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What is the difference between parameters calculated from the STF and MTF functions?

The in situ FIRe system uses both STF and MTF protocols. STF protocols measure changes in chlorophyll fluorescence that occur during a short (100 - 400 us) but intense (>40,000 umol photons m-2s-1) flash of light whereas the MTF approach measures the fluorescence induced by a weaker modulated pulsed source with an intensity of ~ 3,000 to 10,000 umol photons m-2s-1 to modify fluorescence yields.

The STF approach also fundamentally differs from the MTF approach in that the STF fully reduces the primary electron acceptor, QA, allowing a simultaneous single closure event of all photosystem II (PSII) reaction centers whereas the MTF technique generates multiple photochemical charge separations that fully reduces QA, the secondary acceptor, QB, and plastoquinone (PQ).

So, the STF and MTF Fv/Fm data are different and will show different values, because the techniques used to measure them are different. Most scientists now accept that the STF Fv/Fm values are the most appropriate for use in productivity models. Further more, given that the STF protocol is much shorter than the MTF protocol it is more appropriate for moving waters, which is important in the context of an in-situ system where the water is constantly being flushed through the sample volume.