This paper proposes a novel approach to comparing cell colony images taken at different times on a Petri dish. The objective is to provide an assistive tool for microbiologists to quantify the loss of cell colonies on two Petri dishes, by mapping cell colonies between a pair of images. This problem is highly non-trivial, as the shape, size and position of the corresponding colonies vary randomly. In addition, the cell colony images for comparison are taken at different times and from slightly different perspectives (i.e. effects of shearing), and this amplifies the complexity of the problem. Experiments show that approaches purely based on SIFT or SURF, or algorithms used in astronomy, do not perform well on the problem domain. We therefore introduce a new approach to addressing these problems. A novel iterative technique that combines triangulation algorithms with the RANSAC alignment algorithm is proposed. Through hundreds of experiments, we demonstrate the efficacy of the new algorithm in comparison to existing ones found in the literature.