Table 2.

Comparison of the major properties of fluorophore classes used for investigating PCWs. Properties are highlighted in 3 different colours to indicate, in the case of PCW imaging, if they are advantageous (in green), detrimental (in red) or in-between (in orange). Please note that these are general trends and should be adjusted to specific applications.

		Small Fluorescent Molecules	Fluorescent Proteins	Quantum Dots
Spectral properties	Brightness	Low to medium	Medium	High
	Photostability	Low, prone to photobleaching	Low, prone to photobleaching	High
	Stokes shift	Narrow	Narrow	Large
	Lifetime	Long	Long	Short
	Available at various excitation/emission λ	Yes	Yes	Yes
Physical properties	Size (hydrodynamic diameter)	Small <1 nm	Medium >3 nm Prone to oligomerization	Large >10 nm
Chemical properties	Preparation	Commercial or lab dyes	Commercial genes	Commercial or lab
	Labelling	Several derivatives can react with many functions DoL can be difficult to determine	Recombinant cloning DoL is known by construction	Difficult to control with accuracy
	Conjugate stability	High	Medium	Weak
Other		Hydrophilic or hydrophobic Generic small fluorophores are cheap		Blinking (decreases QY), possibly toxic