Embodiments related to methods of use of an image analysis system for identifying residual cancer cells after surgery are disclosed. In some embodiments, the image analysis system collects a surgical site image and indicates on a display one or more locations of the identified cancer cells. In some embodiments, the method for identifying residual cancer cells comprises determining and selecting a portion of the surgical site image responsive to an intensity parameter; modifying the selected portion of the surgical site image to determine one or more groups of residual cancer cells based on size; and identifying at least one of the one or more groups of residual cancer cells from the modified portion of the surgical site image using a local-based threshold.