A medical system comprising: a light source apparatus configured to emit excitation light in a wavelength band including a first wavelength band for exciting a first fluorescent substance accumulated in a subject part inside a body cavity and a second wavelength band that is different from the first wavelength band; a treatment instrument including a second fluorescent substance that is configured to be excited by light in the second wavelength band, the treatment instrument being configured so as to enable treatment of the subject part to be performed; an image pickup section configured to pick up an image of first fluorescence emitted, upon application of the excitation light, from the first fluorescent substance accumulated in the subject part, and an image of second fluorescence emitted, upon the application of the excitation light, from the second fluorescent substance arranged in a vicinity of the subject part, to generate a fluorescence image; an information storing section configured to store shape information including information on a shape and size of the second fluorescent substance; and an operation section configured to perform an operation to calculate a scaling factor based on the shape information and a size of a draw region of the second fluorescence which is a region drawn in a shape matching or substantially matching the shape information in the fluorescence image, and further perform an operation to estimate a size of a region in which the first fluorescence is generated, based on the calculated scaling factor and a size of a draw region of the first fluorescence which is a region drawn in a shape that is different from the shape information in the fluorescence image. a light source apparatus configured to emit excitation light in a wavelength band including a first wavelength band for exciting a first fluorescent substance accumulated in a subject part inside a body cavity and a second wavelength band that is different from the first wavelength band; a treatment instrument including a second fluorescent substance that is configured to be excited by light in the second wavelength band, the treatment instrument being configured so as to enable treatment of the subject part to be performed; an image pickup section configured to pick up an image of first fluorescence emitted, upon application of the excitation light, from the first fluorescent substance accumulated in the subject part, and an image of second fluorescence emitted, upon the application of the excitation light, from the second fluorescent substance arranged in a vicinity of the subject part, to generate a fluorescence image; an information storing section configured to store shape information including information on a shape and size of the second fluorescent substance; and an operation section configured to perform an operation to calculate a scaling factor based on the shape information and a size of a draw region of the second fluorescence which is a region drawn in a shape matching or substantially matching the shape information in the fluorescence image, and further perform an operation to estimate a size of a region in which the first fluorescence is generated, based on the calculated scaling factor and a size of a draw region of the first fluorescence which is a region drawn in a shape that is different from the shape information in the fluorescence image.