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Pigments absorb light, transform it into energy, and provide reaction sites for photosynthesis; thus, the quantification of pigment distribution is vital to plant research. Traditional methods for the quantification of pigments are time-consuming and not suitable for the high-throughput digitization of rice pigment distribution. In this study, using a hyperspectral imaging system, we developed an integrated image analysis pipeline for automatically processing enormous amounts of hyperspectral data. We also built models for accurately quantifying 4 pigments (chlorophyll a, chlorophyll b, total chlorophyll and carotenoid) from rice leaves and determined the important bands (700-760  nm ) associated with these pigments. At the tillering stage, the  R  2  values and mean absolute percentage errors of the models were 0.827–0.928 and 6.94–12.84%, respectively. The hyperspectral data and these models can be combined for digitizing the distribution of the chlorophyll with high resolution (0.11  mm/pixel ). In summary, the integrated hyperspectral image analysis pipeline and selected models can be used to quantify the chlorophyll distribution in rice leaves. The use of this technique will benefit rice functional genomics and rice breeding.

Accurate Digitization of the Chlorophyll Distribution of Individual Rice Leaves Using Hyperspectral Imaging and an Integrated Image Analysis Pipeline