PyGen

PyGen is a dynamic cellular simulation tool designed for modelling cellular interactions within diverse three-dimensional tissue architectures. This tool leverages various mechanical, geometric, and life-event forces to mirror the adaptability of cellular spatial configurations across varied tissue landscapes.

Requirements

Ensure you have the following packages installed:

• numpy
• scipy
• h5py
• imageio
• vispy
• python 3

You can typically install these using pip:

pip install numpy scipy h5py imageio vispy

Codebase

The project comprises four main files:

1. runme.py: The primary script for executing simulations.
2. pygen.py: The central engine fo the simulation.
3. simulation.py: Designed for executing visualisations in real time.
4. playback.py: It contains a class for visualising evolution through files.

Usage

To use PyGen, follow these steps:

1. Clone or download this repository to your local computer.
2. Navigate to the project directory.
3. Run the simulation using the following command:

python runme.py --type [simulation_type] --C [initial_number_of_cells] --S [time_steps] --B [geometric_background]

Parameters:

• simulation_type: Determines the mode of the simulation.

  • realtime: Visualize the evolution in real time.
  • offline: For larger simulations. Records the evolution in a file before visualization.
  • file: To visualize pre-recorded simulations.

• initial_number_of_cells: The initial number of cells in the ensemble. (Integer value.)

• time_steps: Define the number of simulation steps. (Integer value.)

• geometric_background: Specifies the target geometry of the tissue architecture. Options include:

  • sphere
  • torus
  • wfoil
  • wknot
  • cylinder
  • beltrami
  • cylinder

Alternatively, you can import or generate your own point clouds utilising the notebook generate_points.ipynb within tools.

Tweaking Additional Parameters:

Within runme.py, users can adjust several parameters for more refined simulations:

    """ 
        Adjustable parameters for the simulation
    """
    a = 1e-2 * np.ones((N_cells))     # Cell-cell repulsion
    k = 1e-2 * np.ones((N_cells))     # Cell-cell adhesion
    l0 = 1e-2                         # Cell-cell equilibrium distance
    gamma = 1.0 * np.ones((N_cells))  # Cell-tissue surface tension
    division = 100                    # Integer values for cell divisions
    death = 50                        # Integer values for cell deaths

Adjust these parameters as needed to fit your specific requirements.

Example

Edit the runme.py file, then tweak these parameters:

    a = 1e-2 * np.ones((N_cells))
    k = 1e-2 * np.ones((N_cells))
    l0 = 1e-2
    gamma = 1.0 * np.ones((N_cells))
    division = 100
    death = 50

Open a terminal window, go to the folder's project and execute the following command line:

python runme.py --type file --C 500 --S 3000 --B foil

This will execute a simulation file containing 500 cells evolving over a foil background. In the simulation, 100 cells will be divided, while 50 of them will be killed.

Maintenance

For any further queries or issues, feel free to open an issue on this repository or contact the maintainer.

jesus [dot] fuentes [at] uni [dot] lu