Accurate quantification of root and shoot growth is essential for assessing plant development, but manual measurement methods are laborious and fail to capture the actual geometry of plant structures. This study presents a novel semi-automated system for non-destructive measurement of tomato (Solanum lycopersicum) root and shoot growth in an aeroponic setup. The low-cost system integrates a Raspberry Pi computer for automated image acquisition, custom software for user-guided annotation of root and shoot paths, and algorithms to extract length measurements from the annotated images. Tomato seedlings were grown aeroponically and imaged at regular intervals. Root and shoot paths were manually traced on the images using a mouse interface, enabling measurement of actual curved path lengths. The semi-automated system yielded shoot and root length measurements that were 30% and 40% longer, respectively, than manual linear methods by accounting for the contorted geometry of shoots and roots. It reduced measurement time by approximately 50% while increasing consistency threefold compared to conventional destructive techniques. This open-source platform provides a novel tool for researchers to efficiently and reliably quantify critical plant phenotypic traits in a non-destructive manner. Integration with aeroponic culture enables temporal studies of dynamic growth responses to environmental conditions. The framework can be readily adapted for phenotyping diverse crop species and will accelerate plant biology and breeding research efforts.