A microscopy system includes a microscope apparatus that has an objective and a correction device correcting for a spherical aberration, and a refractive index calculator that calculates a refractive index of a sample at a target position in the sample on the basis of a plurality of target set values each of which is a set value of the correction device and each of which corresponds to an amount of spherical aberration that occurs in the microscope apparatus when an observation target plane is situated at a different position in the sample in an optical-axis direction of the objective.