In this research, we have concentrated on trajectory extraction based on image segmentation and data association in order to provide an economic and complete solution for rapid microfluidic cell migration experiments. We applied region scalable active contour model to segment the individual cells and then employed the ellipse fitting technique to process touching cells. Subsequently, we have also introduced a topology based technique to associate the cells between consecutive frames. This scheme achieves satisfactory segmentation and tracking results on the datasets acquired by our microfluidic platform.