EU-GAN: A root inpainting network for improving 2D soil-cultivated root phenotyping

Abstract

Beyond its fundamental roles in nutrient uptake and plant anchorage, the root system critically influences crop development and stress tolerance. Rhizobox enables in situ and nondestructive phenotypic detection of roots in soil, serving as a cost-effective root imaging method. However, the opacity of the soil often results in intermittent gaps in the root images, which reduces the accuracy of the root phenotype calculations. We present a root inpainting method built upon Generative Adversarial Networks (GANs) architecture In addition, we built a hybrid root inpainting dataset (HRID) that contains 1206 cotton root images with real gaps and 7716 rice root images with generated gaps. Compared with computer simulation root images, our dataset provides real root system architecture (RSA) and root texture information. Our method avoids cropping during training by instead utilizing downsampled images to provide the overall root morphology. The model is trained using binary cross-entropy loss to distinguish between root and non-root pixels. Additionally, Dice loss is employed to mitigate the challenge of imbalanced data distribution Additionally, we remove the skip connections in U-Net and introduce an edge attention module (EAM) to capture more detailed information. Compared with other methods, our approach significantly improves the recall rate from 17.35 % to 35.75 % on the test dataset of 122 cotton root images, revealing improved inpainting capabilities. The trait error reduction rates (TERRs) for the root area, root length, convex hull area, and root depth are 76.07 %, 68.63 %, 48.64 %, and 88.28 %, respectively, enabling a substantial improvement in the accuracy of root phenotyping. The codes for the EU-GAN and the 8922 labeled images are open-access, which could be reused by researchers in other AI-related work. This method establishes a robust solution for root phenotyping, thereby increasing breeding program efficiency and advancing our understanding of root system dynamics.