Bacterial colony enumeration is an essential tool for many widely used biomedical assays. However, bacterial colony enumerating is a low throughput, time consuming and labor intensive process since there might exist hundreds or thousands of colonies on a Petri dish, and the counting process is often manually performed by well-trained technicians. In this paper, we introduce a fully automatic yet cost-effective bacterial colony counter. Our proposed method can recognize chromatic and achromatic images and thus can deal with both color and clear medium. In addition, our proposed method can also accept general digital camera images as its input. The whole process includes detecting dish/plate regions, identifying colonies, separating aggregated colonies, and finally reporting consistent and accurate counting results. Our proposed counter has a promising performance in terms of both precision and recall, and is flexible and efficient in terms of labor- and time-savings.