In optical microscopy, the most relevant refractive indices from the point of view of the image acquistion are the Lens Refractive Index and the Medium Refractive Index. A mismatch between these two indices will cause several serious problems, like Spherical Aberration, reduction of the effective Numerical Aperture by Total Internal Reflection, and Fishtank Effect. The Mismatch Distorts Psf!!!
Fortunately, the theoretical PSF in Huygens will adapt to the image-depth and correct for the mismatch.
See Acquisition Pitfalls and Spherical Aberration.