BODIPY staining, an alternative to the Nile Red fluorescence method for the evaluation of intracellular lipids in microalgae

► We optimize BODIPY 505/515 for microalgae with difference cell wall characteristics. ► We compare BODIPY 505/515 to Nile Red. ► We find that BODIPY 505/515 does not photobleach like Nile Red. ► BODIPY 505/515 does not accumulate in organelles or cell structures, other than lipid bodies. ► BODIPY 505/515 is more versatile than Nile Red in advanced techniques like CSLM.