The paper is addressed to detect the parameters of a sphere-center coordinates and radius based on a stack of CT slices. It is proposing a new hierarchical Hough transform approach. In the first step, all slices are taken into consideration sequentially and a 2D accumulator array is used to obtain the coordinates (x"0,y"0), the projecting value of the sphere center into every X-Y-plane. In this step, also a new type of 2D Hough transform for circle or circular detection is proposed based on an effective point filtering. In the second step, the radii of the circles in the different slices are obtained using 1D accumulator arrays. In the last step, the coordinate z"0 and the radius R of the sphere are acquired using a 2D planar Hough transform based on the correlation between the radii of circles, the coordinates z of the slice and the sphere radius. The hierarchical Hough transform is applied to analyze the structure of femoral head of human hip joints. Compared to the established Hough transform techniques for 3D object detection, the hierarchical Hough transform reduces storage space and calculation time significantly and it has a good robustness to noise in the images.
Cardiac arrhythmia is currently investigated from two different points of view. One considers ECG bio-signal analysis and investigates heart rate variability, baroreflex control, heart rate turbulence, alternans phenomena, etc. The other involves building computer models of the heart based on ion channels, bio-domain models and forward calculations to finally reach ECG and body surface potential maps. Both approaches aim to support the cardiologist in better understanding of arrhythmia, improving diagnosis and reliable risk stratification, and optimizing therapy. This article summarizes recent results and aims to trigger new research to bridge the different views.
E. Hughes, B. Taccardi, and F. B. Sachse. A heuristic streamline placement technique for visualization of electrical current flow. In J Flow Visualization and Image Processing, vol. 13(1) , pp. 53-66, 2006
Streamline techniques are frequently applied for scientific visualization of two- and three-dimensional electric fields. Streamline distributions are expected to reflect important features of the underlying fields such as the locations of sources and sinks as well as variations of the field density. Streamline techniques fulfilling these demands in arbitrary fields are currently not developed.In this work, we present a heuristic technique, which aims at creating a linear relationship between a streamline distribution and the density of an underlying electric current field. The technique is based on a sequential optimization algorithm for placement of seed points of streamlines. In each step, a set of random trial seed points is created. Each point of the trial set is temporarily added to the set of best seed points. Streamlines are generated from the enhanced set and the fit of their distribution and the field density is determined. The best point is selected and added to the set of best seed points. The iteration ends after generation of a pre-given number of best seed points. Several examples illustrate results of this technique applied to electric current fields of small complexity and in more extensive cardiothoracic electric fields. Additionally, we characterized, with statistical studies, the influence of parameters of the algorithm on the relationship between streamline distribution and field density.
Investigating the mechanisms underlying the genesis and conduction of electrical excitation in the atria at physiological and pathological states is of great importance. To provide knowledge concerning the mechanisms of excitation, we constructed a biophysical detailed and anatomically accurate computer model of human atria that incorporates both structural and electrophysiological heterogeneities. The three-dimensional geometry was extracted from the visible female dataset. The sinoatrial node (SAN) and atrium, including crista terminalis (CT), pectinate muscles (PM), appendages (APG) and Bachmann's bundle (BB) were segmented in this work. Fibre orientation in CT, PM and BB was set to local longitudinal direction. Descriptions for all used cell types were based on modifications of the Courtemanche et al. model of a human atrial cell. Maximum conductances of Ito, IKr and ICa,L were modified for PM, CT, APG and atrioventricular ring to reproduce measured action potentials (AP). Pacemaker activity in the human SAN was reproduced by removing IK1, but including If, ICa,T, and gradients of channel conductances as described in previous studies for heterogeneous rabbit SAN. Anisotropic conduction was computed with a monodomain model using the finite element method. The transversal to longitudinal ratio of conductivity for PM, CT and BB was 1:9. Atrial working myocardium (AWM) was set to be isotropic. Simulation of atrial electrophysiology showed initiation of APs in the SAN centre. The excitation spread afterwards to the periphery near to the region of the CT and preferentially towards the atrioventricular region. The excitation extends over the right atrium along PM. Both CT and PM activated the right AWM. Earliest activation of the left atrium was through BB and excitation spread over to the APG. The conduction velocities were 0.6ms-1 for AWM, 1.2ms-1 for CT, 1.6ms-1 for PM and 1.1ms-1 for BB at a rate of 63bpm. The simulations revealed that bundles form dominant pathways for atrial conduction. The preferential conduction towards CT and along PM is comparable with clinical mapping. Repolarization is more homogeneous than excitation due to the heterogeneous distribution of electrophysiological properties and hence the action potential duration.
OBJECT: Multiple contrasts are often helpful for a comprehensive diagnosis. In 3D abdominal MRI, breath-hold techniques are preferred for single contrast acquisitions to avoid respiratory artifacts. In this paper, highly accelerated parallel MRI is used to acquire large 3D abdominal volumes with two different contrasts within a single breath-hold. MATERIAL AND METHODS: In vivo studies have been performed on six healthy volunteers, combining T (1)- and T (2)-weighted, gradient- or spin-echo based scans, as well as water/fat resolved imaging in a single breath-hold. These 3D scans were acquired with an acceleration factor of six, using a prototype 32-element receive array. RESULTS: The presented approach was tested successfully on all volunteers. The whole liver area was covered by a FOV of 350 x 250 x 200 mm(3) for all scans with reasonable spatial resolution. Arbitrary scan protocols generating different contrasts have been shown to be combinable in this single breath-hold approach. Good spatial correspondence with negligible spatial offset was achieved for all different scan combinations acquired in overall breath-hold times between 15 and 25 s. CONCLUSION: Enabled by highly parallel imaging technology, this study demonstrates the technical feasibility and the promising image quality of single breath-hold dual contrast MRI.
PURPOSE: To demonstrate a rapid MR technique that combines imaging and R2* mapping based on a single radial multi-gradient-echo (rMGE) data set. The technique provides a fast method for online monitoring of the administration of (super-)paramagnetic contrast agents as well as image-guided drug delivery. MATERIALS AND METHODS: Data are acquired using an rMGE sequence, resulting in interleaved undersampled radial k-spaces representing different echo times (TEs). These data sets are reconstructed separately, yielding a series of images with different TEs used for pixelwise R2* mapping. A fast numerical algorithm implemented on a real-time reconstruction platform provides online estimation of the relaxation rate R2*. Simultaneously the images are summed for the computation of a high-resolution image. RESULTS: Convenient high-resolution R2* maps of phantoms and the liver of a healthy volunteer were obtained. In addition to stable intrinsic baseline maps, the proposed technique provides particularly accurate results for the high relaxation rates observed during the presence of (super-)paramagnetic contrast agents. Assuming that the change in R2* is proportional to the concentration of the agent, the technique offers a rough estimate for dynamic dosage. CONCLUSION: The simultaneous online display of morphological and parametric information permits convenient, quantitative surveillance of contrast-agent administration.
M. Reumann, M. Mohr, O. Dössel, and A. Diez. Vorlesung, Übung und Tutorium im koordinierten Zusammenspiel. Ein Lehr-/Lernpaket schnüren - Grundlagenveranstaltung. Berendt, Brigitte, 2006.
Book Chapters (1)
O. Dössel. Mathematische Modelle vom Herzen. In Debatte - Mathematisierung der Natur, Berlin-Brandenburgische Akademie der Wissenschaften, pp. 83-85, 2006
Mathematisierung der NaturStreitgespräche in den Wissenschaftlichen Sitzungen der Versammlung der Berlin-Brandenburgischen Akademie der Wissenschaftenam 10. Dezember 2004 und 27. Mai 2005
Conference Contributions (31)
J. Bohnert, M. Reumann, T. Faber, and O. Dössel. Investigation of curative ablation techniques for atrial fibrillation in a computer model. In Gemeinsame Jahrestagung der Deutschen, der Österreichischen und der Schweizerischen Gesellschaft für Biomedizinische Technik, 2006
O. Dössel. Funktionelle Computermodelle des Patienten für Diagnose und Therapie. In VDE-Kongress 2006 - Innovations for Europe - Fachtagungsberichte der ITG/BMBF - GMM - ETG - GMA - DGBMT, pp. 443-447, 2006
Nachdem in der Vergangenheit statische Computermodelle von der Anatomie des Patienten entwickelt wurden, stehen heute funktionelle Modelle im Vordergrund der Forschung, in denen beispielsweise Bewegungsabläufe oder physiologische Prozesse im Körper modelliert werden. Zielsetzung ist das bessere Verständnis der funktionellen Prozesse (Grundlagenforschung), die vertiefende Diagnose (Etiologie, Erkennen der Ursachen einer Erkrankung) und die systematische Optimierung der Therapie. Daneben können auch Lern-Werkzeuge für Ärzte daraus abgeleitet werden (Learning and Training). Um zu diesen Zielen zu gelangen, müssen funktionelle Vorgänge im Körper quantitativ verstanden und modelliert werden (Mathematical Physiology, Computational Biology). Erst die mathematische Beschreibung erlaubt die sichere Vorhersage. Vor Erreichen dieses Zieles ist viel Grundlagenforschung nötig, da viele funktionelle Abläufe im Körper noch nicht quantitativ bekannt sind. Oft bedeutet dies, dass Erkrankungen bis zur zellulären Ursache und bis zu den komplexen biologischen Regelkreisen mathematisch beschrieben werden müssen
P. Jones, W. Cascio, and F. B. Sachse. Design of an experimental setup for confocal imaging of cardiac microstructure. In Proc. 2nd Annual Mountain West Biomedical Engineering Conference, 2006
D. U. J. Keller, G. Seemann, D. L. Weiss, and O. Dössel. Detailed anatomical modeling of human ventricles based on diffusion tensor MRI. In Gemeinsame Jahrestagung der Deutschen, der Österreichischen und der Schweizerischen Gesellschaft für Biomedizinische Technik, vol. 50/1, 2006
Atrial fibrillation (AF) is a common cardiac disease with high rates of morbidity, leading to major personal and NHS costs. Computer modeling of AF using a detailed cellular model with realistic 3D anatomical geometry allows investigation of the underlying ionic mechanisms in far more detail than in a physiology laboratory. We have developed a 3D virtual human atrium that combines detailed cellular electrophysiology, including ion channel kinetics and homeostasis of ionic concentrations, with anatomical detail. The segmented anatomical structure and multi-variable nature of the system makes the 3D simulations of AF large and computationally intensive. The computational demands are such that a full problem solving environment requires access to resources of High Performance Computing (HPC), High Performance Visualization (HPV), remote data repositories and a backend infrastructure. This is a classic example of eScience and Gridenabled computing. Initial work has been carried out using multiple processor machines with shared memory architectures. As spatial resolution of anatomical models increases, requirement of HPC resources is predicted to increase many-fold ( ~ 1 10 teraflops). Distributed computing is essential, both through massively parallel systems (a single supercomputer) and multiple parallel systems made accessible through the Grid.
T. G. McNary, K. Sohn, B. Taccardi, and F. B. Sachse. Mechano-Electrical feedback mechanisms in cardiac tissue: Experimental setup and preliminary measurement results. In Proc. 2nd Annual Mountain West Biomedical Engineering Conference, 2006
In the diagnosis of coronary artery disease, 3D-multi-slice computed tomography (MSCT) has recently become more and more important. In this work, an anatomical-based method for the segmentation of atherosclerotic coronary arteries in MSCT is presented. This technique is able to bridge severe stenosis, image artifacts or even full vessel occlusions. Different anatomical structures (aorta, blood-pool of the heart chambers, coronary arteries and their orifices) are detected successively to incorporate anatomical knowledge into the algorithm. The coronary arteries are segmented by a simulated wave propagation method to be able to extract anatomically spatial relations from the result. In order to bridge segmentation breaks caused by stenosis or image artifacts, the spatial location, its anatomical relation and vessel curvature-propagation are taken into account to span a dynamic search space for vessel bridging and gap closing. This allows the prevention of vessel misidentifications and improves segmentation results significantly. The robustness of this method is proven on representative medical data sets.
M. S. Renno, Y. Shang, J. Sweeney, and O. Dössel. Segmentation of 4D cardiac images: investigation on statistical shape models. In Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference, vol. 1, pp. 3086-3089, 2006
The purpose of this research was two-fold: (1) to investigate the properties of statistical shape models constructed from manually segmented cardiac ventricular chambers to confirm the validity of an automatic 4-dimensional (4D) segmentation model that uses gradient vector flow (GVF) images of the original data and (2) to develop software to further automate the steps necessary in active shape model (ASM) training. These goals were achieved by first constructing ASMs from manually segmented ventricular models by allowing the user to cite entire datasets for processing using a GVF-based landmarking procedure and principal component analysis (PCA) to construct the statistical shape model. The statistical shape model of one dataset was used to regulate the segmentation of another dataset according to its GVF, and these results were then analyzed and found to accurately represent the original cardiac data when compared to the manual segmentation results as the golden standard.
M. Reumann, J. Bohnert, and O. Dössel. Simulating pulmonary vein activity leading to atrial fibrillation using a rule-based approach on realistic anatomical data. In Conf Proc IEEE Eng Med Biol Soc., vol. 1, pp. 3943-3946, 2006
Atrial fibrillation (AF) is the most common cardiac arrhythmia leading to a high rate of stroke. The underlying mechanisms of initiation and maintenance of AF are not fully understood. Several findings suggest a multitude of factors to leave the atria vulnerable to AF. In this work, a rule-based approach is taken to simulate the initiation of AF in a computer model for the purpose of generating a model with which the influence of anatomical structures, electrophysiological properties of the atria and arrhythmogenic activity can be evaluated. Pulmonary vein firing has been simulated leading to AF in 65.7 % of all simulations. The excitation pattern generated resemble chaotic excitation behavior, which is characteristic for AF as well as stable reentrant circuits responsible for atrial flutter. The findings compare well with literature. In future, the presented computer model of AF can be used in therapy planning such as ablation therapy or overdrive pacing.
Question: The mechanisms responsible for atrial fibrillation (AF) are not completely understood. Various conduction velocities and realistic anatomical structures of the atria are implemented into a computer model showing the influence of complex anatomical structures on the initiation and maintenance of AF.Method Used: In a computer model of the Visible Female heart (National Library of Medicine, Bethseda, Maryland, USA), the initiation of AF was simulated by pulmonary vein (PV) firing. The anatomical model had a resolution of 1,696,740 tissue voxel with 0.33 mm voxel side length. 32 foci around all pulmonary veins were set. The excitation propagation was simulated using an adaptive cellular automaton. Electrophysiological parameters depending on different tissue types can be set. In this work, only the conduction velocity was reduced compared to physiological data.Results: The initiation of AF through ectopic foci creates re-entrant circuits and quasi-chaotic excitation pattern in the computer model. 8 of 16 foci in the left superior, 3 of 4 foci in the left inferior, 5 of 8 foci in the right superior and 4 of 4 foci in the right inferior PV created AF after only 1.5 s. The excitation pattern shows stable re-entrant circuits as well as chaotic behavior. A breakup of stable re-entrant circuits was also observed when simulating the pathology for 17.5 s. The other foci caused self-terminating rotors.Conclusion: Computer models of the excitation propagation of the heart can be used to simulate AF initiated by triggers in the PV. A reduction in conduction velocity caused the establishment of re-entrant circuits and quasi-chaotic behavior. The complex model of the Visible Female heart showed the importance of anatomical structures in the maintenance of AF. Future work will include an improvement of the computer model by incorporating heterogeneities of atrial tissue and an implementation of individual patient models for therapy planning.
M. Reumann, B. Osswald, S. Hagl, and O. Dössel. Computer aided evaluation of preventive atrial antitachycardial pacing. In 15th World Congress in Cardiac Electrophysiology and Cardiac Techniques - Cardiostim 2006. Europace, vol. 8(Supplement 1) , pp. 213-216, 2006
M. Reumann, B. Osswald, S. Hagl, and O. Dössel. Computer-based Evaluation of Atrial Antitachycardial Pacing to Prevent Atrial Fibrillation on Realistic Anatomical Data. In Gemeinsame Jahrestagung der Deutschen, der Österreichischen und der Schweizerischen Gesellschaft für Biomedizinische Technik, 2006
F. B. Sachse. Modeling of Cardiac Contraction. In 3rd International Symposium of Cell/Biodynamics Simulation Project. Medical Systems Biology of the Heart, pp. 3, 2006
Computational modeling and simulation can provide important insights into the electrical and electrophysiological properties of cells, tissues, and organs. Commonly, the modeling is based on Maxwell's and Poisson's equations for electromagnetic and electric fields, respectively, and numerical techniques are applied for field calculation such as the finite element and finite differences methods. Focus of this work are finite element methods, which are based on an element-wise discretization of the spatial domain. These methods can be classified on the element's geometry, e.g. triangles, tetrahedrons and hexahedrons, and the underlying interpolation functions, e.g. polynomials of various order. Aim of this work is to describe finite element-based approaches and their application to extend the problem-solving environment SCIRun/BioPSE. Finite elements of various types were integrated and methods for interpolation and integration were implemented. General methods for creation of finite element system matrices and boundary conditions were incorporated. The extension provides flexible means for geometric modeling, physical simulation, and visualization with particular application in solving bioelectric field problems.
F. B. Sachse, G. Seemann, and B. Taccardi. Relationship of Strain and Conduction Velocity in Cardiac Muscle in the High Strain Range. In Biophys. J (Annual Meeting Abstracts), pp. 2644, 2006
S. Seitz, A. Khawaja, and O. Dössel. PCA-based method for clustering T-waves. In Gemeinsame Jahrestagung der Deutschen, der Österreichischen und der Schweizerischen Gesellschaft für Biomedizinische Technik, 2006
Y. Shang, G. Su, and O. Dössel. Hierarchical 3D shape model for segmentation of 4D MR cardiac images. In Lecture Notes in Computer Science. Medical Imaging and Augmented Reality, vol. 4091, pp. 333-340, 2006
A novel method for the segmentation of 4D MR cardiac images is introduced in this paper. The method improves the traditional active shape model method by adopting an 3D spatially hierarchical expression of the shape model, which is used as an internal regulation force during the segmentation process. Generation of the landmarks for constructing the shape model is based on the active surface method itself utilizing the long range image force, gradient vector flow (GVF). For constructing hierarchical statistical shape models, initial landmarking is done on a manually segmented training set with different spatial resolutions. Principal component analysis is then used to derive the hierarchical expression of the shape model. Experimental results for 4D MR cardiac image segmentation are presented.
J. P. Thiele, and O. Dössel. Fast optical recording of membrane potential in rat trabecular muscle with a triggered CCD-system: a preliminary study. In Gemeinsame Jahrestagung der Deutschen, der Österreichischen und der Schweizerischen Gesellschaft für Biomedizinische Technik, vol. 51(V 175) , 2006
J. Bohnert. Untersuchung von Ablationslinienführungen zur Therapie von Vorhofflimmern am Computermodell. Institut für Biomedizinische Technik, Universität Karlsruhe (TH). Dissertation. 2006
A. Khawaja. Automatic ECG analysis using principal component analysis and wavelet transformation. Universitätsverlag. Dissertation. 2006
The main objective of this book is to analyse and detect small changes in ECG waves and complexes that indicate cardiac diseases and disorders. Detecting predisposition to Torsade de Points (TDP) by analysing the beat-to-beat variability in T wave morphology is the main core of this work. The second main topic is detecting small changes in QRS complex and predicting future QRS complexes of patients. Moreover, the last main topic is clustering similar ECG components in different groups.
M. B. Mohr. A hybrid deformation model of ventricular myocardium. Universität Karlsruhe (TH). Dissertation. 2006
Student Theses (3)
Y. Jiang. Modeling and imaging of the repolarization of the human heart. Institut für Biomedizinische Technik, Universität Karlsruhe (TH). Masterarbeit. 2006
D. U. J. Keller. Detailed anatomical and electrophysiological modeling of human ventricles based on diffusion tensor MRI. Institute of Biomedical Engineering, Universität Karlsruhe (TH). Diplomarbeit. 2006
The importance of a detailed model characterizing the fiber orientation of the ventricular my- ocardium is unquestioned when it comes to simulating excitation conduction processes. It was therefore the scope of this work to provide the necessary tools to create rules that describe the fiber orientation in various parts of both left and right ventricle. This was not previously possible, as a single rule was utilized for the complete left ventricle whereas the right ventricle could not be characterized at all. The additional rules were created by subdividing the ventricular anatomy in a certain number of segments. A single rule was now determined for every automatically generated segment that characterizes the course of the fiber orientation. The number of segments can be set depending on the desired density with which the rules, describing the muscle fiber orientation, are determined. A higher number of rules leads to a more realistic description of the genuine fiber orientation. On the other hand however, a large number of rules is more difficult to create and verify.The results presented in chapter 6 underline, that a single rule as it has previously been used is not able to depict the regional differences of the fiber orientation. Especially the transverse an- gle showed variations from apex to base that are in agreement with other literature reports (see [18, 19]). The transmural fluctuations of the transverse angles agreed with the work of Scollan  while the presence of a non-zero transverse angle conflicted with reports from Rijcken, Bovendeerd and Ubbink at the same time [24, 25].The generated results should be confirmed by the investigation of additional DTMRI datasets. An increased spatial resolution of the datasets would furhermore support the extraction of rules from the right ventricle which was very problematic in the dataset at hand, due to the limited number of voxels that constitute the right ventricular wall.Future work should focus on the definition of additional subdivisions in the left ventricular apex. Presently, there is no reasonable allocation implemented and an extraction of fiber orientation rules therefore not possible (see chapter 6). Additionally, the manual segmentation procedure which turned out to be time-consuming and slightly inaccurate can be improved by including the available information inherent in the diffusion data (see chapter 5.5). Finally, it is important to investigate the full impact of the created fiber orientation model which is only possible by simulating the excitation conduction process in the complete ventricle. As a prerequisite for these simulations, the encountered problems described in chapter 7 have to be overcome and the concept of exchanging data based on shared-memory should be extended to allow the handling of datasets with a high spatial resolution.
S. Seitz. Analyse der T-Welle des EKG mit Hilfe von Cluster-Verfahren. Institut für Biomedizinische Technik. Diplomarbeit. 2006