This protocols describes the use of a hand-held sensor to estimate polyphenols and cholorphyl content of leaves based on absorbance and transmitance of specific wavelenghts of visible and near infrared light.The instrument does not directly measure these chemical concentrations, but measures reflectance and absorbance indices that have been demonstrated to relate to leaf level concentrations.We use it to measure Chlorophyll, anthocyanin, and a nitrogen balance index.Chlorophyll Concentration (μg/cm2): The instrument is factory calibrated to measure leaf chlorophyll concentration.\textrm{Chl}=\frac{\textrm{NIR} - \textrm{Red}}{\textrm{Red}}Flavanol Index (Flv)\textrm{Flv} = \log \frac{\textrm{NIR fluo excited red}}{\textrm{NIR fluo excited UV-A}}Anthocyanin Index\textrm{Anth} = \log \frac{\textrm{NIR fluo excited red}}{\textrm{NIR fluo excited green}}Nitrogen Balance Index (NBI): a relative measure of nitrogen status\textrm{NBI}=\frac{\textrm{Flavanol Index}}{\textrm{Flavonol Index}}Note that hte instrument documentation does not provide specific wavelenghts, only approximate wavelengths in this diagram (from ):