An observation apparatus comprising a plurality of components, the components comprising: at least one light source adapted to emit illumination light used to observe a specimen; an illumination optical system (10, 30, 40) adapted to radiate the illumination light emitted from the light source onto the specimen; a deflecting section adapted to change an area of the specimen to be irradiated with the illumination light; an observation optical system adapted to collect light from the specimen; at least one light detector (25, 37) adapted to detect the light collected by the observation optical system; an image generation section adapted to generate an image from the light detected by the light detector (25, 37); and a control section adapted to: control the at least one light source to emit light having a first wavelength used to excite a fluorescent substance supplied to the specimen, wherein the fluorescent substance is configured to specifically bind to or be expressed in a stimulus target included in the specimen, and control the image generation section to extract a fluorescence image of the fluorescent substance based on fluorescence produced from the fluorescent substance when the light having the first wavelength is radiated; control the at least one light source to emit light having a second wavelength used to stimulate the stimulus target; and control the at least one light source to emit light having a third wavelength used to acquire an image of the specimen, and control the image generation section to generate an image of the specimen that includes the stimulus target; characterized in that the control section is further adapted to select areas of the fluorescent image of the fluorescent substance as stimulus target areas to be irradiated with the light having the second wavelength, and to control the illumination optical system to emit the light having the second wavelength onto the position of the extracted fluorescence image of the fluorescent substance through the deflecting section. at least one light source adapted to emit illumination light used to observe a specimen; an illumination optical system (10, 30, 40) adapted to radiate the illumination light emitted from the light source onto the specimen; a deflecting section adapted to change an area of the specimen to be irradiated with the illumination light; an observation optical system adapted to collect light from the specimen; at least one light detector (25, 37) adapted to detect the light collected by the observation optical system; an image generation section adapted to generate an image from the light detected by the light detector (25, 37); and a control section adapted to: control the at least one light source to emit light having a first wavelength used to excite a fluorescent substance supplied to the specimen, wherein the fluorescent substance is configured to specifically bind to or be expressed in a stimulus target included in the specimen, and control the image generation section to extract a fluorescence image of the fluorescent substance based on fluorescence produced from the fluorescent substance when the light having the first wavelength is radiated; control the at least one light source to emit light having a second wavelength used to stimulate the stimulus target; and control the at least one light source to emit light having a third wavelength used to acquire an image of the specimen, and control the image generation section to generate an image of the specimen that includes the stimulus target; characterized in that the control section is further adapted to select areas of the fluorescent image of the fluorescent substance as stimulus target areas to be irradiated with the light having the second wavelength, and to control the illumination optical system to emit the light having the second wavelength onto the position of the extracted fluorescence image of the fluorescent substance through the deflecting section. control the at least one light source to emit light having a first wavelength used to excite a fluorescent substance supplied to the specimen, wherein the fluorescent substance is configured to specifically bind to or be expressed in a stimulus target included in the specimen, and control the image generation section to extract a fluorescence image of the fluorescent substance based on fluorescence produced from the fluorescent substance when the light having the first wavelength is radiated; control the at least one light source to emit light having a second wavelength used to stimulate the stimulus target; and control the at least one light source to emit light having a third wavelength used to acquire an image of the specimen, and control the image generation section to generate an image of the specimen that includes the stimulus target; characterized in that the control section is further adapted to select areas of the fluorescent image of the fluorescent substance as stimulus target areas to be irradiated with the light having the second wavelength, and to control the illumination optical system to emit the light having the second wavelength onto the position of the extracted fluorescence image of the fluorescent substance through the deflecting section.