The optimization of plants has long focused on the above-ground parts. Recently, new efforts are being made to exploit the potential below ground. To this end, our partners at the FZJ have developed an imaging system which enables imaging the root system throughout the growth of the plants using MRI. Besides qualitative analysis, a precise quantitative description of the root system is of utmost importance, requiring state-of-the-art image analysis to effectively detect thin roots in a resolution and signal to noise-limited scenario. As part of this project we incorporate recent developments in AI-based image segmentation into established root extraction pipelines with the goal of improving the precision, sensitivity and robustness of the reconstructed root trees.