Imaging techniques heavily rely on the fluorophores they use. GFP was a great breakthrough because it allowed labeling specific targets, photoconvertable GFP variants were a great breakthrough because they allowed generation of single fluorescent molecules and this lead to development of a whole array of tracking and superresolution techniques.
However, GFP variants were always pretty bad fluorophores as compared to organic dyes due to their low quantum yield, pH and redox-potential sensitivity. Organic dyes, good as they are, had issues with selective labeling and thus were mostly used in vitro.
It seems that it might be about to change. Lee at al. report a novel strategy for labeling proteins of interest in vivo with organic dyes. They use HaloTag technology by Promega and label a whole bunch of proteins both in mammalian cells and bacteria with photoactivatable azido DCDHF labels.
And it works beautifully. The only problem is that HaloTag is even bigger than GFP - 33 kD. That's a lot.
Lee at al. Superresolution imaging of targeted proteins in fixed and living cells using photoactivatable organic fluorophores. JACS 2010 vol. 132 (43) pp. 15099-15101 PIMD 20936809
Lord at al. Azido push-pull fluorophores photoactivate to produce bright fluorescent labels. J Phys Chem B 2010 vol. 114 (45) pp. 14154-14167 PIMD 19860443