ReaDDy-Cell is a whole-cell digital twin simulation framework built on the ReaDDy particle-based reaction-diffusion platform. This implementation enables simulation of mitochondrial dynamics and intracellular transport directly from 4D lattice light-sheet microscopy (LLSM) data. For full details, check out our preprint on BioxRiv! Whole-cell particle-based digital twin simulations from 4D lattice light-sheet microscopy data
- Active Transport (Untreated Control)
- ️Intermediate Perturbation (Nocodazole 30 min)
- Passive Transport (Nocodazole 60 min)
- ReaDDy-Made-Models (RMM): Image-guided stochastic procedural generation method for constructing particle-based models from imaging data.
- Automated Digital Twin Construction: Factory methods for building spatially explicit, particle-based models of mitochondria, microtubules, plasma membrane, and nuclear membrane from live-cell imaging data.
- Passive & Active Transport Dynamics: Simulates mitochondrial diffusion and directed motor-driven active transport along microtubule topologies.
- In-Browser Visualization: Simulation trajectories are rendered using Simularium.
- OS: Ubuntu 20.04+
- Conda: Miniconda or Anaconda
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Create and activate a conda environment:
conda create -n readdy-cell python=3.11 conda activate readdy-cell
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Install python and build dependencies:
pip install -r requirements.txt
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Set up conan for C++ dependencies:
conan profile detect
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Compile the project:
./compile.sh
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Run the simulation:
cd readdy_cell python main.py -
Visualize the trajectory:
Open Simularium Visualizer in your browser and drop the
.simulariumfile onto the window to visualize.
ReaDDy-Cell builds upon the excellent work of the ReaDDy project. We thank the original authors and contributors for making their software open-source and extensible.