An improved U-Net-based in situ root system phenotype segmentation method for plants.

Abstract

The condition of plant root systems plays an important role in plant growth and development. The Minirhizotron method is an important tool to detect the dynamic growth and development of plant root systems. Currently, most researchers use manual methods or software to segment the root system for analysis and study. This method is time-consuming and requires a high level of operation. The complex background and variable environment in soils make traditional automated root system segmentation methods difficult to implement. Inspired by deep learning in medical imaging, which is used to segment pathological regions to help determine diseases, we propose a deep learning method for the root segmentation task. U-Net is chosen as the basis, and the encoder layer is replaced by the ResNet Block, which can reduce the training volume of the model and improve the feature utilization capability; the PSA module is added to the up-sampling part of U-Net to improve the segmentation accuracy of the object through multi-scale features and attention fusion; a new loss function is used to avoid the extreme imbalance and data imbalance problems of backgrounds such as root system and soil. After experimental comparison and analysis, the improved network demonstrates better performance. In the test set of the peanut root segmentation task, a pixel accuracy of 0.9917 and Intersection Over Union of 0.9548 were achieved, with an F1-score of 95.10. Finally, we used the Transfer Learning approach to conduct segmentation experiments on the corn in situ root system dataset. The experiments show that the improved network has a good learning effect and transferability.

Plant phenotyping relevance

植物根系画像から根系表現型を抽出するセグメンテーション手法を開発し、性能比較と別作物データセットでの転移性検証を行っており、方法が研究の中心である。

Code and data availability

The supplied blocks describe self-collected peanut/corn minirhizotron root image datasets and an improved U-Net model, but contain no data availability statement, public repository deposit, or author code/model release. The only URL mentioned (Labelme) is a generic annotation tool, not a paper-specific asset.

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