Funding awarded: Next-Generation Simulation & Learning in Imaging-Based Biomedicine
Published:
We are excited to announce that the project Next-Generation Simulation and Learning in Imaging-Based Biomedicine (“FEniCS-in-the-Wild”) has been selected for funding by the Essential Open Source Software for Science (EOSS) program.
The EOSS program supports software maintenance, growth, development, and community engagement for open source tools critical to science, leveraging funding from The Chan-Zuckerberg Initiative, The Kavli Foundation and The Wellcome Trust. The project’s mission is to develop and integrate open computational geometry and simulation technology enabling digital twins in biomedicine via next-generation imaging-based modeling, simulation, optimization and learning.
Addressing knowledge and technology gaps
Over the last decades, biomedical imaging has advanced tremendously. For example, extremely detailed microscopy-based reconstructions of brain tissue are now openly available, while multimodal magnetic resonance imaging are widely collected as part of standard clinical practice. However, embedding such imaging data into most modeling and simulation pipelines remains time-consuming and error-prone. The FEniCS-in-the-Wild project aims to address this challenge by research and technology development for integrating state-of-the-art computational geometry and simulation technology platforms.
“This technology will form a backbone for digital twins in biomedicine: virtual models that can be used to understand and predict physiological responses affecting human health and disease,” says Chief Research Scientist Marie E. Rognes.
Collaborative effort for cutting-edge solutions
The project brings together the open source FEniCS Project (FEniCS) finite element software team at Simula Research Laboratory and the wildmeshing-toolkit (Wildmeshing) computational geometry team at the Courant Institute for Mathematical Sciences, New York University. The unified ambition is to establish a user-efficient pipeline for imaging-based multiphysics simulations across scales, with techniques such as uncertainty quantification, data assimilation, and scientific machine learning as inherently added value. The technology development and integration will be driven by use cases from biomedical research including clinical neurology, orthopedic surgery, and molecular biology.
“We are thrilled about this opportunity for our software projects, FEniCS and Wildmeshing, to join forces to create an integrated platform for next-generation imaging-based modeling, simulation, optimization and learning,” Rognes adds.
Project aims
To achieve its overarching ambition, the project aims to improve:
Usability: To make the integrated use of FEniCS and wildmeshing accessible to a broad user base, through continuous integration, unified documentation, and end-to-end tutorials;
Accessibility: To create a plugin for the popular biomedical software 3D Slicer to support the automatic creation of digital twins of biomedical systems;
Multiscale geometric representations: To extend wildmeshing to multi-material meshing and insertion of co-dimensional objects (tendons, cartilages) essential for many target applications;
Multiscale modeling and simulation: To improve support for biomedical simulations in FEniCS including multiscale features such as vasculature-tissue or membrane-cell interaction models.
Project details
The FEniCS-in-the-Wild project is hosted by Simula with the Courant Institute as the main partner and will be led by Marie E. Rognes. The duration of the project is two years, with a planned start date of July 1, 2024. For more information, see the announcement.
Associated contacts
Henrik Nicolay Finsberg
Email Henrik NicolayMarie E. Rognes
Email Marie E.Jørgen Dokken
Email Jørgen