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In this paper, the link-based cluster ensemble (LCE) method is utilized to improve cloud classification and satellite precipitation estimation. High resolution Satellite Precipitation Estimation (SPE) is based on the Precipitation Estimation from Remotely Sensed Imagery using an Artificial Neural Network Cloud Classification (PERSIANN-CCS) algorithm. This modified SPE with the incorporation of LCE involves the following four steps: 1) segmentation of infrared cloud images into patches; 2) cloud patch feature extraction; 3) clustering cloud patches using LCE; and 4) dynamic application of brightness temperature (Tb) and rain-rate relationships, derived using satellite observations. In order to cluster the cloud patches, the LCE method combines multiple data partitions from different clustering methods. The results show that using the cluster ensemble increases the performance of rainfall estimates compared to the SPE algorithm using a Self Organizing Map (SOM) neural network. The false alarm ratio (FAR), probabilities of detection (POD), equitable threat score (ETS), and bias are used as quantitative measures to assess the performance of the algorithm. It is shown that both the ETS and bias provide improvement in the summer and winter seasons. Almost 5% ETS improvement is obtained at some threshold values for the winter season using the cluster ensemble.