to improve the myocardial feature selection. The technique is validated on a challenging dataset of CP-BOLD MR and standard CINE MR acquired in baseline and ischemic condition across 10 canine subjects. The proposed method significantly outperforms standard cardiac segmentation techniques, including segmentation via registration, level sets and supervised methods for myocardial segmentation.}, language = {en} } @inproceedings{MukhopadhyayOksuzBevilacquaetal.2015, author = {Mukhopadhyay, Anirban and Oksuz, Ilkay and Bevilacqua, Marco and Dharmakumar, Rohan and Tsaftaris, Sotirios}, title = {Unsupervised myocardial segmentation for cardiac MRI}, volume = {LNCS 9351}, booktitle = {Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015}, doi = {10.1007/978-3-319-24574-4_2}, pages = {12 -- 20}, year = {2015}, abstract = {Though unsupervised segmentation was a de-facto standard for cardiac MRI segmentation early on, recently cardiac MRI segmentation literature has favored fully supervised techniques such as Dictionary Learning and Atlas-based techniques. But, the benefits of unsupervised techniques e.g., no need for large amount of training data and better potential of handling variability in anatomy and image contrast, is more evident with emerging cardiac MR modalities. For example, CP-BOLD is a new MRI technique that has been shown to detect ischemia without any contrast at stress but also at rest conditions. Although CP-BOLD looks similar to standard CINE, changes in myocardial intensity patterns and shape across cardiac phases, due to the heart's motion, BOLD effect and artifacts affect the underlying mechanisms of fully supervised segmentation techniques resulting in a significant drop in segmentation accuracy. In this paper, we present a fully unsupervised technique for segmenting myocardium from the background in both standard CINE MR and CP-BOLD MR. We combine appearance with motion information (obtained via Optical Flow) in a dictionary learning framework to sparsely represent important features in a low dimensional space and separate myocardium from background accordingly. Our fully automated method learns background-only models and one class classifier provides myocardial segmentation. The advantages of the proposed technique are demonstrated on a dataset containing CP-BOLD MR and standard CINE MR image sequences acquired in baseline and ischemic condition across 10 canine subjects, where our method outperforms state-of-the-art supervised segmentation techniques in CP-BOLD MR and performs at-par for standard CINE MR.}, language = {en} } @inproceedings{OksuzMukhopadhyayBevilacquaetal.2015, author = {Oksuz, Ilkay and Mukhopadhyay, Anirban and Bevilacqua, Marco and Dharmakumar, Rohan and Tsaftaris, Sotirios}, title = {Dictionary Learning Based Image Descriptor for Myocardial Registration of CP-BOLD MR}, volume = {9350}, booktitle = {Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015}, publisher = {Springer}, doi = {10.1007/978-3-319-24571-3_25}, pages = {205 -- 213}, year = {2015}, abstract = {Cardiac Phase-resolved Blood Oxygen-Level-Dependent (CP- BOLD) MRI is a new contrast agent- and stress-free imaging technique for the assessment of myocardial ischemia at rest. The precise registration among the cardiac phases in this cine type acquisition is essential for automating the analysis of images of this technique, since it can potentially lead to better specificity of ischemia detection. However, inconsistency in myocardial intensity patterns and the changes in myocardial shape due to the heart's motion lead to low registration performance for state- of-the-art methods. This low accuracy can be explained by the lack of distinguishable features in CP-BOLD and inappropriate metric defini- tions in current intensity-based registration frameworks. In this paper, the sparse representations, which are defined by a discriminative dictionary learning approach for source and target images, are used to improve myocardial registration. This method combines appearance with Gabor and HOG features in a dictionary learning framework to sparsely represent features in a low dimensional space. The sum of squared differences of these distinctive sparse representations are used to define a similarity term in the registration framework. The proposed descriptor is validated on a challenging dataset of CP-BOLD MR and standard CINE MR acquired in baseline and ischemic condition across 10 canines.}, language = {en} } @inproceedings{SalehSahuZafaretal.2015, author = {Saleh, Salah and Sahu, Manish and Zafar, Zuhair and Berns, Karsten}, title = {A Multimodal Nonverbal Human-robot Communication System}, booktitle = {VI International Conference on Computational Bioengineering}, year = {2015}, abstract = {Socially interactive robot needs the same behaviors and capabilities of human to be accepted as a member in human society. The environment, in which this robot should operate, is the human daily life. The interaction capabilities of current robots are still limited due to complex inter-human interaction system. Humans usually use different types of verbal and nonverbal cues in their communication. Facial expression and head movement are good examples of nonverbal cues used in feedback. This paper presents a biological inspired system for Human-Robot Interaction (HRI). This system is based on the interactive model of inter-human communication proposed by Schramm. In this model, the robot and its interaction partner can be send and receive information at the same time. For example, if the robot is talking, it also perceive the feedback of the human via his/her nonverbal cues. In this work, we are focusing on recognizing the facial expression of human. The proposed facial expression recognition technique is based on machine learning. Multi SVMs have been used to recognize the six basic emotions in addition to the neutral expression. This technique uses only the depth information, acquired by Kinect, of human face.}, language = {en} } @misc{TackKobayashiGaueretal.2015, author = {Tack, Alexander and Kobayashi, Yuske and Gauer, Tobias and Schlaefer, Alexander and Werner, Ren{\´e}}, title = {Bewegungsfeldsch{\"a}tzung in artefaktbehafteten 4D-CT-Bilddaten: Vergleich von paar- und gruppenweiser Registrierung}, volume = {Supplement 1}, journal = {21st Annual Meeting of the German-Society-for-Radiation-Oncology}, edition = {191}, publisher = {Springer}, address = {Strahlentherapie und Onkologie}, doi = {10.1007/s00066-015-0847-x}, pages = {65 -- 65}, year = {2015}, abstract = {In der Strahlentherapie von Lungentumoren kann mittels Dosisakkumulation der Einfluss von Atembewegungen auf statisch geplante Dosisverteilungen abgesch{\"a}tzt werden. Grundlage sind 4D-CT-Daten des Patienten, aus denen mittels nicht-linearer Bildregistrierung eine Sequenz von Bewegungsfeldern berechnet wird. Typischerweise werden Methoden der paarweisen Bildregistrierung eingesetzt, d.h. konsekutiv zwei Atemphasen aufeinander registriert. Hierbei erfolgt i.d.R. eine physiologisch nicht plausible Anpassung der Felder an CT-Bewegungsartefakte. Gruppenweise Registrierungsans{\"a}tze ber{\"u}cksichtigen hingegen gleichzeitig s{\"a}mtliche Bilddaten des 4D-CT-Scans und erm{\"o}glichen die Integration von zeitlichen Konsistenzbetrachtungen. In diesem Beitrag wird der potentielle Vorteil der gruppen- im Vergleich zur paarweisen Registrierung in artefaktbehafteten 4D-CT-Daten untersucht.}, language = {de} } @misc{TitschackBaum2014, author = {Titschack, J{\"u}rgen and Baum, Daniel}, title = {Advanced computed tomography analyses of cold-water coral mound cores: new insights into mound formation processes}, journal = {Poster, 19th International Sedimentological Congress, Geneva, Switzerland, 2014, August 18 - 22}, year = {2014}, language = {en} } @misc{TitschackBaum2015, author = {Titschack, J{\"u}rgen and Baum, Daniel}, title = {Ambient occlusion - a powerful algorithm to segment skeletal intrapores and gastral cavities in dendrophyllid cold-water corals}, journal = {Poster, 31st IAS Meeting of Sedimentology, 2015, June 22-25, Krak{\´o}w, Poland}, year = {2015}, language = {en} } @article{KastenReininghausHotzetal.2016, author = {Kasten, Jens and Reininghaus, Jan and Hotz, Ingrid and Hege, Hans-Christian and Noack, Bernd and Daviller, Guillaume and Morzyński, Marek}, title = {Acceleration feature points of unsteady shear flows}, volume = {68}, journal = {Archives of Mechanics}, number = {1}, pages = {55 -- 80}, year = {2016}, abstract = {A framework is proposed for extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance. The minima of the acceleration magnitude, i.e. a superset of the acceleration zeros, are extracted and discriminated into vortices and saddle points --- based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These features are tracked in time with a robust algorithm for tracking features. Thus a space-time hierarchy of the minima is built and vortex merging events are detected. The acceleration feature extraction strategy is applied to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of pressure field and minima of λ2.}, language = {en} } @misc{KastenReininghausHotzetal.2015, author = {Kasten, Jens and Reininghaus, Jan and Hotz, Ingrid and Hege, Hans-Christian and Noack, Bernd and Daviller, Guillaume and Morzyński, Marek}, title = {Acceleration feature points of unsteady shear flows}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58397}, year = {2015}, abstract = {A framework is proposed for extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance. The minima of the acceleration magnitude, i.e. a superset of the acceleration zeros, are extracted and discriminated into vortices and saddle points --- based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These features are tracked in time with a robust algorithm for tracking features. Thus a space-time hierarchy of the minima is built and vortex merging events are detected. The acceleration feature extraction strategy is applied to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of pressure field and minima of λ2.}, language = {en} } @misc{OsterlandBennProhaskaetal.2015, author = {Osterland, Marc and Benn, Andreas and Prohaska, Steffen and Sch{\"u}tte, Christof}, title = {Single Cell Tracking in Phase-Contrast Microscopy}, journal = {EMBL Symposium 2015 - Seeing is Believing - Imaging the Processes of Life}, year = {2015}, abstract = {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.}, language = {en} } @masterthesis{Schotte2015, type = {Bachelor Thesis}, author = {Schotte, Merlind}, title = {Automatische Dickenbestimmung der mineralisierten Schicht in Skelettelementen von Knorpelfischen anhand von CT- Bilddaten}, year = {2015}, abstract = {Diese Bachelorarbeit beschäftigt sich mit der Entwicklung eines allgemeinen Verfahrens, welches die Dicke der mineralisierten Schicht von Haikieferelementen automatisch bestimmt. Dabei soll das Verfahren die Dicke näherungsweise im zweidimensionalen (2D) Raum sowie im dreidimensionalen (3D) Raum anhand von Computertomografie-Scans berechnen (im Folgenden als zweidimensionaler bzw. dreidimensionaler Fall bezeichnet). Es werden drei mögliche Verfahren eingef{\"u}hrt und im Anschluss auf ihre Verwendbarkeit analysiert. F{\"u}r die Implementierung zur Dickenbestimmung wird der Kern der Rayburst Sampling Methode verwendet und im Weiteren f{\"u}r den 2D-Raum durch kleinere Optimierungen verbessert. Die Überpr{\"u}fung der Genauigkeit des f{\"u}r den zweidimensionalen Fall entwickelten Programms erfolgt manuell. F{\"u}r einen Vergleich im 3D-Raum wird ein zweites Verfahren programmiert, das auf der Berechnung der Isoflächen basiert. Diese Arbeit ist in den Bereich der angewandten Mathematik mit dem Schwerpunkt Informatik einzuordnen. Das entwickelte Programm wird im Anschluss Anwendung im Bereich der Biologie am Max-Planck-Institut f{\"u}r Grenzflächen- und Kolloidforschung Potsdam-Golm finden.}, language = {de} } @phdthesis{Weber2015, author = {Weber, Britta}, title = {Reconstruction of Microtubule Centerlines from Electron Tomograms}, year = {2015}, abstract = {The organization of the mitotic spindle, a structure that separates the chromosomes during cell division, is an active research topic in molecular cell biology. It is composed of microtubules, elongated tubular macromolecules with a diameter of 25 nm. The only volumetric imaging technique that is available to a wide community and provides the required resolution to capture details about microtubules is electron tomography. However, the automatic detection of microtubules in electron tomograms is a difficult task due to the low contrast of the data. Furthermore, thick samples have to be cut into 300 nm thin sections before electron tomography can be applied. Software for automatically segmentation and stitching of the microtubules are not available and therefore these tasks have to be performed manually. Unfortunately, manual segmentation is time consuming for large samples and manual stitching of the tomograms is often infeasible due to the lack of prominent features for registration. Conclusions drawn from electron tomographic data is currently mostly based on either small samples containing few microtubules or single sections of complex structures. Consequently, simple properties, such as the length of microtubules in the spindle or their number, are still unknown for most model organisms. In this thesis, we present methods for 1) an automatic segmentation of microtubule centerlines in electron tomograms, and 2) an automatic stitching of the lines extracted from serial sections. For the centerline segmentation, we use 3D template matching and exploit knowledge about shape of microtubules and microscopy artifacts to design the templates. For the registration of the lines, we present a way to model the orientation of lines as a mixture of Fisher-Mises distributions where we estimate transformation parameters with the expectation maximization algorithm. The final line matching problem is formulated in terms of a probabilistic graphical model. To find the correct correspondences of line ends, we use belief propagation. We handle the poor convergence properties of this algorithm by detecting ambiguous and conflicting assignments of lines automatically. An expert can then influence the final output of the algorithm by solving conflicts manually. A detailed error analysis on true biological data and assessment of the reliability of the results is the prerequisite for analyzing the resulting line representations of the microtubules. To this end, the developed workflow for segmenting and stitching of microtubule centerlines is evaluated on plasticembedded samples of C. elegans early embryos and of spindles from X. laevis egg extracts. Our results suggest that the output of the presented algorithms together with little manual correction is of sufficient quality to allow a detailed analysis of dense microtubule networks. Finally, we exemplarily show results for the centrosome of a C. elegans mitotic spindle.}, language = {en} } @phdthesis{Poethkow2015, author = {P{\"o}thkow, Kai}, title = {Modeling, Quantification and Visualization of Probabilistic Features in Fields with Uncertainties}, year = {2015}, abstract = {Eine grundlegende Eigenschaft von naturwissenschaftlichen Daten ist, dass der wahre Wert einer Gr{\"o}ße nicht beliebig genau bestimmbar ist. Es ist lediglich m{\"o}glich, ihn durch Intervalle einzugrenzen oder die Unsicherheit durch eine Wahrscheinlichkeitsverteilung zu charakterisieren. Dies gilt f{\"u}r alle reellwertigen Daten, sowohl f{\"u}r Mess-, als auch f{\"u}r Simulationsergebnisse. Beispiele sind Messungen von grundlegenden physikalischen Gr{\"o}ßen wie Geschwindigkeit oder auch langfristige Temperaturvorhersagen, die durch Klimamodelle berechnet werden. Die Unsicherheit von Ergebnissen ist eine wichtige Information, die in Natur- und Ingenieurwissenschaften h{\"a}ufig durch Konfidenzintervalle in 1D-Plots und Tabellen angezeigt wird. Im Gegensatz dazu ist es bisher bei der Visualisierung von 2D- und 3D-Daten mithilfe von Standardmethoden meist unm{\"o}glich, die Datenunsicherheit zu repr{\"a}sentieren. Diese Arbeit stellt wahrscheinlichkeitstheoretisch fundierte Methoden vor, die die Analyse und Visualisierung von Skalar-, Vektor- und Tensorfeldern mit Unsicherheiten erm{\"o}glichen. Der Fokus liegt dabei auf der Extraktion von raumzeitlichen geometrischen und topologischen Merkmalen aus den Feldern (z.B. Isokonturen und kritische Punkte). Wir nutzen parametrische und nichtparametrische Zufallsfelder, um Variabilit{\"a}t und r{\"a}umliche Korrelation mathematisch zu modellieren. Die Wahrscheinlichkeitsverteilungen werden aus Ensemble-Datens{\"a}tzen gesch{\"a}tzt, die mehrere Simulationsergebnisse (z.B. basierend auf variierenden Simulationsparametern) zusammenfassen. Wir untersuchen die Konditionszahlen von Merkmalsextraktionsmethoden, um die Sensitivit{\"a}t, d.h. die Verst{\"a}rkung oder Abschw{\"a}chung der Unsicherheit der Ergebnisse relativ zu Unsicherheiten in den Eingangsdaten abzusch{\"a}tzen. Wir stellen einen allgemeiner Ansatz f{\"u}r die probabilistische Merkmalsextraktion vor, der die Basis f{\"u}r die Berechnung r{\"a}umlicher Wahrscheinlichkeitsverteilungen von verschiedenen Merkmalen in Skalar-, Vektor- und Tensorfeldern bildet. In diesem Framework werden Wahrscheinlichkeiten f{\"u}r die Existenz von Merkmalen aus lokalen Randverteilungen und formalen Merkmalsdefinitionen berechnet. Numerisch k{\"o}nnen die Wahrscheinlichkeiten durch Monte-Carlo­-Integration bestimmt werden. Um den hohen Rechenaufwand dieses Ansatzes zu vermeiden, schlagen wir schnelle Berechnungsmethoden vor, wobei Merkmalswahrscheinlichkeiten n{\"a}herungsweise mit Hilfe von Surrogatfunktionen bzw. Lookup-Tabellen gesch{\"a}tzt werden. Die vorgeschlagenen Methoden werden anhand von Daten aus Klima- und Biofluidmechaniksimulationen sowie aus der medizinischen Bildgebung qualitativ und quantitativ evaluiert.}, language = {en} } @article{ZahnGrotjohannRammetal.2016, author = {Zahn, Robert and Grotjohann, Sarah and Ramm, Heiko and Zachow, Stefan and Pumberger, Matthias and Putzier, Michael and Perka, Carsten and Tohtz, Stephan}, title = {Influence of pelvic tilt on functional acetabular orientation}, volume = {25}, journal = {Technology and Health Care}, number = {3}, publisher = {IOS Press}, doi = {10.3233/THC-161281}, pages = {557 -- 565}, year = {2016}, language = {en} } @article{LemanisKornZachowetal.2016, author = {Lemanis, Robert and Korn, Dieter and Zachow, Stefan and Rybacki, Erik and Hoffmann, Ren{\´e}}, title = {The Evolution and Development of Cephalopod Chambers and Their Shape}, volume = {11}, journal = {PLOS ONE}, number = {3}, doi = {10.1371/journal.pone.0151404}, year = {2016}, abstract = {The Ammonoidea is a group of extinct cephalopods ideal to study evolution through deep time. The evolution of the planispiral shell and complexly folded septa in ammonoids has been thought to have increased the functional surface area of the chambers permitting enhanced metabolic functions such as: chamber emptying, rate of mineralization and increased growth rates throughout ontogeny. Using nano-computed tomography and synchrotron radiation based micro-computed tomography, we present the first study of ontogenetic changes in surface area to volume ratios in the phragmocone chambers of several phylogenetically distant ammonoids and extant cephalopods. Contrary to the initial hypothesis, ammonoids do not possess a persistently high relative chamber surface area. Instead, the functional surface area of the chambers is higher in earliest ontogeny when compared to Spirula spirula. The higher the functional surface area the quicker the potential emptying rate of the chamber; quicker chamber emptying rates would theoretically permit faster growth. This is supported by the persistently higher siphuncular surface area to chamber volume ratio we collected for the ammonite Amauroceras sp. compared to either S. spirula or nautilids. We demonstrate that the curvature of the surface of the chamber increases with greater septal complexity increasing the potential refilling rates. We further show a unique relationship between ammonoid chamber shape and size that does not exist in S. spirula or nautilids. This view of chamber function also has implications for the evolution of the internal shell of coleoids, relating this event to the decoupling of soft-body growth and shell growth.}, language = {en} } @misc{KnoetelSeidelWeaveretal.2015, author = {Kn{\"o}tel, David and Seidel, Ronald and Weaver, James C. and Baum, Daniel and Dean, Mason N.}, title = {Segmentation of the Tessellated Mineralized Endoskeleton of Sharks and Rays}, journal = {Poster, Tomography for Scientific Advancement symposium (ToScA), Manchester, UK, September 3 - 4, 2015}, year = {2015}, abstract = {The cartilaginous endoskeletons of sharks and rays are covered by tiles of mineralized cartilage called tesserae that enclose areas of unmineralized cartilage. These tesselated layers are vital to the growth as well as the material properties of the skeleton, providing both flexibility and strength. An understanding of the principles behind the tiling of the mineralized layer requires a quantitative analysis of shark and ray skeletal tessellation. However, since a single skeletal element comprises several thousand tesserae, manual segmentation is infeasible. We developed an automated segmentation pipeline that, working from micro-CT data, allows quantification of all tesserae in a skeletal element in less than an hour. Our segmentation algorithm relies on aspects we have learned of general tesseral morphology. In micro-CT scans, tesserae usually appear as round or star-shaped plate-like tiles, wider than deep and connected by mineralized intertesseral joints. Based on these observations, we exploit the distance map of the mineralized layer to separate individual tiles using a hierarchical watershed algorithm. Utilizing a two-dimensional distance map that measures the distance in the plane of the mineralized layer only greatly improves the segmentation. We developed post-processing techniques to quickly correct segmentation errors in regions where tesseral shape differs from the assumed shape. Evaluation of our results is done qualitatively by visual comparison with raw datasets, and quantitatively by comparison to manual segmentations. Furthermore, we generate two-dimensional abstractions of the tiling network based on the neighborhood, allowing representation of complex, biological forms as simpler geometries. We apply our newly developed techniques to the analysis of the left and right hyomandibulae of four ages of stingray enabling the first quantitative analyses of the tesseral tiling structure, while clarifying how these patterns develop across ontogeny.}, language = {en} } @misc{KnoetelSeidelHosnyetal.2016, author = {Kn{\"o}tel, David and Seidel, Ronald and Hosny, Ahmed and Zaslansky, Paul and Weaver, James C. and Baum, Daniel and Dean, Mason N.}, title = {Understanding the Tiling Rules of the Tessellated Mineralized Endoskeleton of Sharks and Rays}, journal = {Poster, Euro Bio-inspired Materials 2016, Potsdam, Germany, February 22 - 25, 2016}, year = {2016}, abstract = {The endoskeletons of sharks and rays are composed of an unmineralized cartilaginous core, covered in an outer layer of mineralized tiles called tesserae. The tessellated layer is vital to the growth as well as the material properties of the skeletal element, providing both flexibility and strength. However, characterizing the relationship between tesseral size and shape, and skeletal growth and mechanics is challenging because tesserae are small (a few hundred micrometers wide), anchored to the surrounding tissue in complex three-dimensional ways, and occur in huge numbers. Using a custom-made semi-automatic segmentation algorithm, we present the first quantitative and three-dimensional description of tesserae in micro-CT scans of whole skeletal elements. Our segmentation algorithm relies on aspects we have learned of general tesseral morphology. We exploit the distance map of the mineralized layer to separate individual tiles using a hierarchical watershed algorithm. Additionally, we have developed post-processing techniques to quickly correct segmentation errors. Our data reveals that the tessellation is not regular, with tesserae showing a great range of shapes, sizes and number of neighbors. This is partly region-dependent: for example, thick, columnar tesserae are arranged in series along convex edges with small radius of curvature (RoC), whereas more brick-or disc-shaped tesserae are found in planar areas. We apply our newly developed techniques on the left and right hyomandibula (skeletal elements supporting the jaws) from four different ages of a stingray species, to clarify how tiling patterns develop across ontogeny and differ within and between individuals. We evaluate the functional consequences of tesseral morphologies using finite element analysis and 3d-printing, for a better understanding of shark skeletal mechanics, but also to extract fundamental engineering design principles of tiling arrangements on load-bearing three-dimensional objects.}, language = {en} } @article{KnightTullyKaplanetal.2016, author = {Knight, James C and Tully, Philip J and Kaplan, Bernhard and Lansner, Anders and Furber, Steve}, title = {Large-scale simulations of plastic neural networks on neuromorphic hardware}, volume = {10:37}, journal = {Frontiers in Neuroanatomy}, doi = {10.3389/fnana.2016.00037}, year = {2016}, abstract = {SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Rather than using bespoke analog or digital hardware, the basic computational unit of a SpiNNaker system is a general-purpose ARM processor, allowing it to be programmed to simulate a wide variety of neuron and synapse models. This flexibility is particularly valuable in the study of biological plasticity phenomena. A recently proposed learning rule based on the Bayesian Confidence Propagation Neural Network (BCPNN) paradigm offers a generic framework for modeling the interaction of different plasticity mechanisms using spiking neurons. However, it can be computationally expensive to simulate large networks with BCPNN learning since it requires multiple state variables for each synapse, each of which needs to be updated every simulation time-step. We discuss the trade-offs in efficiency and accuracy involved in developing an event-based BCPNN implementation for SpiNNaker based on an analytical solution to the BCPNN equations, and detail the steps taken to fit this within the limited computational and memory resources of the SpiNNaker architecture. We demonstrate this learning rule by learning temporal sequences of neural activity within a recurrent attractor network which we simulate at scales of up to 2.0 × 10^4 neurons and 5.1 × 10^7 plastic synapses: the largest plastic neural network ever to be simulated on neuromorphic hardware. We also run a comparable simulation on a Cray XC-30 supercomputer system and find that, if it is to match the run-time of our SpiNNaker simulation, the super computer system uses approximately 45× more power. This suggests that cheaper, more power efficient neuromorphic systems are becoming useful discovery tools in the study of plasticity in large-scale brain models.}, language = {en} } @misc{SeidelKnoetelBaumetal.2014, author = {Seidel, Ronald and Kn{\"o}tel, David and Baum, Daniel and Weaver, James C. and Dean, Mason N.}, title = {Material and structural characterization of mineralized elasmobranch cartilage - lessons in repeated tiling patterns in mechanically loaded 3D objects}, journal = {Poster, Tomography for Scientific Advancement symposium (ToScA), London, UK, September 1 - 3, 2014}, year = {2014}, abstract = {Biological tissues achieve a wide range of properties and function, however with limited components. The organization of these constituent parts is a decisive factor in the impressive properties of biological materials, with tissues often exhibiting complex arrangements of hard and soft materials. The "tessellated" cartilage of the endoskeleton of sharks and rays, for example, is a natural composite of mineralized polygonal tiles (tesserae), collagen fiber bundles, and unmineralized cartilage, resulting in a material that is both flexible and strong, with optimal stiffness. The properties of the materials and the tiling geometry are vital to the growth and mechanics of the system, but had not been investigated due to the technical challenges involved. We use high-resolution materials characterization techniques (qBEI, µCT) to show that tesserae exhibit great variability in mineral density, supporting theories of accretive growth mechanisms. We present a developmental series of tesserae and outline the development of unique structural features that appear to function in load bearing and energy dissipation, with some structural features far exceeding cortical bone's mineral content and tissue stiffness. To examine interactions among tesserae, we developed an advanced tiling-recognition-algorithm to semi-automatically detect and isolate individual tiles in microCT scans of tesseral mats. The method allows quantification of shape variation across a wide area, allowing localization of regions of high/low reinforcement or flexibility in the skeleton. The combination of our material characterization and visualization techniques allows the first quantitative 3d description of anatomy and material properties of tesserae and the organization of tesseral networks in elasmobranch mineralized cartilage, providing insight into form-function relationships of the repeating tiled pattern. We aim to combine detailed knowledge of intra-tesseral morphology and mineralization to model the relationships of tesseral shapes and skeletal surface curvature, to understand fundamental tiling laws important for complex, mechanically loaded 3d objects.}, language = {en} } @inproceedings{JacomeEggelerPoethkowetal.2015, author = {J{\´a}come, Leonardo Agudo and Eggeler, Gunter and P{\"o}thkow, Kai and Paetsch, Olaf and Hege, Hans-Christian}, title = {Three-Dimensional Characterization of Superdislocation Interactions in the High Temperature and Low Stress Creep Regime of Ni-Base Superalloy Single Crystals}, booktitle = {Proceedings of CREEP 2015 - 13th International Conference on Creep and Fracture of Engineering Materials and Structures, May 31 - June 4, 2015, Toulouse, France}, pages = {16 -- 17}, year = {2015}, abstract = {Monocrystaline Ni-base superalloys are the material of choice for first row blades in jet engine gas turbines. Using a novel visualization tool for 3D reconstruction and visualization of dislocation line segments from stereo-pairs of scanning transmission electron microscopies, the superdislocation substructures in Ni-base superalloy LEK 94 (crept to ε = 26\%) are characterized. Probable scenarios are discussed, how these dislocation substructures form.}, language = {en} } @misc{BojarovskiHegeLieetal.2015, author = {Bojarovski, Stefan and Hege, Hans-Christian and Lie, Han Cheng and Weber, Marcus}, title = {Topological analysis and visualization of scalar functions characterizing conformational transitions of molecules on multiple time-scales}, journal = {Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany}, year = {2015}, abstract = {Molecular processes such as protein folding or ligand-receptor-binding can be understood by analyzing the free energy landscape. Those processes are often metastable, i.e. the molecular systems remain in basins around local minima of the free energy landscape, and in rare cases undergo gauche transitions between metastable states by passing saddle-points of this landscape. By discretizing the configuration space, this can be modeled as a discrete Markov process. One way to compute the transition rates between conformations of a molecular system is by utilizing Transition Path Theory and the concept of committor functions. A fundamental problem from the computational point of view is that many time-scales are involved, ranging from 10^(-14) sec for the fastest motion to 10^(-6) sec or more for conformation changes that cause biological effects. The goal of our work is to provide a better understanding of such transitions in configuration space on various time-scales by analyzing characteristic scalar functions topologically and geometrically. We are developing suitable visualization and interaction techniques to support our analysis. For example, we are analyzing a transition rate indicator function by computing and visualizing its Reeb graph together with the sets of molecular states corresponding to maxima of the transition rate indicator function. A particular challenge is the high dimensionality of the domain which does not allow for a straightforward visualization of the function. The computational topology approach to the analysis of the transition rate indicator functions for a molecular system allows to explore different time scales of the system by utilizing coarser or finer topological partitioning of the function. A specific goal is the development of tools for analyzing the hierarchy of these partitionings. This approach tackles the analysis of a complex and sparse dataset from a different angle than the well-known spectral analysis of Markov State Models.}, language = {en} } @article{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}, volume = {35}, journal = {Computer Graphics Forum}, number = {2}, doi = {10.1111/cgf.12832}, 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 Rn 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} } @article{SahuMoermanMewesetal.2016, author = {Sahu, Manish and Moerman, Daniil and Mewes, Philip and Mountney, Peter and Rose, Georg}, title = {Instrument State Recognition and Tracking for Effective Control of Robotized Laparoscopic Systems}, volume = {5}, journal = {International Journal of Mechanical Engineering and Robotics Research}, number = {1}, doi = {10.18178/ijmerr.5.1.33-38}, pages = {33 -- 38}, year = {2016}, abstract = {Surgical robots are an important component for delivering advanced paradigm shifting technology such as image guided surgery and navigation. However, for robotic systems to be readily adopted into the operating room they must be easy and convenient to control and facilitate a smooth surgical workflow. In minimally invasive surgery, the laparoscope may be held by a robot but controlling and moving the laparoscope remains challenging. It is disruptive to the workflow for the surgeon to put down the tools to move the robot in particular for solo surgery approaches. This paper proposes a novel approach for naturally controlling the robot mounted laparoscope's position by detecting a surgical grasping tool and recognizing if its state is open or close. This approach does not require markers or fiducials and uses a machine learning framework for tool and state recognition which exploits naturally occurring visual cues. Furthermore a virtual user interface on the laparoscopic image is proposed that uses the surgical tool as a pointing device to overcome common problems in depth perception. Instrument detection and state recognition are evaluated on in-vivo and ex-vivo porcine datasets. To demonstrate the practical surgical application and real time performance the system is validated in a simulated surgical environment.}, language = {en} } @inproceedings{TackKobayashiGaueretal.2015, author = {Tack, Alexander and Kobayashi, Yuske and Gauer, Tobias and Schlaefer, Alexander and Werner, Ren{\´e}}, title = {Groupwise Registration for Robust Motion Field Estimation in Artifact-Affected 4D CT Images}, booktitle = {ICART: Imaging and Computer Assistance in Radiation Therapy: A workshop held on Friday 9th October as part of MICCAI 2015 in Munich, Germany. MICCAI workshop. 2015.}, pages = {18 -- 25}, year = {2015}, abstract = {Precise voxel trajectory estimation in 4D CT images is a prerequisite for reliable dose accumulation during 4D treatment planning. 4D CT image data is, however, often affected by motion artifacts and applying standard pairwise registration to such data sets bears the risk of aligning anatomical structures to artifacts - with physiologically unrealistic trajectories being the consequence. In this work, the potential of a novel non-linear hybrid intensity- and feature-based groupwise registration method for robust motion field estimation in artifact-affected 4D CT image data is investigated. The overall registration performance is evaluated on the DIR-lab datasets; Its robustness if applied to artifact-affected data sets is analyzed using clinically acquired data sets with and without artifacts. The proposed registration approach achieves an accuracy comparable to the state-of-the-art (subvoxel accuracy), but smoother voxel trajectories compared to pairwise registration. Even more important: it maintained accuracy and trajectory smoothness in the presence of image artifacts - in contrast to standard pairwise registration, which yields higher landmark-based registration errors and a loss of trajectory smoothness when applied to artifact-affected data sets.}, language = {en} } @article{FournierPalidworShcherbininetal.2013, author = {Fournier, David and Palidwor, Gareth A. and Shcherbinin, Sergey and Szengel, Angelika and Schaefer, Martin H. and Perez-Iratxeta, Carol and Andrade-Navarro, Miguel A.}, title = {Functional and Genomic Analyses of Alpha-Solenoid Proteins}, journal = {PLoS ONE Journal}, doi = {10.1371/journal.pone.0079894}, year = {2013}, abstract = {Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/.}, language = {en} } @misc{Grewe2015, author = {Grewe, Carl Martin}, title = {3D Digital Morphology of Human Faces}, journal = {Anthropologie der Wahrnehmung. Marsilius-Sommerakademie Heidelberg, 14.-20. September}, year = {2015}, language = {en} } @misc{Sahu2016, type = {Master Thesis}, author = {Sahu, Manish}, title = {Instrument Gesture Recognition and Tracking for Effective Control of Laparoscopic Tracking and Guidance Device}, year = {2016}, language = {en} } @misc{MukhopadhyayKumarBhandarkar2016, author = {Mukhopadhyay, Anirban and Kumar, Arun and Bhandarkar, Suchendra}, title = {Joint Geometric Graph Embedding for Partial Shape Matching in Images}, journal = {IEEE Winter Conference on Applications of Computer Vision}, edition = {IEEE Winter Conference on Applications of Computer Vision (WACV)}, publisher = {IEEE}, pages = {1 -- 9}, year = {2016}, abstract = {A novel multi-criteria optimization framework for matching of partially visible shapes in multiple images using joint geometric graph embedding is proposed. The proposed framework achieves matching of partial shapes in images that exhibit extreme variations in scale, orientation, viewpoint and illumination and also instances of occlusion; conditions which render impractical the use of global contour-based descriptors or local pixel-level features for shape matching. The proposed technique is based on optimization of the embedding distances of geometric features obtained from the eigenspectrum of the joint image graph, coupled with regularization over values of the mean pixel intensity or histogram of oriented gradients. It is shown to obtain successfully the correspondences denoting partial shape similarities as well as correspondences between feature points in the images. A new benchmark dataset is proposed which contains disparate image pairs with extremely challenging variations in viewing conditions when compared to an existing dataset [18]. The proposed technique is shown to significantly outperform several state-of-the-art partial shape matching techniques on both datasets.}, language = {en} } @article{HermannPohlTremblayetal.2016, author = {Hermann, Gunter and Pohl, Vincent and Tremblay, Jean Christophe and Paulus, Beate and Hege, Hans-Christian and Schild, Axel}, title = {ORBKIT - A modular Python toolbox for cross-platform post-processing of quantum chemical wavefunction data}, volume = {37}, journal = {Journal of Computational Chemistry}, number = {16}, doi = {10.1002/jcc.24358}, pages = {1511 -- 1520}, year = {2016}, abstract = {ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wave function, as well as several grid-independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by user-written modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT offers routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is open-source under GNU-LGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations.}, language = {en} } @article{GoubergritsOsmanMevertetal.2016, author = {Goubergrits, Leonid and Osman, Jan and Mevert, Ricardo and Kertzscher, Ulrich and P{\"o}thkow, Kai and Hege, Hans-Christian}, title = {Turbulence in blood damage modeling}, volume = {39}, journal = {The International Journal of Artificial Organs}, number = {4}, doi = {10.5301/ijao.5000476}, pages = {147 -- 210}, year = {2016}, abstract = {Purpose: To account for the impact of turbulence in blood damage modeling, a novel approach based on the generation of instantaneous flow fields from RANS simulations is proposed. Methods: Turbulent flow in a bileaflet mechanical heart valve was simulated using RANS-based (SST k-ω) flow solver using FLUENT 14.5. The calculated Reynolds shear stress (RSS) field is transformed into a set of divergence-free random vector fields representing turbulent velocity fluctuations using procedural noise functions. To consider the random path of the blood cells, instantaneous flow fields were computed for each time step by summation of RSS-based divergence-free random and mean velocity fields. Using those instantaneous flow fields, instantaneous pathlines and corresponding point-wise instantaneous shear stresses were calculated. For a comparison, averaged pathlines based on mean velocity field and respective viscous shear stresses together with RSS values were calculated. Finally, the blood damage index (hemolysis) was integrated along the averaged and instantaneous pathlines using a power law approach and then compared. Results: Using RSS in blood damage modeling without a correction factor overestimates damaging stress and thus the blood damage (hemolysis). Blood damage histograms based on both presented approaches differ. Conclusions: A novel approach to calculate blood damage without using RSS as a damaging parameter is established. The results of our numerical experiment support the hypothesis that the use of RSS as a damaging parameter should be avoided.}, language = {en} } @article{WilliePapPerkaetal.2015, author = {Willie, Bettina M. and Pap, Thomas and Perka, Carsten and Schmidt, Carsten Oliver and Eckstein, Felix and Arampatzis, Adamantios and Hege, Hans-Christian and Madry, Henning and Vortkamp, Andrea and Duda, Georg}, title = {OVERLOAD - Rolle der Gelenk{\"u}berlastung in der prim{\"a}ren Arthrose - Die Krankheitsprogression verstehen und vermeiden}, volume = {74}, journal = {Zeitschrift f{\"u}r Rheumatologie}, doi = {10.1007/s00393-014-1561-2}, pages = {618 -- 621}, year = {2015}, abstract = {Intakte Gelenke sind eine Voraussetzung f{\"u}r das Funktionieren des Skeletts und die Mobilit{\"a}t im Lebensalltag. Ein gesunder Bewegungsapparat ist die Grundlage f{\"u}r die Funktionsf{\"a}higkeit des Herz-Kreislauf-Systems wie auch der Immunabwehr. Bewegungs- und Physiotherapie sowie verschiedene Formen der Patientenaktivit{\"a}t stellen essenzielle klinische Ans{\"a}tze in der Behandlung von neurodegenerativen Erkrankungen, Schlaganfall, Diabetes und Krebs dar. Kommt es zu degenerativen Ver{\"a}nderungen von Gelenken, bedeutet dies eine wesentliche Beeintr{\"a}chtigung der Mobilit{\"a}t. N{\"a}chtliche Schmerzen und Schlafst{\"o}rungen treten in fortgeschrittenen Stadien auf und sind besonders belastend. Arthrose wird auch als degenerative Gelenkerkrankung bezeichnet. Sie geht mit Ver{\"a}nderungen in der Struktur und Zusammensetzung des Gelenkknorpels wie auch des verkalkten Knorpels, der subchondralen Kortikalis, der subchondralen Spongiosa, des Meniskus, der Gelenkkapsel und der Synovialis einher, was schließlich zur Degeneration dieser Gewebe f{\"u}hrt, aus denen sich die Synovialgelenke zusammensetzen.}, language = {de} } @misc{SieberKuhnHegeetal.2015, author = {Sieber, Moritz and Kuhn, Alexander and Hege, Hans-Christian and Paschereit, C. Oliver and Oberleithner, Kilian}, title = {A Graphical Representation of the Spectral Proper Orthogonal Decomposition}, journal = {68th Annual Meeting of the APS Division of Fluid Dynamics, Gallery of Fluid Motion, Nov 22-24, 2015, Boston, MA, USA.}, year = {2015}, abstract = {We consider the spectral proper orthogonal decomposition (SPOD) for experimental data of a turbulent swirling jet. This newly introduced method combines the advantages of spectral methods, such as Fourier decomposition or dynamic mode decomposition, with the energy-ranked proper orthogonal decomposition (POD). This poster visualizes how the modal energy spectrum transitions from the spectral purity of Fourier space to the sparsity of POD space. The transition is achieved by changing a single parameter - the width of the SPOD filter. Each dot in the 3D space corresponds to an SPOD mode pair, where the size and color indicates its spectral coherence. What we notice is that neither the Fourier nor the POD spectrum achieves a clear separation of the dynamic phenomena. Scanning through the graph from the front plane (Fourier) to the back plane (POD), we observe how three highly coherent SPOD modes emerge from the dispersed Fourier spectrum and later branch out into numerous POD modes. The spatial properties of these three individual SPOD modes are displayed in the back of the graph using line integral convolution colored by vorticity. The first two modes correspond to single-helical global instabilities that are well known for these flows. Their coexistence, however, has not been observed until now. The third mode is of double- helical shape and has not been observed so far. For this considered data set and many others, the SPOD is superior in identification of coherent structures in turbulent flows. Hopefully, it gives access to new fluid dynamic phenomena and enriches the available methods.}, language = {en} } @inproceedings{PaetschBaumProhaskaetal.2015, author = {Paetsch, Olaf and Baum, Daniel and Prohaska, Steffen and Ehrig, Karsten and Meinel, Dietmar and Ebell, Gino}, title = {3D Corrosion Detection in Time-dependent CT Images of Concrete}, booktitle = {DIR-2015 Proceedings}, year = {2015}, abstract = {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.}, language = {en} } @misc{KnoetelSeidelProhaskaetal.2017, author = {Kn{\"o}tel, David and Seidel, Ronald and Prohaska, Steffen and Dean, Mason N. and Baum, Daniel}, title = {Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65785}, year = {2017}, abstract = {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.}, language = {en} } @article{KnoetelSeidelProhaskaetal.2017, author = {Kn{\"o}tel, David and Seidel, Ronald and Prohaska, Steffen and Dean, Mason N. and Baum, Daniel}, title = {Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage}, journal = {PLOS ONE}, doi = {10.1371/journal.pone.0188018}, year = {2017}, abstract = {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.}, language = {en} } @misc{JoachimskyAmbellanZachow2017, author = {Joachimsky, Robert and Ambellan, Felix and Zachow, Stefan}, title = {Computerassistierte Auswahl und Platzierung von interpositionalen Spacern zur Behandlung fr{\"u}her Gonarthrose}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66064}, year = {2017}, abstract = {Degenerative Gelenkerkrankungen, wie die Osteoarthrose, sind ein h{\"a}ufiges Krankheitsbild unter {\"a}lteren Erwachsenen. Hierbei verringert sich u.a. der Gelenkspalt aufgrund degenerierten Knorpels oder gesch{\"a}digter Menisci. Ein in den Gelenkspalt eingebrachter interpositionaler Spacer soll die mit der Osteoarthrose einhergehende verringerte Gelenkkontaktfl{\"a}che erh{\"o}hen und so der teilweise oder vollst{\"a}ndige Gelenkersatz hinausgez{\"o}gert oder vermieden werden. In dieser Arbeit pr{\"a}sentieren wir eine Planungssoftware f{\"u}r die Auswahl und Positionierung eines interpositionalen Spacers am Patientenmodell. Auf einer MRT-basierten Bildsegmentierung aufbauend erfolgt eine geometrische Rekonstruktion der 3D-Anatomie des Kniegelenks. Anhand dieser wird der Gelenkspalt bestimmt, sowie ein Spacer ausgew{\"a}hlt und algorithmisch vorpositioniert. Die Positionierung des Spacers ist durch den Benutzer jederzeit interaktiv anpassbar. F{\"u}r jede Positionierung eines Spacers wird ein Fitness-Wert zur Knieanatomie des jeweiligen Patienten berechnet und den Nutzern R{\"u}ckmeldung hinsichtlich Passgenauigkeit gegeben. Die Software unterst{\"u}tzt somit als Entscheidungshilfe die behandelnden {\"A}rzte bei der patientenspezifischen Spacerauswahl.}, language = {de} } @misc{leRoux2017, type = {Master Thesis}, author = {le Roux, Gabriel}, title = {Development and Evaluation of Algorithms for 3D Facial Motion Estimation from Stereo Videos}, pages = {52}, year = {2017}, language = {en} } @misc{Zaenker2017, type = {Master Thesis}, author = {Z{\"a}nker, Martin}, title = {Estimating Human Face Reflectance from Single-Shot Multiview Data}, year = {2017}, language = {en} } @misc{KramerNoackBaumetal.2017, author = {Kramer, Tobias and Noack, Matthias and Baum, Daniel and Hege, Hans-Christian and Heller, Eric J.}, title = {Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66338}, year = {2017}, abstract = {Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term obser- vations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial dis- tribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending.}, language = {en} } @phdthesis{Zachow2005, author = {Zachow, Stefan}, title = {Computergest{\"u}tzte 3D Osteotomieplanung in der Mund-Kiefer-Gesichtschirurgie unter Ber{\"u}cksichtigung der r{\"a}umlichen Weichgewebeanordnung}, isbn = {3899631986}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10432}, year = {2005}, abstract = {In der Arbeit wird die computergest{\"u}tzte Planung von chirurgisch gesetzten Knochenfrakturen bzw. Knochenschnitten (sogenannten Osteotomien) an dreidimensionalen, computergrafischen Sch{\"a}delmodellen, sowie die Umpositionierung separierter kn{\"o}cherner Segmente im Kontext der rekonstruktiven MKG-Chirurgie behandelt. Durch die 3D Modellierung und Visualisierung anatomischer Strukturen, sowie der 3D Osteotomie- und Umstellungsplanung unter Einbeziehung der resultierenden Weichgewebedeformation wird den Chirurgen ein Werkzeug an die Hand gegeben, mit dem eine Therapieplanung am Computer durchgef{\"u}hrt und diese in Hinblick auf Funktion und {\"A}sthetik bewertet werden kann. Unterschiedliche Strategien k{\"o}nnen dabei erprobt und in ihrer Auswirkung erfasst werden. Dazu wird ein methodischer Ansatz vorgestellt, der zum einen die chirurgische Planung im Vergleich zu existierenden Ans{\"a}tzen deutlich verbessert und zum anderen eine robuste Weichgewebeprognose, durch den Einsatz geeigneter Planungsmodelle und eines physikalisch basierten Weichgewebemodells unter Nutzung numerischer L{\"o}sungsverfahren in die Planung integriert. Die Visualisierung der Planungsergebnisse erlaubt sowohl eine anschauliche und {\"u}berzeugende, pr{\"a}operative Patientenaufkl{\"a}rung, als auch die Demonstration m{\"o}glicher Vorgehensweisen und deren Auswirkungen f{\"u}r die chirurgische Ausbildung. Ferner erg{\"a}nzen die Planungsdaten die Falldokumentation und liefern einen Beitrag zur Qualit{\"a}tssicherung. Die Arbeit ist in sieben Kapitel gegliedert und wie folgt strukturiert: Zuerst wird die medizinische Aufgabenstellung bei der chirurgischen Rekonstruktion von Knochenfehlbildungen und -fehlstellungen in der kraniofazialen Chirurgie sowie die daraus resultierenden Anforderungen an die Therapieplanung beschrieben. Anschließend folgt ein umfassender {\"U}berblick {\"u}ber entsprechende Vorarbeiten zur computergest{\"u}tzten Planung knochenverlagernder Operationen und eine kritische Bestandsaufnahme der noch vorhandenen Defizite. Nach der Vorstellung des eigenen Planungsansatzes wird die Generierung individueller, qualitativ hochwertiger 3D Planungsmodelle aus tomografischen Bilddaten beschrieben, die den Anforderungen an eine intuitive, 3D Planung von Umstellungsosteotomien entsprechen und eine Simulation der daraus resultierenden Weichgewebedeformation mittels der Finite-Elemente Methode (FEM) erm{\"o}glichen. Die Methoden der 3D Schnittplanung an computergrafischen Modellen werden analysiert und eine 3D Osteotomieplanung an polygonalen Sch{\"a}delmodellen entwickelt, die es erm{\"o}glicht, intuitiv durch Definition von Schnittlinien am 3D Knochenmodell, eine den chirurgischen Anforderungen entsprechende Schnittplanung unter Ber{\"u}cksichtigung von Risikostrukturen durchzuf{\"u}hren. Separierte Knochensegmente lassen sich im Anschluss interaktiv umpositionieren und die resultierende Gesamtanordnung hinsichtlich einer funktionellen Rehabilitation bewerten. Aufgrund des in dieser Arbeit gew{\"a}hlten, physikalisch basierten Modellierungsansatzes kann unter Ber{\"u}cksichtigung des gesamten Weichgewebevolumens aus der Knochenverlagerung direkt die resultierende Gesichtsform berechnet werden. Dies wird anhand von 13 exemplarischen Fallstudien anschaulich demonstriert, wobei die Prognosequalit{\"a}t mittels postoperativer Fotografien und postoperativer CT-Daten {\"u}berpr{\"u}ft und belegt wird. Die Arbeit wird mit einem Ausblick auf erweiterte Modellierungsans{\"a}tze und einem Konzept f{\"u}r eine integrierte, klinisch einsetzbare Planungsumgebung abgeschlossen.}, language = {de} }