In this paper, we propose a novel geodesic distance based clustering approach for delineating boundaries of touching cells. In specific, the Riemannian metric is firstly adopted to integrate the spatial distance and intensity variation. Then the distance between any two given pixels under this metric is computed as the geodesic distance in a propagational way, and the K-means-like algorithm is deployed in clustering based on the propagational distance. The proposed method was validated to segment the touching Madin-Darby Canine Kidney (MDCK) epithelial cell images for measuring their N-Ras protein expression patterns inside individual cells. The experimental results and comparisons demonstrate the advantages of the proposed method in massive cell segmentation and robustness to the initial seeds selection, varying intensity contrasts and high cell densities in microscopy images.