Which method is used to attach fluorophores in single molecule fluorescence microscopy?

Fluorophores for single-molecule microscopy can come in several different flavors. Fluorophores can be genetically encoded fluorescent proteins, which are frequently used for live-cell imaging (e.g. EosFP, Dronpa, or PA-mCherry), or various synthetic dyes such as Alexa.

These emitters, when not genetically encoded, can be linked to the molecule of interest using one of several options: immunolabeling with either a molecule-specific primary antibody combined with an emitter-fused secondary antibody or a small antibody fragment such a nanobodies or single-chain antibodies fused to the emitter, or alternatively binding of the emitter to a small protein tag.