Simulation: Particles dont "disappear" when out of focus

[weidtn]

For my work, I'm interested in the z-dimension of magnetic beads. When I move the microscope's focal plane through the particles, they first appear by getting sharper, come into the best focus, and then disappear by getting blurry again if I keep moving the focal plane.

I can not replicate this behavior in the simulations. The particle gets bigger and bigger and eventually blocks the whole image. I expected the particles to look like the particles in this: https://github.com/softmatterlab/DeepTrack2/blob/develop/examples/paper-examples/5-inline_holography_3d_tracking.ipynb But when I'm doing my own simulations I get something like this:

[BenjaminMidtvedt]

This is likely due to matplotlib automatically normalizing the shown images for you. Try fixing vmin and vmax in imshow, it should correctly show that particle becomes weaker.

[weidtn]

I think that solved the problem. Thank you!