It is always a tremendous problem to have an estimation of intracellular pH since in cyanobacteria two important "separated" compartment occured and have very different pH, I mean cytosol and thylakoids. So the fluorescent probe signal could be a result of a mixing of two different signal emitted by the two compartment. In anyway, you should take care in the choice of the probe.

Thank you so mch sir. My organism is Spirulina platensis i specifically want to check the cytosolic pH so could u suggest me some dyes then. Yes offcourse you are right as the thyllakoid pH is always 1 unit higher then the cytosolic.