Composite geometries

[lauriejy]

Hello,
First of all, thanks to the developers for releasing DeepTrack, it's a really powerful tool! I'm trying to use it to generate fluorescence and brightfield spherical and ellipsoidal shells similar to the issue here, #46. I've tried to use the following code to do so, but I don't get the intended output:

outer = Sphere(
    refractive_index=1.33,
    intensity=1,            # Squared magnitude of the field
    position_unit="meter",  # Units of position (default meter)
    position=(64, 64),      # Position of the particle
    radius=30e-6,            # Radius of the sphere
    upsample=2,              # Amount the resolution is upsampled for accuracy
    
)
inner = Sphere(
    refractive_index=1.33,
    intensity=0,           # Squared magnitude of the field
    position_unit="meter",  # Units of position (default meter)
    position=(64, 64),      # Position of the particle
    radius=29e-6,            # Radius of the sphere
    upsample=2,              # Amount the resolution is upsampled for accuracy
   
)

hollow_shell = outer & inner
imaged_scatterer = fluorescence_optics(hollow_shell)

Is there another way of doing what I want?

[BenjaminMidtvedt]

@lauriejy Sure! Intensities in deeptrack are additive. So your inner would need to have the negative of the outer particle's intensity. You can add this as a relation between the two if you want:

outer = Sphere(
    refractive_index=1.33,
    intensity=1,            # Squared magnitude of the field
    position_unit="meter",  # Units of position (default meter)
    position=(64, 64),      # Position of the particle
    radius=30e-6,            # Radius of the sphere
    upsample=2,              # Amount the resolution is upsampled for accuracy
    
)
inner = Sphere(
    refractive_index=1.33,
    intensity=outer.intensity * -1,           # Squared magnitude of the field
    position_unit="meter",  # Units of position (default meter)
    position=(64, 64),      # Position of the particle
    radius=29e-6,            # Radius of the sphere
    upsample=2,              # Amount the resolution is upsampled for accuracy
   
)

hollow_shell = outer & inner
imaged_scatterer = fluorescence_optics(hollow_shell)