@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} } @misc{ZachowZilskeHege2007, author = {Zachow, Stefan and Zilske, Michael and Hege, Hans-Christian}, title = {3D reconstruction of individual anatomy from medical image data: Segmentation and geometry processing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10440}, number = {07-41}, year = {2007}, abstract = {For medical diagnosis, visualization, and model-based therapy planning three-dimensional geometric reconstructions of individual anatomical structures are often indispensable. Computer-assisted, model-based planning procedures typically cover specific modifications of "virtual anatomy" as well as numeric simulations of associated phenomena, like e.g. mechanical loads, fluid dynamics, or diffusion processes, in order to evaluate a potential therapeutic outcome. Since internal anatomical structures cannot be measured optically or mechanically in vivo, three-dimensional reconstruction of tomographic image data remains the method of choice. In this work the process chain of individual anatomy reconstruction is described which consists of segmentation of medical image data, geometrical reconstruction of all relevant tissue interfaces, up to the generation of geometric approximations (boundary surfaces and volumetric meshes) of three-dimensional anatomy being suited for finite element analysis. All results presented herein are generated with amira ® - a highly interactive software system for 3D data analysis, visualization and geometry reconstruction.}, language = {en} } @phdthesis{Baum2007, author = {Baum, Daniel}, title = {A Point-Based Algorithm for Multiple 3D Surface Alignment of Drug-Sized Molecules}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-fudissthesis000000002759-2}, school = {Freie Universit{\"a}t Berlin}, year = {2007}, abstract = {One crucial step in virtual drug design is the identification of new lead structures with respect to a pharmacological target molecule. The search for new lead structures is often done with the help of a pharmacophore, which carries the essential structural as well as physico-chemical properties that a molecule needs to have in order to bind to the target molecule. In the absence of the target molecule, such a pharmacophore can be established by comparison of a set of active compounds. In order to identify their common features,a multiple alignment of all or most of the active compounds is necessary. Moreover, since the "outer shape" of the molecules plays a major role in the interaction between drug and target, an alignment algorithm aiming at the identification of common binding properties needs to consider the molecule's "outer shape", which can be approximated by the solvent excluded surface. In this thesis, we present a new approach to molecular surface alignment based on a discrete representation of shape as well as physico-chemical properties by points distributed on the solvent excluded surface. We propose a new method to distribute points regularly on a surface w.r.t. a smoothly varying point density given on that surface. Since the point distribution algorithm is not restricted to molecular surfaces, it might also be of interest for other applications. For the computation of pairwise surface alignments, we extend an existing point matching scheme to surface points, and we develop an efficient data structure speeding up the computation by a factor of three. Moreover, we present an approach to compute multiple alignments from pairwise alignments, which is able to handle a large number of surface points. All algorithms are evaluated on two sets of molecules: eight thermolysin inhibitors and seven HIV-1 protease inhibitors. Finally, we compare the results obtained from surface alignment with the results obtained by applying an atom alignment approach.}, language = {en} } @misc{Clasen2005, type = {Master Thesis}, author = {Clasen, Malte}, title = {Beleuchtung von Landschaften in interaktiver Darstellung}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9906}, school = {Zuse Institute Berlin (ZIB)}, year = {2005}, abstract = {Inhalt dieser Diplomarbeit ist ein Beleuchtungs- und Visualisierungsmodell f{\"u}r Pflanzen im interaktiven Landschaftsrendering. Ziel ist die qualitativ hochwertige Darstellung von einzelnen Individuen nahe des Betrachters, der seine Position in einer ansonsten statischen Szene frei w{\"a}hlen kann. Um dies zu erreichen wird zun{\"a}chst vorgestellt, wie ausgehend von einfachen 3D-Modellen und Materialien ein physikalisch basiertes Reflexionsmodell parametrisiert werden kann. Grund hierf{\"u}r ist der oftmals vorhandene umfangreiche Datenbestand, der auf die OpenGL-Materialien oder {\"a}hnliche Shader optimiert ist. Anschließend wird gezeigt, wie die Echtzeit-Renderingtechniken Shadow Mapping und Precomputed Radiance Transfer kombiniert werden k{\"o}nnen, um sowohl exakte hochfrequente direkte Beleuchtung als auch niederfrequentes indirektes Streulicht zu ber{\"u}cksichtigen. Diese Kombination wird an Hand der Pfad-Notation des Monte-Carlo-Path-Tracing eingef{\"u}hrt und begr{\"u}ndet.}, language = {de} } @phdthesis{Kaehler2005, author = {K{\"a}hler, Ralf}, title = {Accelerated Volume Rendering on Structured Adaptive Meshes}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-2005002769}, year = {2005}, abstract = {Multi-scale phenomena are abundant in many application fields. Representing and numerically simulating such processes is a challenging task since quite different scales have to be resolved, which often requires enormous amounts of storage and computational power. An important strategy in this context is adaptivity, i.e. local adjustment of the spatio-temporal resolution to the details to be resolved. A standard representation therefore are hierarchical, locally refined grids. A specific adaptive approach for solving partial differential equations, usually called AMR (Adaptive Mesh Refinement), was introduced in 1984. The basic idea is to combine the simplicity of structured grids and the advantages of local refinement. In this numerical scheme the computations are started on a set of coarse, potentially overlapping structured grids, that cover the computational domain. Local error criteria are applied to detect regions that require higher resolution. These are covered by subgrids with decreasing mesh spacing, which do not replace, but rather overlap the refined regions of the coarser patches. The equations are advanced on the finer subgrids and the refinement procedure recursively continues until all cells fulfill the considered error criteria, giving rise to a hierarchy of nested levels of refinement. In 1989 a variant of this scheme, called Structured Adaptive Mesh Refinement (SAMR), which reduces some of the complexity of the original approach, was proposed. While the separate subgrids in the AMR scheme could be rotated against each other, in SAMR they are aligned with the major axes of the coordinate system, which for example simplifies the computation of fluxes of (conserved) quantities through the cell faces. SAMR has become more and more popular in the last decade, and nowadays it is applied in many domains like hydrodynamics, meteorology and in particular in cosmology and relativistic astrophysics. Due to this growing popularity, an increasing number of scientists is in need of appropriate interactive visualization techniques to interpret and analyze AMR simulation data. Tools for both, 2D analysis to quantitatively convey the information within single slices and 3D representations to apprehend the overall structure are required. In this thesis we develop direct and indirect volume visualization algorithms for scalar fields that are defined on structured Adaptive Mesh Refinement (SAMR) grids. In particular algorithms for planar slicing and the display of height fields, C0-continuous isosurface extraction, software-, and hardware-based direct volume rendering and temporal interpolation for cell-, and vertex-centered data on unrestricted SAMR grids are proposed. Additionally we investigate the applicability of SAMR data structures for accelerated software-, and hardware-based volume rendering of large 3D scalar data.}, language = {en} } @misc{GreweZachow2021, author = {Grewe, C. Martin and Zachow, Stefan}, title = {Release of the FexMM for the Open Virtual Mirror Framework}, doi = {10.12752/8532}, year = {2021}, abstract = {THIS MODEL IS FOR NON-COMMERCIAL RESEARCH PURPOSES. ONLY MEMBERS OF UNIVERSITIES OR NON-COMMERCIAL RESEARCH INSTITUTES ARE ELIGIBLE TO APPLY. 1. Download, fill, and sign the form available from: https://media.githubusercontent.com/media/mgrewe/ovmf/main/data/fexmm_license_agreement.pdf 2. Send the signed form to: fexmm@zib.de NOTE: Use an official email address of your institution for the request.}, language = {en} } @article{vonLindheimHarikrishnanDoerffeletal.2021, author = {von Lindheim, Johannes and Harikrishnan, Abhishek and D{\"o}rffel, Tom and Klein, Rupert and Koltai, Peter and Mikula, Natalia and M{\"u}ller, Annette and N{\´e}vir, Peter and Pacey, George and Polzin, Robert and Vercauteren, Nikki}, title = {Definition, detection and tracking of persistent structures in atmospheric flows}, journal = {arXiv}, arxiv = {http://arxiv.org/abs/2111.13645}, year = {2021}, abstract = {Long-lived flow patterns in the atmosphere such as weather fronts, mid-latitude blockings or tropical cyclones often induce extreme weather conditions. As a consequence, their description, detection, and tracking has received increasing attention in recent years. Similar objectives also arise in diverse fields such as turbulence and combustion research, image analysis, and medical diagnostics under the headlines of "feature tracking", "coherent structure detection" or "image registration" - to name just a few. A host of different approaches to addressing the underlying, often very similar, tasks have been developed and successfully used. Here, several typical examples of such approaches are summarized, further developed and applied to meteorological data sets. Common abstract operational steps form the basis for a unifying framework for the specification of "persistent structures" involving the definition of the physical state of a system, the features of interest, and means of measuring their persistence.}, language = {en} } @article{TackAmbellanZachow2021, author = {Tack, Alexander and Ambellan, Felix and Zachow, Stefan}, title = {Towards novel osteoarthritis biomarkers: Multi-criteria evaluation of 46,996 segmented knee MRI data from the Osteoarthritis Initiative}, volume = {16}, journal = {PLOS One}, number = {10}, doi = {10.1371/journal.pone.0258855}, year = {2021}, abstract = {Convolutional neural networks (CNNs) are the state-of-the-art for automated assessment of knee osteoarthritis (KOA) from medical image data. However, these methods lack interpretability, mainly focus on image texture, and cannot completely grasp the analyzed anatomies' shapes. In this study we assess the informative value of quantitative features derived from segmentations in order to assess their potential as an alternative or extension to CNN-based approaches regarding multiple aspects of KOA. Six anatomical structures around the knee (femoral and tibial bones, femoral and tibial cartilages, and both menisci) are segmented in 46,996 MRI scans. Based on these segmentations, quantitative features are computed, i.e., measurements such as cartilage volume, meniscal extrusion and tibial coverage, as well as geometric features based on a statistical shape encoding of the anatomies. The feature quality is assessed by investigating their association to the Kellgren-Lawrence grade (KLG), joint space narrowing (JSN), incident KOA, and total knee replacement (TKR). Using gold standard labels from the Osteoarthritis Initiative database the balanced accuracy (BA), the area under the Receiver Operating Characteristic curve (AUC), and weighted kappa statistics are evaluated. Features based on shape encodings of femur, tibia, and menisci plus the performed measurements showed most potential as KOA biomarkers. Differentiation between non-arthritic and severely arthritic knees yielded BAs of up to 99\%, 84\% were achieved for diagnosis of early KOA. Weighted kappa values of 0.73, 0.72, and 0.78 were achieved for classification of the grade of medial JSN, lateral JSN, and KLG, respectively. The AUC was 0.61 and 0.76 for prediction of incident KOA and TKR within one year, respectively. Quantitative features from automated segmentations provide novel biomarkers for KLG and JSN classification and show potential for incident KOA and TKR prediction. The validity of these features should be further evaluated, especially as extensions of CNN- based approaches. To foster such developments we make all segmentations publicly available together with this publication.}, language = {en} } @article{TackShestakovLuedkeetal.2021, author = {Tack, Alexander and Shestakov, Alexey and L{\"u}dke, David and Zachow, Stefan}, title = {A deep multi-task learning method for detection of meniscal tears in MRI data from the Osteoarthritis Initiative database}, journal = {Frontiers in Bioengineering and Biotechnology, section Biomechanics}, doi = {10.3389/fbioe.2021.747217}, pages = {28 -- 41}, year = {2021}, abstract = {We present a novel and computationally efficient method for the detection of meniscal tears in Magnetic Resonance Imaging (MRI) data. Our method is based on a Convolutional Neural Network (CNN) that operates on a complete 3D MRI scan. Our approach detects the presence of meniscal tears in three anatomical sub-regions (anterior horn, meniscal body, posterior horn) for both the Medial Meniscus (MM) and the Lateral Meniscus (LM) individually. For optimal performance of our method, we investigate how to preprocess the MRI data or how to train the CNN such that only relevant information within a Region of Interest (RoI) of the data volume is taken into account for meniscal tear detection. We propose meniscal tear detection combined with a bounding box regressor in a multi-task deep learning framework to let the CNN implicitly consider the corresponding RoIs of the menisci. We evaluate the accuracy of our CNN-based meniscal tear detection approach on 2,399 Double Echo Steady-State (DESS) MRI scans from the Osteoarthritis Initiative database. In addition, to show that our method is capable of generalizing to other MRI sequences, we also adapt our model to Intermediate-Weighted Turbo Spin-Echo (IW TSE) MRI scans. To judge the quality of our approaches, Receiver Operating Characteristic (ROC) curves and Area Under the Curve (AUC) values are evaluated for both MRI sequences. For the detection of tears in DESS MRI, our method reaches AUC values of 0.94, 0.93, 0.93 (anterior horn, body, posterior horn) in MM and 0.96, 0.94, 0.91 in LM. For the detection of tears in IW TSE MRI data, our method yields AUC values of 0.84, 0.88, 0.86 in MM and 0.95, 0.91, 0.90 in LM. In conclusion, the presented method achieves high accuracy for detecting meniscal tears in both DESS and IW TSE MRI data. Furthermore, our method can be easily trained and applied to other MRI sequences.}, language = {en} } @misc{TackShestakovLuedkeetal.2021, author = {Tack, Alexander and Shestakov, Alexey and L{\"u}dke, David and Zachow, Stefan}, title = {A deep multi-task learning method for detection of meniscal tears in MRI data from the Osteoarthritis Initiative database}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-84415}, year = {2021}, abstract = {We present a novel and computationally efficient method for the detection of meniscal tears in Magnetic Resonance Imaging (MRI) data. Our method is based on a Convolutional Neural Network (CNN) that operates on a complete 3D MRI scan. Our approach detects the presence of meniscal tears in three anatomical sub-regions (anterior horn, meniscal body, posterior horn) for both the Medial Meniscus (MM) and the Lateral Meniscus (LM) individually. For optimal performance of our method, we investigate how to preprocess the MRI data or how to train the CNN such that only relevant information within a Region of Interest (RoI) of the data volume is taken into account for meniscal tear detection. We propose meniscal tear detection combined with a bounding box regressor in a multi-task deep learning framework to let the CNN implicitly consider the corresponding RoIs of the menisci. We evaluate the accuracy of our CNN-based meniscal tear detection approach on 2,399 Double Echo Steady-State (DESS) MRI scans from the Osteoarthritis Initiative database. In addition, to show that our method is capable of generalizing to other MRI sequences, we also adapt our model to Intermediate-Weighted Turbo Spin-Echo (IW TSE) MRI scans. To judge the quality of our approaches, Receiver Operating Characteristic (ROC) curves and Area Under the Curve (AUC) values are evaluated for both MRI sequences. For the detection of tears in DESS MRI, our method reaches AUC values of 0.94, 0.93, 0.93 (anterior horn, body, posterior horn) in MM and 0.96, 0.94, 0.91 in LM. For the detection of tears in IW TSE MRI data, our method yields AUC values of 0.84, 0.88, 0.86 in MM and 0.95, 0.91, 0.90 in LM. In conclusion, the presented method achieves high accuracy for detecting meniscal tears in both DESS and IW TSE MRI data. Furthermore, our method can be easily trained and applied to other MRI sequences.}, language = {en} } @inproceedings{HanikHegevonTycowicz2022, author = {Hanik, Martin and Hege, Hans-Christian and von Tycowicz, Christoph}, title = {A Nonlinear Hierarchical Model for Longitudinal Data on Manifolds}, booktitle = {2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI)}, arxiv = {http://arxiv.org/abs/2202.01180}, doi = {10.1109/ISBI52829.2022.9761465}, pages = {1 -- 5}, year = {2022}, abstract = {Large longitudinal studies provide lots of valuable information, especially in medical applications. A problem which must be taken care of in order to utilize their full potential is that of correlation between intra-subject measurements taken at different times. For data in Euclidean space this can be done with hierarchical models, that is, models that consider intra-subject and between-subject variability in two different stages. Nevertheless, data from medical studies often takes values in nonlinear manifolds. Here, as a first step, geodesic hierarchical models have been developed that generalize the linear ansatz by assuming that time-induced intra-subject variations occur along a generalized straight line in the manifold. However, this is often not the case (e.g., periodic motion or processes with saturation). We propose a hierarchical model for manifold-valued data that extends this to include trends along higher-order curves, namely B{\´e}zier splines in the manifold. To this end, we present a principled way of comparing shape trends in terms of a functional-based Riemannian metric. Remarkably, this metric allows efficient, yet simple computations by virtue of a variational time discretization requiring only the solution of regression problems. We validate our model on longitudinal data from the osteoarthritis initiative, including classification of disease progression.}, language = {en} } @misc{AmbellanHanikvonTycowicz2021, author = {Ambellan, Felix and Hanik, Martin and von Tycowicz, Christoph}, title = {Morphomatics: Geometric morphometrics in non-Euclidean shape spaces}, doi = {10.12752/8544}, year = {2021}, abstract = {Morphomatics is an open-source Python library for (statistical) shape analysis developed within the geometric data analysis and processing research group at Zuse Institute Berlin. It contains prototype implementations of intrinsic manifold-based methods that are highly consistent and avoid the influence of unwanted effects such as bias due to arbitrary choices of coordinates.}, language = {en} } @article{GreweLiuHildebrandtetal.2022, author = {Grewe, Carl Martin and Liu, Tuo and Hildebrandt, Andrea and Zachow, Stefan}, title = {The Open Virtual Mirror Framework for Enfacement Illusions - Enhancing the Sense of Agency With Avatars That Imitate Facial Expressions}, journal = {Behavior Research Methods}, publisher = {Springer}, doi = {10.3758/s13428-021-01761-9}, year = {2022}, language = {de} } @article{JainSinghSinghetal.2025, author = {Jain, Toshit and Singh, Upkar and Singh, Varun and Boda, Vijay Kumar and Hotz, Ingrid and Vadhiyar, Sathish S. and Vinayachandran, P. N. and Natarajan, Vijay}, title = {A Scalable System for Visual Analysis of Ocean Data}, volume = {44}, journal = {Computer Graphics Forum}, number = {1}, doi = {10.1111/cgf.15279}, pages = {e15279}, year = {2025}, language = {en} } @inproceedings{AmbellanZachowvonTycowicz2021, author = {Ambellan, Felix and Zachow, Stefan and von Tycowicz, Christoph}, title = {Geodesic B-Score for Improved Assessment of Knee Osteoarthritis}, booktitle = {Proc. Information Processing in Medical Imaging (IPMI)}, arxiv = {http://arxiv.org/abs/2104.01107}, doi = {10.1007/978-3-030-78191-0_14}, pages = {177 -- 188}, year = {2021}, abstract = {Three-dimensional medical imaging enables detailed understanding of osteoarthritis structural status. However, there remains a vast need for automatic, thus, reader-independent measures that provide reliable assessment of subject-specific clinical outcomes. To this end, we derive a consistent generalization of the recently proposed B-score to Riemannian shape spaces. We further present an algorithmic treatment yielding simple, yet efficient computations allowing for analysis of large shape populations with several thousand samples. Our intrinsic formulation exhibits improved discrimination ability over its Euclidean counterpart, which we demonstrate for predictive validity on assessing risks of total knee replacement. This result highlights the potential of the geodesic B-score to enable improved personalized assessment and stratification for interventions.}, language = {en} } @article{HembusAmbellanZachowetal.2021, author = {Hembus, Jessica and Ambellan, Felix and Zachow, Stefan and Bader, Rainer}, title = {Establishment of a rolling-sliding test bench to analyze abrasive wear propagation of different bearing materials for knee implants}, volume = {11}, journal = {Applied Sciences}, number = {4}, doi = {10.3390/app11041886}, pages = {15}, year = {2021}, abstract = {Currently, new materials for knee implants need to be extensively and expensive tested in a knee wear simulator in a realized design. However, using a rolling-sliding test bench, these materials can be examined under the same test conditions but with simplified geometries. In the present study, the test bench was optimized, and forces were adapted to the physiological contact pressure in the knee joint using the available geometric parameters. Various polymers made of polyethylene and polyurethane articulating against test wheels made of cobalt-chromium and aluminum titanate were tested in the test bench using adapted forces based on ISO 14243-1. Polyurethane materials showed distinctly higher wear rates than polyethylene materials and showed inadequate wear resistance for use as knee implant material. Thus, the rolling-sliding test bench is an adaptable test setup for evaluating newly developed bearing materials for knee implants. It combines the advantages of screening and simulator tests and allows testing of various bearing materials under physiological load and tribological conditions of the human knee joint. The wear behavior of different material compositions and the influence of surface geometry and quality can be initially investigated without the need to produce complex implant prototypes of total knee endoprosthesis or interpositional spacers.}, language = {en} } @misc{TackAmbellanZachow2021, author = {Tack, Alexander and Ambellan, Felix and Zachow, Stefan}, title = {Towards novel osteoarthritis biomarkers: Multi-criteria evaluation of 46,996 segmented knee MRI data from the Osteoarthritis Initiative (Supplementary Material)}, volume = {16}, journal = {PLOS One}, number = {10}, doi = {10.12752/8328}, year = {2021}, abstract = {Convolutional neural networks (CNNs) are the state-of-the-art for automated assessment of knee osteoarthritis (KOA) from medical image data. However, these methods lack interpretability, mainly focus on image texture, and cannot completely grasp the analyzed anatomies' shapes. In this study we assess the informative value of quantitative features derived from segmentations in order to assess their potential as an alternative or extension to CNN-based approaches regarding multiple aspects of KOA A fully automated method is employed to segment six anatomical structures around the knee (femoral and tibial bones, femoral and tibial cartilages, and both menisci) in 46,996 MRI scans. Based on these segmentations, quantitative features are computed, i.e., measurements such as cartilage volume, meniscal extrusion and tibial coverage, as well as geometric features based on a statistical shape encoding of the anatomies. The feature quality is assessed by investigating their association to the Kellgren-Lawrence grade (KLG), joint space narrowing (JSN), incident KOA, and total knee replacement (TKR). Using gold standard labels from the Osteoarthritis Initiative database the balanced accuracy (BA), the area under the Receiver Operating Characteristic curve (AUC), and weighted kappa statistics are evaluated. Features based on shape encodings of femur, tibia, and menisci plus the performed measurements showed most potential as KOA biomarkers. Differentiation between healthy and severely arthritic knees yielded BAs of up to 99\%, 84\% were achieved for diagnosis of early KOA. Substantial agreement with weighted kappa values of 0.73, 0.73, and 0.79 were achieved for classification of the grade of medial JSN, lateral JSN, and KLG, respectively. The AUC was 0.60 and 0.75 for prediction of incident KOA and TKR within 5 years, respectively. Quantitative features from automated segmentations yield excellent results for KLG and JSN classification and show potential for incident KOA and TKR prediction. The validity of these features as KOA biomarkers should be further evaluated, especially as extensions of CNN-based approaches. To foster such developments we make all segmentations publicly available together with this publication.}, language = {en} } @article{SekuboyinaHusseiniBayatetal.2021, author = {Sekuboyina, Anjany and Husseini, Malek E. and Bayat, Amirhossein and L{\"o}ffler, Maximilian and Liebl, Hans and Li, Hongwei and Tetteh, Giles and Kukačka, Jan and Payer, Christian and Štern, Darko and Urschler, Martin and Chen, Maodong and Cheng, Dalong and Lessmann, Nikolas and Hu, Yujin and Wang, Tianfu and Yang, Dong and Xu, Daguang and Ambellan, Felix and Amiranashvili, Tamaz and Ehlke, Moritz and Lamecker, Hans and Lehnert, Sebastian and Lirio, Marilia and de Olaguer, Nicol{\´a}s P{\´e}rez and Ramm, Heiko and Sahu, Manish and Tack, Alexander and Zachow, Stefan and Jiang, Tao and Ma, Xinjun and Angerman, Christoph and Wang, Xin and Brown, Kevin and Kirszenberg, Alexandre and Puybareau, {\´E}lodie and Chen, Di and Bai, Yiwei and Rapazzo, Brandon H. and Yeah, Timyoas and Zhang, Amber and Xu, Shangliang and Hou, Feng and He, Zhiqiang and Zeng, Chan and Xiangshang, Zheng and Liming, Xu and Netherton, Tucker J. and Mumme, Raymond P. and Court, Laurence E. and Huang, Zixun and He, Chenhang and Wang, Li-Wen and Ling, Sai Ho and Huynh, L{\^e} Duy and Boutry, Nicolas and Jakubicek, Roman and Chmelik, Jiri and Mulay, Supriti and Sivaprakasam, Mohanasankar and Paetzold, Johannes C. and Shit, Suprosanna and Ezhov, Ivan and Wiestler, Benedikt and Glocker, Ben and Valentinitsch, Alexander and Rempfler, Markus and Menze, Bj{\"o}rn H. and Kirschke, Jan S.}, title = {VerSe: A Vertebrae labelling and segmentation benchmark for multi-detector CT images}, volume = {73}, journal = {Medical Image Analysis}, doi = {10.1016/j.media.2021.102166}, year = {2021}, abstract = {Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision support systems for diagnosis, surgery planning, and population-based analysis of spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms tackling the labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the results of this evaluation and further investigate the performance variation at the vertebra level, scan level, and different fields of view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top-performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The VerSe content and code can be accessed at: https://github.com/anjany/verse.}, language = {en} } @article{SipiranLazoLopezetal.2021, author = {Sipiran, Ivan and Lazo, Patrick and Lopez, Cristian and Bagewadi, Nihar and Bustos, Benjamin and Dao, Hieu and Gangisetty, Shankar and Hanik, Martin and Ho-Thi, Ngoc-Phuong and Holenderski, Mike and Jarnikov, Dmitri and Labrada, Arniel and Lengauer, Stefan and Licandro, Roxane and Nguyen, Dinh-Huan and Nguyen-Ho, Thang-Long and P{\´e}rez Rey, Luis A. and Pham, Bang-Dang and Pham, Minh-Khoi and Preiner, Reinhold and Schreck, Tobias and Trinh, Quoc-Huy and Tonnaer, Loek and von Tycowicz, Christoph and Vu-Le, The-Anh}, title = {SHREC 2021: Retrieval of Cultural Heritage Objects}, volume = {100}, journal = {Computers and Graphics}, doi = {10.1016/j.cag.2021.07.010}, pages = {1 -- 20}, year = {2021}, abstract = {This paper presents the methods and results of the SHREC'21 contest on a dataset of cultural heritage (CH) objects. We present a dataset of 938 scanned models that have varied geometry and artistic styles. For the competition, we propose two challenges: the retrieval-by-shape challenge and the retrieval-by-culture challenge. The former aims at evaluating the ability of retrieval methods to discriminate cultural heritage objects by overall shape. The latter focuses on assessing the effectiveness of retrieving objects from the same culture. Both challenges constitute a suitable scenario to evaluate modern shape retrieval methods in a CH domain. Ten groups participated in the contest: thirty runs were submitted for the retrieval-by-shape task, and twenty-six runs were submitted for the retrieval-by-culture challenge. The results show a predominance of learning methods on image-based multi-view representations to characterize 3D objects. Nevertheless, the problem presented in our challenges is far from being solved. We also identify the potential paths for further improvements and give insights into the future directions of research.}, language = {en} } @article{MoewisKaiserTrepczynskietal.2021, author = {Moewis, Philippe and Kaiser, Ren{\´e} and Trepczynski, Adam and von Tycowicz, Christoph and Krahl, Leonie and Ilg, Ansgar and Holz, Johannes and Duda, Georg}, title = {Patient specific resurfacing implant knee surgery in subjects with early osteoarthritis results in medial pivot and lateral femoral rollback during flexion: A retrospective pilot study}, journal = {Knee Surgery, Sports Traumatology, Arthroscopy}, doi = {10.1007/s00167-021-06749-8}, year = {2021}, abstract = {Purpose. Metallic resurfacing implants have been developed for the treatment of early, focal, small, condylar and trochlear osteoarthritis (OA) lesions. They represent an option for patients who are either too young to fulfill the criteria for total knee arthroplasty (TKA) or too old for biological treatment. Although relevant clinical evidence has been collected for different resurfacing types, the in vivo post-operative knee kinematics remains unknown. The present study aims to measure and analyse the knee joint kinematics in subjects with patient-specific Episealer implants Methods. Retrospective study design. Fluoroscopic analyses during high flexion activities (unloaded flexion-extension and loaded lunge) were conducted at >12 months post-surgery in ten Episealer knees. The post-operative knee joint kinematics was compared to equally assessed kinematic from ten healthy knees, twenty G-Curve TKA knees and 10 J-Curve knees. Pre- and postoperative clinical data of the Episealer knees were collected using a visual analog scale (VAS), the EQ 5d Health Questionnaire and the Knee Injury and Osteoarthritis Outcome Score (KOOS). Results. During unloaded flexion-extension and loaded lunge, the medial condyle in the Episealer knees remained relative stationary, indicating a medial pivot, while the lateral condyle translated consistently towards posterior. Similarly, reduced movement of the medial condyle and posterior translation of the lateral condyle was also observed in the healthy knees, although to a lesser extent. In contrast, the kinematics of both TKA cohorts during unloaded flexion-extension showed a tendency towards anterior displacement in the medial compartment, which led to significant differences in comparison with the Episealer knees. In the lateral compartment, a certain degree of femoral rollback was noted in the G-Curve TKA cohort. Improved scores were observed in the Episealer subjects between the preoperative and 1-year postoperative follow-up. Conclusion. At 12 months postsurgery, a physiological-like knee kinematics was observed in the group of patient-specific reconstructed chondral/osteochondral lesions by means of a resurfacing Episealer implant strategy. Considering that these patients are physically active and do not fulfill the criteria for TKA, the group is hard to be compared to TKA patients which usually are less active and more challenging. Nevertheless, the comparison to either healthy knee kinematics as well as to TKA reconstructed knees with different implant designs showed a more physiological-like kinematics in the resurfacing implants that seems more appropriate for such a patient group. Despite positive results, careful clinical follow-up of treated patients is recommended for the long-term OA progression. Further investigations need to be encouraged not only in larger patient groups but also in a prospective manner to assess the pre- to postoperative kinematic changes.}, language = {en} } @misc{Punjabi2021, type = {Master Thesis}, author = {Punjabi, Dev}, title = {Orientation-invariant Dense Correspondence using Graph Convolutional Neural Networks}, pages = {41}, year = {2021}, language = {en} } @misc{AmbellanZachowvonTycowicz2021, author = {Ambellan, Felix and Zachow, Stefan and von Tycowicz, Christoph}, title = {Geodesic B-Score for Improved Assessment of Knee Osteoarthritis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81930}, year = {2021}, abstract = {Three-dimensional medical imaging enables detailed understanding of osteoarthritis structural status. However, there remains a vast need for automatic, thus, reader-independent measures that provide reliable assessment of subject-specific clinical outcomes. To this end, we derive a consistent generalization of the recently proposed B-score to Riemannian shape spaces. We further present an algorithmic treatment yielding simple, yet efficient computations allowing for analysis of large shape populations with several thousand samples. Our intrinsic formulation exhibits improved discrimination ability over its Euclidean counterpart, which we demonstrate for predictive validity on assessing risks of total knee replacement. This result highlights the potential of the geodesic B-score to enable improved personalized assessment and stratification for interventions.}, language = {en} } @article{MelnykMontavonKlusetal.2020, author = {Melnyk, Kateryna and Montavon, Gr{\`e}goire and Klus, Stefan and Conrad, Tim}, title = {Graph Kernel Koopman Embedding for Human Microbiome Analysis}, volume = {5}, journal = {Applied Network Science}, number = {96}, doi = {10.1007/s41109-020-00339-2}, year = {2020}, abstract = {More and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, or some cancer types. Thanks to modern high-throughput omics technologies, it becomes possible to directly analyze human microbiome and its influence on the health status. Microbial communities are monitored over long periods of time and the associations between their members are explored. These relationships can be described by a time-evolving graph. In order to understand responses of the microbial community members to a distinct range of perturbations such as antibiotics exposure or diseases and general dynamical properties, the time-evolving graph of the human microbial communities has to be analyzed. This becomes especially challenging due to dozens of complex interactions among microbes and metastable dynamics. The key to solving this problem is the representation of the time-evolving graphs as fixed-length feature vectors preserving the original dynamics. We propose a method for learning the embedding of the time-evolving graph that is based on the spectral analysis of transfer operators and graph kernels. We demonstrate that our method can capture temporary changes in the time-evolving graph on both synthetic data and real-world data. Our experiments demonstrate the efficacy of the method. Furthermore, we show that our method can be applied to human microbiome data to study dynamic processes.}, language = {en} } @article{IravaniConrad2023, author = {Iravani, Sahar and Conrad, Tim}, title = {An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data}, volume = {20}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, number = {1}, doi = {10.1109/tcbb.2022.3141656}, pages = {151 -- 161}, year = {2023}, abstract = {Analyzing mass spectrometry-based proteomics data with deep learning (DL) approaches poses several challenges due to the high dimensionality, low sample size, and high level of noise. Additionally, DL-based workflows are often hindered to be integrated into medical settings due to the lack of interpretable explanation. We present DLearnMS, a DL biomarker detection framework, to address these challenges on proteomics instances of liquid chromatography-mass spectrometry (LC-MS) - a well-established tool for quantifying complex protein mixtures. Our DLearnMS framework learns the clinical state of LC-MS data instances using convolutional neural networks. Based on the trained neural networks, we show how biomarkers can be identified using layer-wise relevance propagation. This enables detecting discriminating regions of the data and the design of more robust networks. One of the main advantages over other established methods is that no explicit preprocessing step is needed in our DLearnMS framework. Our evaluation shows that DLearnMS outperforms conventional LC-MS biomarker detection approaches in identifying fewer false positive peaks while maintaining a comparable amount of true positives peaks.}, language = {en} } @article{RamsConrad2022, author = {Rams, Mona and Conrad, Tim}, title = {Dictionary learning allows model-free pseudotime estimation of transcriptomics data}, volume = {23}, journal = {BMC Genomics}, publisher = {BioMed Central}, doi = {10.1186/s12864-021-08276-9}, year = {2022}, language = {en} } @article{FroehlerElberfeldMoelleretal.2020, author = {Fr{\"o}hler, Bernhard and Elberfeld, Tim and M{\"o}ller, Torsten and Hege, Hans-Christian and De Beenhouwer, Jan and Sijbers, Jan and Kastner, Johann and Heinzl, Christoph}, title = {Analysis and comparison of algorithms for the tomographic reconstruction of curved fibres}, volume = {35}, journal = {Nondestructive Testing and Evaluation}, number = {3}, doi = {10.1080/10589759.2020.1774583}, pages = {328 -- 341}, year = {2020}, abstract = {We present visual methods for the analysis and comparison of the results of curved fibre reconstruction algorithms, i.e., of algorithms extracting characteristics of curved fibres from X-ray computed tomography scans. In this work, we extend previous methods for the analysis and comparison of results of different fibre reconstruction algorithms or parametrisations to the analysis of curved fibres. We propose fibre dissimilarity measures for such curved fibres and apply these to compare multiple results to a specified reference. We further propose visualisation methods to analyse differences between multiple results quantitatively and qualitatively. In two case studies, we show that the presented methods provide valuable insights for advancing and parametrising fibre reconstruction algorithms, and support in improving their results in characterising curved fibres.}, language = {en} } @misc{Dill2018, type = {Master Thesis}, author = {Dill, Sabrina}, title = {Joint Feature Learning and Classification - Deep Learning for Surgical Phase Detection}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81745}, year = {2018}, abstract = {In this thesis we investigate the task of automatically detecting phases in surgical workflow in endoscopic video data. For this, we employ deep learning approaches that solely rely on frame-wise visual information, instead of using additional signals or handcrafted features. While previous work has mainly focused on tool presence and temporal information for this task, we reason that additional global information about the context of a frame might benefit the phase detection task. We propose novel deep learning architectures: a convolutional neural network (CNN) based model for the tool detection task only, called Clf-Net, as well as a model which performs joint (context) feature learning and tool classification to incorporate information about the context, which we name Context-Clf-Net. For the phase detection task lower-dimensional feature vectors are extracted, which are used as input to recurrent neural networks in order to enforce temporal constraints. We compare the performance of an online model, which only considers previous frames up to the current time step, to that of an offline model that has access to past and future information. Experimental results indicate that the tool detection task benefits strongly from the introduction of context information, as we outperform both Clf-Net results and stateof-the-art methods. Regarding the phase detection task our results do not surpass state-of-the-art methods. Furthermore, no improvement of using features learned by the Context-Clf-Net is observed in the phase detection task for both online and offline versions}, language = {en} }