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We present a new signal processing strategy for high frequency color flow mapping in moving tissue environments. A new application of an eigendecomposition-based clutter rejection filter is presented with modifications to deal with high blood-to-clutter ratios (BCR). Additionally, a new method for correcting blood velocity estimates with an estimated tissue motion profile is detailed. The performance of the clutter filter and velocity estimation strategies is quantified using a new swept-scan signal model. In vivo color flow images are presented to illustrate the potential of the system for mapping blood flow in the microcirculation with external tissue motion.