Onco*: An umbrella Python framework for modelling and simulation of oncological scenarios

The umbrella software Onco* provides a workflow for patient-specific tumour simulations. The general framework is exemplarily shown for brain tumours, where users are allowed to input medical image data or work with benchmark geometries. Three pre-processing Python packages generalise the magnetic resonance imaging series of the brain and segments the tumour and the heterogeneous microstructure of the tissue. The interpretation of collected information is followed by numerical simulations in a package, where users have the option to use pre-implemented model set-ups. These model set-ups can be customised, where each entity is editable, providing flexibility for ongoing development in the interdisciplinary field of tumour prediction. Two examples from a provided tutorial demonstrate the workflow and its capabilities from patient-specific and academic geometry input to potential tumour evolutions. • Allows automatic processing of strongly distorted MRI scans due to a tumour disease • Flexible workflow using gold-standard MRI modalities or any available subset as input • Modular design allows easy modification, replacement, and expansion • Its modular setup allows testing, comparing, and improving tasks and their interplay • A bi-phasic porous media model with extendable components serves as test setup