A microscope system comprising: an optical microscope for observing a test object; and a computer connected to the microscope; wherein the microscope comprises an illuminating optical system that illuminates the test object with illumination light from a light source under predetermined illumination conditions, an imaging optical system that forms an image of the test object on the basis of light from the test object, and an image sensor that detects the image of the test object formed by the imaging optical system and outputs an image signal, and wherein the computer comprises an image analyzing unit that acquires an image feature amount of the test object on the basis of the image signal detected by the image sensor, characterized by a storage unit that has stored therein image feature amounts corresponding, respectively, to each of a plurality of sample test objects (SM01-SM10), which were obtained by illuminating the plurality of sample test objects (SM01-SM10) with the illumination light under the predetermined illumination conditions, in correlation with illumination states of illumination light suitable for observation of each of the sample test objects (SM01-SM10), respectively, a comparison unit that compares the image feature amount of the test object with the image feature amounts corresponding to each of the plurality of sample test objects (SM01-SM10), respectively, and specifies an image feature amount of a sample test object closest to the image feature amount of the test object, and a setting unit that sets illumination conditions of the illuminating optical system to an illumination condition suitable of observation of the test object on the basis of the illumination state of the illumination light that is suitable for observation of the sample test object having the image feature amount specified by the comparison unit; wherein the illuminating optical system further comprises a first spatial light modulating device that changes an intensity distribution of the illumination light at a position conjugate to a pupil of the imaging optical system, and the setting unit comprises a device modulating unit that modulates the first spatial light modulating device (90. an optical microscope for observing a test object; and a computer connected to the microscope; wherein the microscope comprises an illuminating optical system that illuminates the test object with illumination light from a light source under predetermined illumination conditions, an imaging optical system that forms an image of the test object on the basis of light from the test object, and an image sensor that detects the image of the test object formed by the imaging optical system and outputs an image signal, and wherein the computer comprises an image analyzing unit that acquires an image feature amount of the test object on the basis of the image signal detected by the image sensor, characterized by a storage unit that has stored therein image feature amounts corresponding, respectively, to each of a plurality of sample test objects (SM01-SM10), which were obtained by illuminating the plurality of sample test objects (SM01-SM10) with the illumination light under the predetermined illumination conditions, in correlation with illumination states of illumination light suitable for observation of each of the sample test objects (SM01-SM10), respectively, a comparison unit that compares the image feature amount of the test object with the image feature amounts corresponding to each of the plurality of sample test objects (SM01-SM10), respectively, and specifies an image feature amount of a sample test object closest to the image feature amount of the test object, and a setting unit that sets illumination conditions of the illuminating optical system to an illumination condition suitable of observation of the test object on the basis of the illumination state of the illumination light that is suitable for observation of the sample test object having the image feature amount specified by the comparison unit; wherein the illuminating optical system further comprises a first spatial light modulating device that changes an intensity distribution of the illumination light at a position conjugate to a pupil of the imaging optical system, and the setting unit comprises a device modulating unit that modulates the first spatial light modulating device (90.