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In this paper,we propose the use of binary partition trees (BPT) to introduce a novel region-based and multi-scale polarimetric SAR (PolSAR) data representation. The BPT structure represents homogeneous regions in the data at different detail levels. The construction process of the BPT is based, firstly, on a region model able to represent the homogeneous areas, and, secondly, on a dissimilarity measure in order to identify similar areas and define the merging sequence. Depending on the final application, a BPT pruning strategy needs to be introduced. In this paper, we focus on the application of BPT PolSAR data representation for speckle noise filtering and data segmentation on the basis of the Gaussian hypothesis, where the average covariance or coherency matrices are considered as a region model. We introduce and quantitatively analyze different dissimilarity measures. In this case, and with the objective to be sensitive to the complete polarimetric information under the Gaussian hypothesis, dissimilarity measures considering the complete covariance or coherency matrices are employed. When confronted to PolSAR speckle filtering, two pruning strategies are detailed and evaluated. As presented, the BPT PolSAR speckle filter defined filters data according to the complete polarimetric information. As shown, this novel filtering approach is able to achieve very strong filtering while preserving the spatial resolution and the polarimetric information. Finally, the BPT representation structure is employed for high spatial resolution image segmentation applied to coastline detection. The analyses detailed in this work are based on simulated, as well as on real PolSAR data acquired by the ESAR system of DLR and the RADARSAT-2 system.