Simulator GUI

Starting the GUI

The GUI can be started from command line by entering trait2d_simulator_gui. The GUI and its components are described below.

Description of the GUI

_images/simulator_gui.png
    1. Select the free diffusion model
    2. Select the hopping difffusion model
  2. Parameter: maximal total length ( Tmax ) in seconds: This is the maximum simulation duration. The simulation might be short if the particle diffuses out of the simulation volume.
  3. Parameter: time step ( dt ) in seconds: This is the temporal discretization of the simulation domain.
  4. Parameter: sandbox length ( L ) in m: This is the physical size of the simulation domain.
  5. Parameter: compartment map pixel size ( dL ) in m: This is the physical discretization of the simulation domain.
  6. Parameter: free diffusion coefficient ( Df ) in m²/s
  7. Parameter: average compartment diameter / length ( HP **) in m. This parameter is used by the hopping diffusion model.
  8. Parameter: Hopping probability ( HL ), between 0 and 1: Describes the probability of hopping diffusion, e.g. the probability of changing hopping diffusion cells.
  9. Parameter: Random generator seeds ( seed , integer): This ia an optional integer used to initialize the random number generator. This is mostly used for reproducibility (initializing a simulation with a given seed will give the same simulation results every time). Keep empty to use a random seed.
  10. Run the diffusion simulation using the diffusion model selected in 1a/1b, and the diffusion parameters described by 2-9. Generate must be used every time the diffusion parameters are changed.
  11. Visualize the simulated diffusion track. Must generate (10) beforehand.
  12. Save the simulated track to a file. Uses the selected file format (13).
  13. Exported track file format. Available formats are .csv, .json, and .pcl.
  14. Load a track file (simulated track, detected track, …). If a track was simulated using a diffusion model, it can be used directly to generate the movie (if load trajectory is not used).
  15. Parameter: resolution ( resolution ) in m/pix: This is the movie physical resolution in m per pixel. If the track’s particle positions are expressed at a finer resolution, they will be rounded to the closest pixel position given by this parameter.
  16. Parameter: signal-to-noise-ration (SNR): Gives the ratio between the signal and the simulated noise. Higher SNR will result in higher particle contrast compared to the background.
  17. Parameter: background intensity: Average background intensity of the simulated movie.
  18. Parameter: Gaussian noise variance: Represents the background noise.
  19. Parameter: Poisson noise variance: If True, Poisson noise will be added to the simulated movie.
  20. Temporal resolution (frame/sec): This is the temporal resolution of the simulated movie. The track positions for all time frames in between the discrete times of the simulated movie are integrated.
  21. Ratio: If set to square, the simulated movie will have the same height and width. Otherwise the movie dimension will be given by the particle’s track positions.
  22. Load PSF: Optional. Used to load a point spread function stack. The Z-axis must be the first dimension of the stack. The middle frame along dimension 0 is used for the convolution.
  23. Generate and show the simulated movie given the loaded track and the simulation parameters.
  24. Save the simulated movie as an image stack.