Create tutorial on creating custom scatterers

[mirjagranfors]

For the biological scatterers:

• should I add other biological scatterers too? E.g. nuclei, mitochondria, actin, microtubuli?

[Pwhsky]

The tutorial looks good, I think it would be good to have a separate tutorial titled DTSG172_biological_scatterers where you show the bacterium and composite scatterers as a continuation/extension of the concept and tools introduced in DTSG171_custom_scatterers, let me know what you think

[JChonpca]

In my opinion, I would like to add it to DTAT321_scatterers, as a supplement to learn dt.Scatter more. Or replace it (Since the new tutorial looks quite good). When I learn those Advanced Topics before I read our original code, I do learn lots from DTAT301_features since it gives a detailed structure of dt.Feature, as well as a custom one. But for other advanced topics, they just try to list all our classes, which I think it is overlaps with our documentation.

[JChonpca]

For changing the refractive index of the scatterer (in each voxel?, to make it much more accurate or differentiable optimization to experimental data). I think we should focus on _create_volume in optics.py. It merges all the scatterer information (intensity for fluorescence microscopy, and refractive index for others) before sending them to the specific microscopy. According to its code, I think it merges at the scatter-level rather than the voxel level, which means it may treat one scatter with only one certain refractive index or intensity.