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Funded project, 2023 Spatial Model Editor
3D Spatial Modelling
Total developer time: 2 years
Contact person: Dr. Sven Sahle, Bioquant, COS
Outline
Spatial Model Editor provides a user friendly GUI editor to create and edit spatial SBML models of bio-chemical reactions and simulate them using the dune-copasi solver for reaction-diffusion systems. The goal of this project is to extend the software from two-dimensional to three-dimensional spatial models, which involves multiple aspects including image segmentation, meshing, PDEs and SBML.
Results
- Added support for import and export of 3d SBML models
- Extended Pixel solver to support 3d and anisotropic voxels
- In progress: Automatic segmentation and meshing of voxel geometry
- In progress: Visualization of generated 3d meshes
