Ballast water provides stability and manoeuvrability to a ship. Foreign harmful aquatic organisms, which
were transferred by ballast water, cause disturbing ecosystem. In order to minimize transference of foreign
harmful aquatic organisms, IMO(International Maritime Organization) adopted the International Convention
for the Control and Management of Ship’s Ballast Water and Sediments in 2004. If the convention take
effect, a port authority might need to check that ballast water is properly disposed of. In this paper, we
propose a method of counting harmful aquatic organisms in ballast water thorough image processing. We
extracted three samples from the ballast water that had been collected at Busan port in Korea. Then we
made three grey-scale images from each sample as experimental data. We made a comparison between the
proposed method and CellProfiler which is a well known cell-counting program based on image processing.
Setting of CellProfiler is empirically chosen from the result of cell count by an expert. After finding a
proper threshold for each image at which the result is similar to that of CellProfiler, we used the average
value as the final threshold. Our experimental results showed that the proposed method is simple but about
ten times faster than CellProfiler without loss of the output quality.