CellSys is a modular software tool designed for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in both 2D and 3D. It implements an agent-based model that treats cells as isotropic, elastic, and adhesive objects, with cell migration modeled by equations of motion. The software includes modules for real-time 3D visualization, VRML 2.0 support, and the ability to vary cell and environment parameters independently. This allows for species-specific simulations and detailed analyses of growth dynamics and links between cellular and multi-cellular phenotypes. CellSys is freely available for non-commercial use and has been used to model liver regeneration and other multi-cellular phenomena, with results validated against experimental data. The software is implemented in ANSI C++ and is cross-platform, with a graphical user interface for interactive exploration and parameter adjustment. Future versions will include additional functionalities, such as modeling of surrounding tissue and vascular networks.CellSys is a modular software tool designed for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in both 2D and 3D. It implements an agent-based model that treats cells as isotropic, elastic, and adhesive objects, with cell migration modeled by equations of motion. The software includes modules for real-time 3D visualization, VRML 2.0 support, and the ability to vary cell and environment parameters independently. This allows for species-specific simulations and detailed analyses of growth dynamics and links between cellular and multi-cellular phenotypes. CellSys is freely available for non-commercial use and has been used to model liver regeneration and other multi-cellular phenomena, with results validated against experimental data. The software is implemented in ANSI C++ and is cross-platform, with a graphical user interface for interactive exploration and parameter adjustment. Future versions will include additional functionalities, such as modeling of surrounding tissue and vascular networks.