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The refractive index (r.i.) of a material is the factor by which electromagnetic radiation is slowed down (relative to vacuum) when it travels inside the material. (Source: Wikipedia).

In optical microscopy, important r.i. are the Lens Refractive Index and the Medium Refractive Index. A mismatch between these two indices will cause several problems like spherical aberration which if known will be corrected for in the Huygens software. For a complete overview see Refractive Index Mismatch.