Remove nested lists in parameter file

[Haydnspass]

Change all nested lists to not nested ones, i.e.

psf_extent: [[-0.5, 39.5], [-0.5, 39.5], None] to

psf_extent: 
   x: [-0.5, 39.5]
   y: [-0.5, 39.5]
   z: None

Reason: Makes it easier for the user to understand what is happening and also easier to parse e.g. in napari.