Abstract: A fluorescence microscope system for imaging a sample having at least two different fluorophores includes an illumination system configured to emit illumination light for exciting the fluorophores; an optical detection system configured to generate images of the sample based on fluorescence light emitted by the excited fluorophores; and a control unit configured to determine whether to image the sample in a concurrent imaging mode or in a sequential imaging mode, based on at least one characteristic of each of the fluorophores and based on at least one parameter of the optical detection system and/or the illumination system. In the concurrent imaging mode, the fluorophores are imaged simultaneously, and in the sequential imaging mode, the fluorophores are divided into a first group and at least one second group, and fluorophores of the first group and the at least one second group are imaged subsequently.