A microscope device, comprising: an illumination optical system arranged to emit activation light for activating a fluorescent substance present in a specimen, excitation light for exciting the activated fluorescent substance, and auxiliary light for exciting a fiducial marker; an image-forming optical system arranged to form a fluorescent image from the fluorescent substance; an imager arranged to image an image formed by the image-forming optical system; an image processor arranged to perform image processing using an imaging result of the imager; and a controller arranged to control the imager, the controller arranged to: cause the activated fluorescent substance to be irradiated with the excitation light and causing the imager to image a fluorescent image from the activated fluorescent substance in a plurality of frame periods in a first period, cause the fiducial marker to be irradiated with the auxiliary light and causing the imager to image a fluorescent image from the fiducial marker in a second period, cause irradiation with the excitation light in the second period to stop or causing intensity of the excitation light in the second period to be reduced to be lower than intensity of the excitation light in the first period, and cause irradiation with the auxiliary light in the first period to stop or causing intensity of the auxiliary light in the first period to be reduced to be lower than intensity of the auxiliary light in the second period, in order to detect the position of the fiducial markers with higher precision, the image processor arranged to correct at least a part of an imaging result obtained in the first period using an imaging result obtained in the second period and generate one image using at least a part of the corrected imaging result, wherein a wavelength of the excitation light and a wavelength of the auxiliary light are different from each other. an illumination optical system arranged to emit activation light for activating a fluorescent substance present in a specimen, excitation light for exciting the activated fluorescent substance, and auxiliary light for exciting a fiducial marker; an image-forming optical system arranged to form a fluorescent image from the fluorescent substance; an imager arranged to image an image formed by the image-forming optical system; an image processor arranged to perform image processing using an imaging result of the imager; and a controller arranged to control the imager, the controller arranged to: cause the activated fluorescent substance to be irradiated with the excitation light and causing the imager to image a fluorescent image from the activated fluorescent substance in a plurality of frame periods in a first period, cause the fiducial marker to be irradiated with the auxiliary light and causing the imager to image a fluorescent image from the fiducial marker in a second period, cause irradiation with the excitation light in the second period to stop or causing intensity of the excitation light in the second period to be reduced to be lower than intensity of the excitation light in the first period, and cause irradiation with the auxiliary light in the first period to stop or causing intensity of the auxiliary light in the first period to be reduced to be lower than intensity of the auxiliary light in the second period, in order to detect the position of the fiducial markers with higher precision, the image processor arranged to correct at least a part of an imaging result obtained in the first period using an imaging result obtained in the second period and generate one image using at least a part of the corrected imaging result, wherein a wavelength of the excitation light and a wavelength of the auxiliary light are different from each other. cause the activated fluorescent substance to be irradiated with the excitation light and causing the imager to image a fluorescent image from the activated fluorescent substance in a plurality of frame periods in a first period, cause the fiducial marker to be irradiated with the auxiliary light and causing the imager to image a fluorescent image from the fiducial marker in a second period, cause irradiation with the excitation light in the second period to stop or causing intensity of the excitation light in the second period to be reduced to be lower than intensity of the excitation light in the first period, and cause irradiation with the auxiliary light in the first period to stop or causing intensity of the auxiliary light in the first period to be reduced to be lower than intensity of the auxiliary light in the second period, in order to detect the position of the fiducial markers with higher precision, the image processor arranged to correct at least a part of an imaging result obtained in the first period using an imaging result obtained in the second period and generate one image using at least a part of the corrected imaging result, wherein a wavelength of the excitation light and a wavelength of the auxiliary light are different from each other.