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This article presents a comprehensive subpixel water mapping algorithm to automatically produce routinely open water fraction maps in the Tibetan Plateau (TP) with the Moderate Resolution Imaging Spectroradiometer (MODIS). A multi-index threshold endmember extraction method was applied to select the endmembers from MODIS images. To incorporate endmember variability, an endmember selection strategy, called the combined use of typical and neighboring endmembers, was adopted in multiple endmember spectral mixture analysis (MESMA), which can assure a robust subpixel water fractions estimation. The accuracy of the algorithm was assessed at both the local scale and regional scale. At the local scale, a comparison using the eight pairs of MODIS/Landsat 8 Operational Land Imager (OLI) water maps demonstrated that subpixels water fractions were well retrieved with a root mean square error (RMSE) of 7.86% and determination coefficient (R2) of 0.98. At the regional scale, the MODIS water fraction map in October 2014 matches well with the TP lake data set and the Global Lake and Wetland Database (GLWD) in both latitudinal and longitudinal distribution. The lake area estimation is more consistent with the reference TP lake data set (difference of −3.15%) than the MODIS Land Water Mask (MOD44W) (difference of −6.39%).

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