Ellerweg, Roland

Hale, Jack

Weir, Phil

Open Repository and Bibliography - Luxembourg

Orchestrating clinical simulation with FEniCSPhil Weir, NUMA Engineering Services Ltd.. phil.weir@flaxandteal.co.uk,Roland Ellerweg, Fraunhofer Institute of Technology, roland.ellerweg@fit.fraunhofer.de,Jack S. Hale, University of Luxembourg, jack.hale@uni.luKeywords: clinical domain model, containerization, web, clinical simulation, Docker, mini-mally invasive cancer treatment.In a clinical research environment, it is necessary to perform simulations where geometryand parameters are configured at runtime, often by users with significant clinical experience, butwithout deep knowledge of programming or numerical tools. Providing an online interface forboth clinical and technical users, not fixed to pre-existing models or medical equipment, requiresadaptable and comprehensive numerical libraries for technical end-users to build upon. FEniCSis well-placed to fulfil this need, supported by the breadth of Python.The Go-Smart EU-FP7 Project (http://gosmart-project.eu) implements this within the fieldof minimally invasive cancer treatments, by establishing a web-based platform for clinical train-ing, numerical model validation and interdisciplinary research [1].Within this project, FEniCS provides steady-state solutions for energy deposition duringmicrowave tumour ablation, using transverse-magnetic axisymmetric Maxwell’s equations cou-pled to Pennes’ bioheat equation, with an empirically-derived nonlinear dependence of electricalparameters on tissue temperature [2]. Integrated FEniCS support assists technical end-users inincorporating their own numerical models of minimally invasive treatments.Figure 1: Go-Smart web interface launching a simulation. The input form is dynamicallygenerated based on the choice of equipment, clinical protocol and a numerical model.The web interface allows users to segment image data, graphically place percutaneous nee-dles and enter clinical procedure steps, which are made available to modellers’ code throughPython objects. Modellers and manufacturers may combine simulation models, clinical proto-cols, patient-specific measurements and equipment parameter sets through the web interface.A Python server, Glossia (https://github.com/go-smart/glossia), enables remote manage-ment of simulations over standard web protocols. All software is containerised using Docker toensure security, efficiency, reproducibility and system independence [3].References[1] P. T. Weir, D. Reuter, R. Ellerweg, T. Alhonnoro, M. Pollari, P. Voglreiter, P. Mariap-pan, R. Flanagan, C. S. Park, S. Payne, E. Staerk, P. Voigt, M. Moche and M. Kolesnik:Go-Smart: Web-based Computational Modeling of Minimally Invasive Cancer TreatmentsIEEE International Conference on e-Health and Bioengineering, 2015.[2] Z. Ji and C. L. Brace: Expanded modeling of temperature-dependent dielectric propertiesfor microwave thermal ablation Physics in medicine and biology, 56.16 (2011): 5249.[3] J. S. Hale, L. Li and G. N. Wells: FEniCS in Linux Containers (poster) FEniCS Workshop,Imperial College London, 2015.

Orchestrating clinical simulations with FEniCS

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Orchestrating clinical simulations with FEniCS

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