Precision agriculture has become a key factor for increasing crop yields by providing essential information to decision makers. In this work, we present a deep learning method for simultaneous segmentation and counting of cranberries to aid in yield estimation and sun exposure predictions. Notably, supervision is done using low cost center point annotations. The approach, named Triple-S Network, incorporates a three-part loss with shape priors to promote better fitting to objects of known shape typical in agricultural scenes. Our results improve overall segmentation performance by more than 6.74% and counting results by 22.91% when compared to state-of-the-art. To train and evaluate the network, we have collected the CRanberry Aerial Imagery Dataset (CRAID), the largest dataset of aerial drone imagery from cranberry fields. This dataset will be made publicly available.