Computational models of cardiac electrophysiology provided insights into arrhythmogenesis and paved the way toward tailored therapies in the last years. To fully leverage in silico models in future research, these models need to be adapted to reflect pathologies, genetic alterations, or pharmacological effects, however. A common approach is to leave the structure of established models unaltered and estimate the values of a set of parameters. Today's high-throughput patch clamp data acquisition methods require robust, unsupervised algorithms that estimate parameters both accurately and reliably. In this work, two classes of optimization approaches are evaluated: gradient-based trust-region-reflective and derivative-free particle swarm algorithms. Using synthetic input data and different ion current formulations from the Courtemanche et al. electrophysiological model of human atrial myocytes, we show that neither of the two schemes alone succeeds to meet all requirements. Sequential combination of the two algorithms did improve the performance to some extent but not satisfactorily. Thus, we propose a novel hybrid approach coupling the two algorithms in each iteration. This hybrid approach yielded very accurate estimates with minimal dependency on the initial guess using synthetic input data for which a ground truth parameter set exists. When applied to measured data, the hybrid approach yielded the best fit, again with minimal variation. Using the proposed algorithm, a single run is sufficient to estimate the parameters. The degree of superiority over the other investigated algorithms in terms of accuracy and robustness depended on the type of current. In contrast to the non-hybrid approaches, the proposed method proved to be optimal for data of arbitrary signal to noise ratio. The hybrid algorithm proposed in this work provides an important tool to integrate experimental data into computational models both accurately and robustly allowing to assess the often non-intuitive consequences of ion channel-level changes on higher levels of integration.
BACKGROUND AND OBJECTIVE: Progress in biomedical engineering has improved the hardware available for diagnosis and treatment of cardiac arrhythmias. But although huge amounts of intracardiac electrograms (EGMs) can be acquired during electrophysiological examinations, there is still a lack of software aiding diagnosis. The development of novel algorithms for the automated analysis of EGMs has proven difficult, due to the highly interdisciplinary nature of this task and hampered data access in clinical systems. Thus we developed a software platform, which allows rapid implementation of new algorithms, verification of their functionality and suitable visualization for discussion in the clinical environment. METHODS: A software for visualization was developed in Qt5 and C++ utilizing the class library of VTK. The algorithms for signal analysis were implemented in MATLAB. Clinical data for analysis was exported from electroanatomical mapping systems. RESULTS: The visualization software KaPAVIE (Karlsruhe Platform for Analysis and Visualization of Intracardiac Electrograms) was implemented and tested on several clinical datasets. Both common and novel algorithms were implemented which address important clinical questions in diagnosis of different arrhythmias. It proved useful in discussions with clinicians due to its interactive and user-friendly design. Time after export from the clinical mapping system to visualization is below 5min. CONCLUSION: KaPAVIE(2) is a powerful platform for the development of novel algorithms in the clinical environment. Simultaneous and interactive visualization of measured EGM data and the results of analysis will aid diagnosis and help understanding the underlying mechanisms of complex arrhythmias like atrial fibrillation.
Conference Contributions (18)
J. Schmid, and O. Dössel. An electromagnetic simulation environment, to construct microwave imaging algorithms. In Biomedizinische Technik. Biomedical Engineering, vol. 58(s1) , 2013
This paper is about the construction of an ultra- wideband microwave (UWB) simulation environment and about the construction of a model of the human head in- cluding regions of stroke. It calculates the propagation of microwaves within a wide frequency range through biolog- ical tissues. The simulations will be used to guide the de- velopment of a new system for early detection of stroke with UWB. The simulation has to be as close as possible to the real physiological properties of human tissues including the dispersive effects.
S. Bauer, T. Oesterlein, J. Schmid, and O. Dössel. Interactive visualization of cardiac anatomy and atrial excitation for medical diagnosis and research. In Current Directions in Biomedical Engineering, vol. 1(1) , pp. 400-404, 2015
State of the art biomedical engineering allows for acquiring enormous amounts of intracardiac data to aid diagnosis and treatment of cardiac arrhythmias. Modern catheters, which are used to acquire electrical information from within the heart, are capable of recording up to 64 channels simultaneously. The software available for data analysis, however, does not provide adequate performance to neither analyze nor visualize the acquired information in an appropriate manner. We present a software package that fascilitates interdisciplinary collaborations between engineers and physicians to adress open questions about pathophysiological mechanisms using data from everyday electrophysiogical studies. Therefore, a package has been compiled that enables algorithm development using MATLAB and subsequent visualization using the VTK C++ class libraries. The resulting application KaPAVIE, which is presented in this paper, is designed to meet the requirements from the clinical side and has been successfully applied in the clinical environment.
Generally, models of cardiac electrophysiology describe physiologic conditions in detail. However, other conditions, such as drug interactions or mutations of ion channels are of interest for research. Therefore, the simulated ion currents have to be fitted to measured voltage or patch clamp data. In this work, three different methods for the model parametrization were compared: one based on Powells algorithm implemented in a modular C++ framework and two optimization techniques realized in Matlab. The latter two approaches differed in solving the ordinary differential equations describing the channel gating. They can either be approximated numerically or solved analytically, since the transmembrane voltage is a piecewise constant function during the applied clamp protocol. All three methods were compared regarding computing time and quality of the fit using least squares. The modular C++ framework was slower than the numerical Matlab method, which took longer than the analytical one. The quality of the fit was similar for almost all analyzed methods. Therefore, the analytical method grants a fast and reliable solution for the calibration of ion current models for applications with constant membrane voltage, as e.g. in case of voltage or patch clamp data.
J. Schmid. Microwave Imaging for Stroke Diagnostics. Dissertation. 2016
Microwave imaging can offer a non-harmful and mobile way of imaging strokes. In this work three imaging algorithms are introduced and the tests whether they are able to image cerebral bleeding are published. Additionally, it contains the development of a phantom with permittivities comparable to a human head.
Student Theses (3)
J. Schmid. Optimierte Parameteranpassung für Simulationen der menschlichen Vorhofelektrophysiologie. Institute of Biomedical Engineering, Karlsruhe Institute of Technology (KIT). Diplomarbeit. 2012