基于VGG-UNet的食用菌菌丝体表型参数自动测量方法

Automated Measurement Method of Phenotypic Parameters of Edible Mushroom Mycelium Based on VGG-UNet

食用菌菌丝体表型特征是食用菌种质资源评价和科学育种的重要依据。针对传统阈值分割方法提取菌丝体区域易受到光照不均、菌丝体不规则生长和培养皿内产生代谢物等因素干扰的问题,制作食用菌菌丝体图像数据集,并提出一种基于深度学习的食用菌菌丝体表型参数自动测量方法。将U-Net网络编码器部分替换为VGG16的前13个卷积层,引入预训练权重,构建适用于菌丝体分割的VGG-UNet模型。测试集上对比实验表明,该模型的平均交并比达到98.18%,比原始U-Net模型高0.93个百分点。经该模型获取菌丝体分割图像后,利用OpenCV相关函数计算菌丝体的半径、周长、面积、覆盖度、圆整度这5个表型参数。将人工测量方法与本文方法进行线性回归分析,得出菌丝体半径、周长、面积和覆盖度的决定系数分别为0.979 5、0.991 5、0.975 0和0.975 0,均方根误差分别为2.20 mm、4.73 mm、176.74 mm^(2)和3.16%。经测试,本文方法能准确地完成食用菌菌丝体表型参数自动测量任务,为食用菌表型分析研究提供理论基础。

Mycelium phenotypic characteristics of edible mushroom are an important basis for the evaluation of edible mushroom germplasm resources and scientific breeding.To address the problems of traditional threshold segmentation method to extract mycelium regions which are easily disturbed by uneven light,irregular growth of mycelium and metabolites produced in the petri dishes,an image dataset of edible mycelium was made and a deep learning-based automatic measurement method for edible mycelium phenotype parameters was proposed.The U-Net network encoder was partially replaced with the first 13 convolutional layers of VGG16,and pre-training weights were introduced to construct a VGG-UNet model applicable to mycelium segmentation.The average cross-merge ratio of this model reached 98.18%,which was 0.93 percentage points higher than that of the original U-Net model.After obtaining mycelium segmentation images by this model,the five phenotypic parameters of radius,perimeter,area,coverage,and roundness of mycelium were calculated by using OpenCV correlation functions.A linear regression analysis was performed between the manual measurement method,and the R2 of mycelium radius,perimeter,area and coverage were 0.9795,0.9915,0.9750 and 0.9750,respectively,and the RMSE were 2.20 mm,4.73 mm,176.74 mm^(2) and 3.16%,respectively.The method was tested to accurately accomplish the task of automatic measurement of phenotypic parameters of edible mycelium,which provided a theoretical basis for the study of phenotypic analysis of edible mushrooms.