Abstract: This paper presents a complete pipeline to perform deep learning-based instance segmentation of different types of grains (e.g., corn, sunflower, soybeans, lentils, chickpeas, mote, and beans). The proposed approach consists of using synthesized image datasets for the training process, which are easily generated according to the category of the instance to be segmented. The synthesized imaging process allows generating a large set of well-annotated grain samples with high variability—as large and high as the user requires. Instance segmentation is performed through a popular deep learning based approach, the Mask R-CNN architecture, but any learning-based instance segmentation approach can be considered. Results obtained by the proposed pipeline show that the strategy of using synthesized image datasets for training instance segmentation helps to avoid the time-consuming image annotation stage, as well as to achieve higher intersection over union and average precision performances. Results obtained with different varieties of grains are shown, as well as comparisons with manually annotated images, showing both the simplicity of the process and the improvements in the performance.