Next-generation simulation and learning in imaging-based biomedicine

This project brings together the FEniCS Project (FEniCSx) finite element software team at Simula Research Laboratory, Oslo, Norway, and the wildmeshing-toolkit (wildmeshing) computational geometry team at the Courant Institute, New York, USA. The overall project ambition is a user-efficient pipeline for imaging-based multiphysics simulations across scales, with advanced techniques such as uncertainty quantification, data assimilation, and physics-based machine learning as inherently added value. The technology development and integration will be driven by use cases from biomedical research through well-established collaborations, including in clinical neurology (brain clearance, drug delivery, and neurovascular coupling), cellular mechanobiology (long-term potentiation), orthopedic surgery (hip joint motion), and molecular biology (autophagy in cancer). To achieve its overarching ambition, the project aims -To make the integrated use of FEniCSx and wildmeshing accessible to a broad user base, through continuous -integration, unified documentation, and end-to-end tutorials (WP1); -To create a plugin for the popular biomedical software 3D Slicer to support the automatic creation of digital twins of biomedical systems (WP2); -To extend wildmeshing to multi-material meshing and insertion of co-dimensional objects (tendons, cartilages) essential for many target applications (WP3); -To improve support for biomedical simulations in FEniCSx including multiscale features such as vasculature-tissue or membrane-cell interaction models (WP4).