In medical image processing, the segmentation of overlapping nuclei is one of the challenging topics, which relates to its application in diagnostic pathology. To achieve the quantification accuracy (ACC) of the diagnosis, we propose an overlapping nuclei segmentation algorithm using the principle of direction-based flow tracking (DBFT). The DBFT, which consists of direction field preparation and direction field tracking, is performed to provide the direction field and the labeled distinct single nucleus. Its performance is validated with 6375 nuclei from 29 images and compared with two popular overlapping objects segmentation methods, i.e., traditional watershed (TWS) and marker-controlled watershed (MCWS). While the sensitivity (SS) of the DBFT, TWS, and MCWS is 0.981, 0.990, and 0.966, respectively, and the corresponding positive predictive value (PPV) is 0.948, 0.831, and 0.910. The ACC values and F 1 measures obtained from the combination of SS and PPV are used as the total performance measures. While the ACC values from DBFT, TWS, and MCWS are 0.930, 0.824, and 0.882, respectively, the corresponding F 1 measures are 0.964, 0.904, and 0.937. The results clearly show that the DBFT is the best among three methods because it provides the maximum numbers on both ACC and F 1 values.