1. A microscope apparatus comprising: a first optical system configured to irradiate an activating light which actives a part of a plurality of fluorescent material included in a sample to a state capable of emitting a fluorescence, a second optical system configured to irradiate an exciting light that excites at least a part of the activated fluorescent material and that causes the fluorescence to emit, an imager, and a controller configured to: calculate fluorescent intensity distribution information of a fluorescent image captured by the imager by classifying a fluorescent intensity distribution of the fluorescent image captured by the imager into multiple levels by prescribed ranges of fluorescent intensity, and control capture of another fluorescent image by setting different intensities of the activating light for each of a plurality of regions of the sample so that different ones of the regions are irradiated with the different intensities of the activating light, the different intensities being set based on the calculated levels, and by setting an intensity of the exciting light to a predetermined intensity.