The increased availability of 3D image data requires improving the efficiency of digital segmentation, currently relying on manual labelling, especially when separating structures into multiple components. Automated and semi-automated methods to streamline segmentation have been developed, such as deep learning and smart interpolation, but require pre-labelled data, and specialized hardware and software. Deep learning models in particular often require the manual creation of extensive training data, particularly for complex multi-class segmentations. Here, we introduce SPROUT, a novel, semi-automated computer vision method providing a time-efficient and user-friendly pipeline for segmenting and parcellating image data. SPROUT generates seeds (representing parts of an object) based on specified density thresholds and erosion of connected components, to achieve element separation. Seeds are grown to obtain fully-parcellated segmentations. We compare SPROUT's performance to that of smart interpolation and apply it to diverse datasets to demonstrate the utility and versatility of this open-source 3D segmentation method.