Wound healing assays is a common two-dimensional migration model, with the spheroid assay three-dimensional migration model recently emerging as being more representative of in vivo migration behaviours. These models provide insight to the overall migration of cells in response to various factors such as biological, chemotactic and molecular agents. However, currently available analysis techniques for these assays fall short on providing quantifiable means to measure regional migration patterns, , which is essential to allow more robust assessment of drug treatments on cell migration in a chemotactic fashion. Therefore, the aim of this study is to develop a finite element (FE) based pipeline that can objectively quantify regional migration patterns of cells. Here, we report that our FE based approach was able to accurately measure changes in overall migration areas compared to the standard ImageJ method. Furthermore, our regional migration analysis provided accurate and quantitative means to analyse the migration pattern seen in the phantom data and our experimental results, giving us confidence that it can be a robust tool for analysing cell migration patterns.