@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} }