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The aim of this article is to illustrate the need for an improved quality assurance in fluorescence microscopy. From the instrument-side, this can be achieved by a better understanding, consideration, and regular control of the instrument-specific parameters and quantities affecting measured fluorescence signals. Particularly, the need for requirements on physical- and chemical-type instrument standards for the characterization and performance validation of spectral fluorescence microscopes (SFMs) is discussed and suitable systems are presented. Special emphasis is given to spectral fluorescence standards and to day-to-day intensity standards for SFMs. Fluorescence standards and well-characterized fluorescence microscopes are the first and essential steps towards the comparability and the understanding of the variability in fluorescence microscopy data in medical and life sciences. In addition, standards enable the distinction between instrument-specific variations and fluorescent label- or probe-related uncertainties as well as generally sample-related effects.