Being able to effectively identify clouds and monitor their evolution is one important step toward more accurate quantitative precipitation estimation and forecast. In this study, a new gradient-based cloud-image segmentation technique is developed using tools from image processing techniques. This method integrates morphological image gradient magnitudes to separable cloud systems and patches boundaries. A varying scale-kernel is implemented to reduce the sensitivity of image segmentation to noise and capture objects with various finenesses of the edges in remote-sensing images. The proposed method is flexible and extendable from single- to multi-spectral imagery. Case studies were carried out to validate the algorithm by applying the proposed segmentation algorithm to synthetic radiances for channels of the Geostationary Operational Environmental Satellites (GOES-R) simulated by a high-resolution weather prediction model. The proposed method compares favorably with the existing cloud-patch-based segmentation technique implemented in the PERSIANN-CCS (Precipitation Estimation from Remotely Sensed Information using Artificial Neural Network - Cloud Classification System) rainfall retrieval algorithm. Evaluation of event-based images indicates that the proposed algorithm has potential to improve rain detection and estimation skills with an average of more than 45% gain comparing to the segmentation technique used in PERSIANN-CCS and identifying cloud regions as objects with accuracy rates up to 98%.