In this chapter, motion of magnetic particles were captured using ultrasound imaging with contrast-enhanced microbubbles. Ultrasound videos were captured and analyzed by the created tracking algorithm to determine the efficiency and accuracy of the algorithm. It is necessary to ensure an efficient and accurate tracking method of the particles in order to evaluate future in vitro or in vivo applications of the microbubbles, when implanted into an enclosed system and imaged using ultrasound. First, it was found that the porous structure of the magnetic microbubbles could be successfully fabricated based on a gas foaming technique, using alginate (low viscosity, 2% (w/v)) as the polymer, mixed homogeneously with sodium carbonate (4%) solution. The reaction between sodium bicarbonate and hydrogen peroxide (32 wt %) in the collecting solution allowed the creation of encapsulated microbubbles. The alginate went under crosslinking in the collecting calcium chloride (25% w/v) solution. Second, it was proven that the encapsulated microbubbles enhanced the resultant ultrasound images, with the air bubbles appearing as bright white spots. In contrast, the solid spheres appeared dull and at times could not be seen under ultrasound. The contrast enhancing properties of the microbubbles allowed the microbubbles to be detected by the tracking algorithm, as compared to the solid spheres which could not be detected at all. Third, ground truth of the (x, y) coordinates of the microbubble centroids were determined using manual selection by the user mouse. Based on the accuracy analysis done, the accuracy of the tracking algorithm was 3.33 pixels, or 0.0354 cm, between the algorithm detected and the manually selected (x, y) coordinates of the centroids. Also, the optimal number of particles to be tracked was up to five particles with an accuracy studies.