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What is in vivo chlorophyll analysis?
In vivo chlorophyll analysis is the fluorescent detection of chlorophyll in living algal and cyanobacteria cells in water.  In this technique, the excitation light from the fluorometer passes through the untreated sample water and excites chlorophyll within the living cells of the algae present.  Due to the nature of light, cells and other dissolved and particulate materials in the water will affect the excitation light before it reaches the chlorophyll molecules.  Examples of interfering materials include other plant pigments and degradation products, dissolved organic matter, turbidity, and cell morphologies.  Therefore, in vivo analysis is a semi-quantitative tool. In vivo numbers should correlate well with each other but rarely can they be used as actual chlorophyll a concentration measurements until correlated with extracted chlorophyll a data.