The simulation below allows to evaluate, how changes in refraction index in cells and interstitial fluid can affect the overall transparency of tissues. This is already the second version of the simulation. I am also working on a more advanced model to include other factors that affect transparency.
In the simulation below, the light is emitted as parallel light beams coming from the top. The light then moves through a layer of 2D-simulated cells. You can control the angle of the falling light, and the refraction index of the (1) cell cytoplasm (nCell), (2) mitochondria (nMitochondria) and (3) outer interstitial fluid (nOuter). The sensor (marked with yellow in the visualization) then counts, how many of the emitted beams have reached it. Result is updated every time that you update the settings.
To see in more detail, how the transparency simulation works, based on a single cell, see the single cell simulation.
Below is also a picture of the experiment results. The parameters were: nOuter = 1.33, nMitochondria = 1.41, and the cell’s cytoplasm refraction index (nCell) was evaluated in the range between 1.33 and 1.55. The chart displays, how many beams have reached the sensor in this simulation.