Super Resolution (SR) imaging has the potential of visualizing the micro-vasculature down to the 10 µm level, but motion induced by breathing, heartbeats, and muscle contractions are often significantly above this level. The paper therefore introduces a method for estimating tissue motion and compensating for this. The processing pipeline is described and validated using Field II simulations of an artificial kidney. In vivo measurements were conducted using a modified bk5000 research scanner (BK Medical, Herlev, Denmark) with a BK 9009 linear array probe employing a pulse amplitude modulation scheme. The left kidney of ten Sprague-Dawley rats were scanned during open laparotomy. A 1:10 diluted SonoVue contrast agent (Bracco, Milan, Italy) was injected through a jugular vein catheter at 100 µl/min. Motion was estimated using speckle tracking and decomposed into contributions from the heartbeats, breathing and residual motion. The estimated peak motions and their precisions were: