The role of the fluorescent dipoles

A fluorescent dipole absorbates and re-emits light of a different wave length The intensity of re-emitted ligth is proportional to the scalar product of the E-field with the dipole vector. This relation is visualized in the image above.

The non-trivial field distribution in the confocal microscope leads therefore to an intensity difference of the re-emitted ligth. You may follow that after scanning the microscope over the dipole, the pattern for the angles theta and phi describing the dipole direction is measured.