There have been studies related to identification of diatoms similar to Skeletonema using FISH techniques. Although they are not unicellular but are microalgae nonetheless, the techniques may come in handy.
One of the problems is the overlapping of fluorescent signal from some of the probes used in FISH and auto-fluorescence of Chlorophyll and other pigments presents in algae.To my knowledge, only some fluorochrome are usable with algae