Identification of optimal fluorophores for use in the <i>Drosophila</i> embryo

The use of fluorescent proteins has become ubiquitous throughout the life sciences as a key method for understanding molecular, cellular, and tissue-scale processes. Genetically encodable fluorophores have enabled stable genetic lines to be generated in a large array of organisms. There are now suites of fluorophores available, particularly in the green and red spectra. Yet, which fluorophore works best in vivo can depend on a range of factors, both extrinsic (e.g., pH and temperature) and intrinsic (e.g., photobleaching and brightness). While fluorophores have been well characterised in cell culture, such measures within in vivo systems are more limited. Here, we present a quantitative screen of nine green and eight red fluorophore lines in <i>Drosophila</i>, with the fluorescent protein expressed from the same genomic location and imaged under identical conditions. We analyse the expression of the fluorophores in both early and late <i>Drosophila</i> embryos. We provide a quantitative analysis of the bleaching and folding rates. We find amongst the green fluorophores that the suitable choice-e.g., mEGFP, mNeonGreen, StayGold-E138D-depends on timing and imaging requirements. For the red fluorophores, mScarlet-I performed consistently well, though no particular fluorophore stood out as ideal under all conditions. These results provide a powerful database for selecting optimal fluorophores for imaging in the <i>Drosophila</i> embryo in green and red channels.