Dual-guided asymmetric MP-former for rice root instance segmentation

Root phenotypic traits such as length and number are critical indicators of plant growth and productivity. However, accurate extraction of these traits remains challenging due to the slender morphology, dense overlap, and frequent occlusion within root systems. Traditional digital image processing methods suffer from low throughput and limited robustness, while most deep learning–based approaches rely on semantic segmentation, which fails to distinguish individual roots and therefore limits their applicability in instance-level phenotypic analysis.To address these limitations, we propose Dual-Guided Asymmetric MP-Former (DGA-MP-Former), a novel instance segmentation model tailored for root phenotyping, with rice roots as a representative case. Building upon the MP-Former framework, our model introduces two key components: the Guided-Enhancement Pixel Decoder (GEPD) and the Asymmetric Dual-Query Decoder (ADQD). The GEPD enhances multi-scale feature representations via Hybrid Convolution Aggregator, Semantic-Guided Fusion Module and Frequency-Guided Feature Enhancement Module, effectively capturing fine root structures and low-contrast regions. ADQD employs asymmetric interaction between semantic and instance queries to improve long-range dependency modeling and instance separation in occluded scenarios.Additionally, we present the Rice Root Segmentation Dataset (RRSD), comprising of 343 high-resolution images with instance-level annotations. Experimental results show that DGA-MP-Former achieves state-of-the-art performance on RRSD, with 57.2% AP 0.5:0.95 and 87.4% AP 0.5 . Importantly, the accurate instance segmentation results enable reliable computation of instance-level geometric traits, such as root perimeter and area. To quantitatively assess phenotypic measurement accuracy, Relative Area Error (RAE) and Relative Perimeter Error (RPE) are further introduced, achieving 26.4% and 20.2%, respectively. These results demonstrate that the proposed method effectively bridges instance segmentation accuracy and phenotypic quantification reliability, supporting high-throughput and precise root phenotyping.