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Molecular brightness is the detected fluorescence signal contributed by one labelled molecule or fluorescent particle under specified illumination and collection conditions. It is often expressed as detected photons per second per particle, or counts per particle per acquisition interval. It depends on the label, its environment and the apparatus, so it is not an intrinsic universal constant of the protein carrying the label.

For one uniformly observed species in a simple additive model, background-subtracted count rate $F$ and mean particle number $N$ satisfy $F=bN$, where $b$ is the molecular brightness. Ten particles with $b=1000$ counts per second and five particles with $b=2000$ counts per second both yield $F=10,000$ counts per second. Mean intensity alone cannot distinguish the two samples. A particle carrying two independent identical labels can approach twice the molecular brightness of one label, but quenching or incomplete labelling can invalidate that comparison.

Yan Chen and colleagues used the distribution of photon counts as particles diffuse through a tiny illuminated observation volume to estimate both molecular brightness and mean occupancy. This uses fluctuations beyond the average, with the illumination profile included in the measurement model.^[ref]

Yan Chen is the first author of the 1999 photon-counting-histogram study in fluorescence fluctuation spectroscopy. The analysis used the distribution of detected photon counts in short intervals to estimate molecular brightness and the average number of fluorescent molecules in the observation volume.^[ref]

Two samples can have the same mean fluorescence while containing different numbers of molecules with different individual brightnesses. Their count distributions can help distinguish these possibilities when interpreted with the instrument's illumination profile and counting statistics. This entry identifies the researcher through that paper's byline and affiliation, without conflating other scientists named Yan Chen.