Automated cell imaging systems have been proposed for faster and more reliable analysis of biological events at the cellular level. The first step of these systems is usually cell segmentation whose success affects the other system steps. Thus, it is critical to implement robust and efficient segmentation algorithms for the design of successful systems. In the literature, the most commonly used methods for cell segmentation are marker controlled watersheds. These watershed algorithms assume that markers one-to-one correspond to cells and identify their boundaries by growing these markers. Thus, it is very important to correctly define the markers for these algorithms. The markers are usually defined by finding local minima/maxima on intensity or gradient values or by applying morphological operations on the corresponding binary image. In this work, we propose a new marker controlled watershed algorithm for live cell segmentation. The main contributions of this algorithm are twofold. First, different than the approaches in the literature, it implements a new supervised learning model for marker detection. In this model, it has been proposed to extract features for each pixel considering its neighbors' intensities and gradients and to decide whether this pixel is a marker pixel or not by a classifier using these extracted features. Second, it has been proposed to group the neighboring pixels based on the direction information and to extract features according to these groups. The experiments on 1954 cells show that the proposed algorithm leads to higher segmentation results compared to other watersheds. © 2014 IEEE.