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What environmental factors cause error in in vivo chlorophyll analysis with the SCUFA?
Temperature has an inverse relationship with fluorescence.  In a vertical profile, as temperature decreases, the fluorescence will increase independent of chlorophyll concentration.  The SCUFA is equipped with temperature compensation to automatically correct data.  

Light history will have significant affects on the fluorescence in algal cells.  Cells will fluoresce more chlorophyll per cell when in darker environments than in well lit zones.  One way of reducing the effects of light is to use the flow-through cap when sampling natural waters.  By using a flow-through cap and an external pump, the algal cells will be dark-adapted before entering the fluorometer, significantly reducing fluorescence error caused by variations in the light history of the cells.
Dissolved organic matter (DOM), chlorophyll degradation products, and turbidity can also affect fluorescence response.  If these factors are suspected to be significant it is worth conducting a quick study to look at the effects by comparing the fluorescence from filtered and non-filtered water samples from below the photic zone where chlorophyll concentrations would be at a minimum.