A novel approach for connecting temporal-ontologies with blood flow simulations.

In this paper an approach for developing a temporal domain ontology for biomedical simulations is introduced. The ideas are presented in the context of simulations of blood flow in aneurysms using the Lattice Boltzmann Method. The advantages in using ontologies are manyfold: On the one hand, ontologies having been proven to be able to provide medical special knowledge e.g., key parameters for simulations. On the other hand, based on a set of rules and the usage of a reasoner, a system for checking the plausibility as well as tracking the outcome of medical simulations can be constructed. Likewise, results of simulations including data derived from them can be stored and communicated in a way that can be understood by computers. Later on, this set of results can be analyzed. At the same time, the ontologies provide a way to exchange knowledge between researchers. Lastly, this approach can be seen as a black-box abstraction of the internals of the simulation for the biomedical researcher as well. This approach is able to provide the complete parameter sets for simulations, part of the corresponding results and part of their analysis as well as e.g., geometry and boundary conditions. These inputs can be transferred to different simulation methods for comparison. Variations on the provided parameters can be automatically used to drive these simulations. Using a rule base, unphysical inputs or outputs of the simulation can be detected and communicated to the physician in a suitable and familiar way. An example for an instantiation of the blood flow simulation ontology and exemplary rules for plausibility checking are given.

Computation of a tetrahedral mesh for striated muscle deformation simulation.

Competing concepts exist regarding surgery for instance of the cleft lip and palate to date. Morphology-based simulations at histological scale may one day be used to help the surgeon predict the possible outcome of a variety of approaches. It however can be a challenge to generate volume meshes that are applicable to the mathematical modelling of three-dimensional spatial modifications. Computation of surface meshes may be considered less delicate. The aim of this study is to design and evaluate a novel algorithm that supports finite element methods. Images of histological serial sections of a striated muscle were segmented. Results of the three-dimensional reconstruction of multiple layers of the polygonal segmentation data characterized the hull of the muscle. The corresponding surface mesh was then converted into a tetrahedral mesh to generate volume. This was achieved by mapping multiple template types onto neighbouring intersection polygons. Muscle contraction was subsequently simulated by mesh deformation. The technique successfully generated volumes and was able to provide data on contraction directions. The mesh supported a novel approach to simulate representations of contraction. However, several drawbacks were evident. Mathematical modelling of scenarios with more than one striated muscle will require considerable modification of the currently presented approach. Future studies need to then evaluate the applicability of volume meshes to represent arrays of three-dimensional biological objects. Surface mesh based mathematical modelling of cleft lip and palate surgery and its results are therefore not yet in reach.

[Mathematical modelling in systems biology. Simulation of the desmoplastic stromal reaction as an example]. / Mathematische Modellierung in der Systembiologie. Beispiel einer Simulation der desmoplastischen Stromareaktion.

A mathematical model of collagen fiber mesh formation was created to evaluate the possible role of chemotaxis and haptotaxis in the histomorphology of a desmoplastic stromal reaction (DSR). Fibroblasts were mathematicaly interpreted as mobile discrete objects, characterized by their velocity and position, both dependent on time. This resulted in cell migration paths, commonly termed "trajectories" which are modulated as stochastic process. The implementation of chemotactic effects requires knowledge of the concentration and distribution of the appropriate chemical substance in the scenario. A simplistic model assumption allows the calculation of a numerical solution of the resulting diffusion equation. Adding haptotaxis necessitates the simulation of the extracellular matrix (ECM). The fiber distribution is modeled as a vector field which contains information on both, fiber density and direction. The production of new fibers is based on ordinary differential equations coupled with the migratory behavior of the cells. Filters help smooth the trajectories. Appropriate visualization allows a direct comparison of the simulation results with histomorphology. Matches between computed data and their real counterparts indicate that the development of mathematical models is appropriate to describe and forecast the course of DSR. This makes systems biology a stepping stone to improving biomedical research.

[Analysis of histological datasets by signal processing methods]. / Signaltheoretische Analyse histologischer Daten im Ortsfrequenzraum.

In the present study, a semi-automatic segmentation and classification algorithm is proposed for the analysis of histological and cytological images. In view of the fact that histological and cytological images usually exhibit poor contrast and blurred outlines, classical segmentation algorithms often fail to detect relevant structures. A new algorithm for texture segmentation based on signal processing methods in combination with machine learning techniques was therefore developed.

[Virtual tissue. Quaoaring]. / Virtuelles Gewebe. Quaoaring.

Virtual tissue can be generated by employing various methods. First steps en route to virtual tissue may encompass the generation of virtual cells. One such approach termed Quaoaring was applied to produce artificial erythrocytes and these were both discocyte and echinocyte in shape. The results were subsequently compared with data gleaned from scanning electron microscopy and atomic force microscopy. Quaoaring has, however, proved to be unsuccessful in creating convincing objects, particularly those which should be echinocytic in appearance.

Registration of biplane angiography and intravascular ultrasound for 3D vessel reconstruction.

UNLABELLED: If planned and applied correctly, intra-vascular brachytherapy (IVB) can significantly reduce the risk of restenosis after interventional treatment of stenotic arteries. OBJECTIVES: In order to facilitate computer-based IVB planning, a three-dimensional reconstruction of the stenotic artery based on intravascular ultrasound (IVUS) sequences is desirable. METHODS: To attain a 3D reconstruction, the frames of the IVUS sequence are properly aligned in space and completed with additional intermediate frames generated by interpolation. The alignment procedure uses additional information that is obtained from biplane X-ray angiography performed simultaneously during the capturing of the IVUS sequence. After IVUS images and biplane angiography data are acquired from the patient, the vessel-wall borders and the IVUS catheter are detected by an active contour algorithm. Next, the twist between adjacent IVUS frames is determined by a sequential triangulation method combined with stochastic analysis. RESULTS: The above procedure results in a 3D volume-model of the vessel, which also contains information from the IVUS modality. This data is sufficient for computer-based intravascular brachytherapy planning. CONCLUSION: The proposed methodology can be used to improve the current state-of-the-art IVB treatment planning by enabling computerized dosage computations on a highly accurate 3D model.

Finite element simulation of skeletal muscular structures obtained from images of histological serial sections.

In this study, we present a method for the three-dimensional reconstruction of objects obtained from histological serial sections (exemplified by those of a pennate striated skeletal muscle) and its application to the finite element method. A hyperelastic material model is used for modeling biological soft tissue. The reconstruction process relies on the direct construction of a volumetric mesh using an octree approach which leads to a stable finite element method. Stability can be expressed in the spectral matrix condition number. To visualize stress patterns within the underlying anatomy the simulation results are projected onto images of the histological scenario.