When do I use photobleaching on purpose?

Photobleaching is often used on purpose to quench autofluorescence when using fluorophores that overlap with tissue autofluorescence. Tissues contain endogenous fluorophores, which give the tissue autofluorescence. These endogenous fluorophores fluoresce at around 488 nm and 520 nm, which are the same wavelengths as GFP (green fluorescent protein) and FITC (fluorescein isothiocyanate) fluorophores respectively. This can make it difficult to differentiate between your true signal and the background autofluorescence. Under these circumstances, using photobleaching can help reduce autofluorescence and minimize the background noise so you can identify your true signal more clearly.