@misc{HoerthBaumKnoeteletal.2015, author = {Hoerth, Rebecca M. and Baum, Daniel and Kn{\"o}tel, David and Prohaska, Steffen and Willie, Bettina M. and Duda, Georg and Hege, Hans-Christian and Fratzl, Peter and Wagermaier, Wolfgang}, title = {Registering 2D and 3D Imaging Data of Bone during Healing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53426}, year = {2015}, abstract = {Purpose/Aims of the Study: Bone's hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro computed tomography (μCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. Materials and Methods: We investigated bone during healing by means of μCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue's calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. Results: We present an approach for the registration of 2D data in a 3D μCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into μCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. Conclusions: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.}, language = {en} } @misc{WeberTranfieldHoeoegetal.2014, author = {Weber, Britta and Tranfield, Erin M. and H{\"o}{\"o}g, Johanna L. and Baum, Daniel and Antony, Claude and Hyman, Tony and Verbavatz, Jean-Marc and Prohaska, Steffen}, title = {Automated stitching of microtubule centerlines across serial electron tomograms}, issn = {1438-0064}, doi = {10.1371/journal.pone.0113222}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52958}, year = {2014}, abstract = {Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts' opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort.}, language = {en} } @misc{KaplanLauferProhaskaetal.2017, author = {Kaplan, Bernhard and Laufer, Jan and Prohaska, Steffen and Buchmann, Jens}, title = {Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography}, issn = {1438-0064}, doi = {10.1117/12.2251945}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-62318}, year = {2017}, abstract = {The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 \% compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data.}, language = {en} } @misc{ZhukovaHiepenKnausetal.2017, author = {Zhukova, Yulia and Hiepen, Christian and Knaus, Petra and Osterland, Marc and Prohaska, Steffen and Dunlop, John W. C. and Fratzl, Peter and Skorb, Ekaterina V.}, title = {The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration}, issn = {1438-0064}, doi = {10.1002/adhm.201601244}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63053}, year = {2017}, abstract = {Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered - mesoporous titania (TMS), and ordered - titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair.}, language = {en} } @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} } @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{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} } @misc{KoberSaderZeilhoferetal.2001, author = {Kober, Cornelia and Sader, Robert and Zeilhofer, Hans-Florian and Prohaska, Steffen and Zachow, Stefan and Deuflhard, Peter}, title = {Anisotrope Materialmodellierung f{\"u}r den menschlichen Unterkiefer}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6574}, number = {01-31}, year = {2001}, abstract = {Im Rahmen der biomechanischen Simulation kn{\"o}cherner Organe ist die Frage nach einer befriedigenden Materialbeschreibung nach wie vor ungel{\"o}st. Computertomographische Datens{\"a}tze liefern eine r{\"a}umliche Verteilung der (R{\"o}ntgen-)Dichte und erm{\"o}glichen damit eine gute Darstellung der individuellen Geometrie. Weiter k{\"o}nnen die verschiedenen Materialbestandteile des Knochens, Spongiosa und Kortikalis, voneinander getrennt werden. Aber die richtungsab{\"a}ngige Information der Materialanisotropie ist verloren. In dieser Arbeit wird ein Ansatz f{\"u}r eine anisotrope Materialbeschreibung vorgestellt, die es erm{\"o}glicht, den Einfluss der individuellen kn{\"o}chernen Struktur auf das makroskopische Materialverhalten abzusch{\"a}tzen.}, language = {de} }