Effect of depth dependent spherical aberrations in 3D structured illumination microscopy.

We model the effect of depth dependent spherical aberration caused by a refractive index mismatch between the mounting and immersion mediums in a 3D structured illumination microscope (SIM). We first derive a forward model that takes into account the effect of the depth varying aberrations on both the illumination and the detection processes. From the model, we demonstrate that depth dependent spherical aberration leads to loss of signal only due to its effect on the detection response of the system, while its effect on illumination leads to phase shifts between orders that can be handled computationally in the reconstruction process. Further, by using the model, we provide guidelines for optical corrections of aberrations with different complexities, and explain how the proposed corrections simplify the forward model. Finally, we show that it is possible to correct both illumination and detection aberrations using a deformable mirror only on the detection path of the microscope.