Bacterial colony enumeration has applications in many different assays such as antibiotic screening, toxicology testing, and genotoxicity measuring. The counting of bacterial colony is usually performed by well-trained technicians manually. However, this manual enumeration process has a very low throughput, and is time consuming and labor intensive in practice. To provide consistent and accurate results and improve the throughput, the existing colony counter devices and software were then developed and commercialized in the market. In this study, we propose a fully automatic colony counter and compare its performance with Clono-Counter, an existing automatic colony counter reported by Niyazi et al. Our proposed method can significantly reduce the manual labor by automatically detecting the dish/plate region and extracting and counting colonies. Our experimental results show that the proposed method outperforms Clono-Counter in terms of Precision, Recall, and F-measures.