Of course their is some limitations. But now almost everything is possible.
y I have passed through the cytometer almost every thing possible. bactreia, liposomes, giant liposomes, isolated mitochondria, chloroplasts, thylacoids... What type of organelles do you planned to study?
It is of importance to do a calibration in FSC/SSC and fluorescence with small beads even if the organelles do not give the same informations than bead. The size of the laser beam is important. The FSC being almost proportional to the wavelength of the laser (example 488 nm) is the organelles are above the 488 nm and have an inverted relationship if under 488 nm. If you need more details contact me at [email protected]