Deep learning-based elaiosome detection in milk thistle seed for efficient high-throughput phenotyping

Milk thistle, Silybum marianum (L.), is a well-known medicinal plant used for the treatment of liver diseases due to its high content of silymarin. The seeds contain elaiosome, a fleshy structure attached to the seeds, which is believed to be a rich source of many metabolites including silymarin. Segmentation of elaiosomes using only image analysis is difficult, and this makes it impossible to quantify the elaiosome phenotypes. This study proposes a new approach for semi-automated detection and segmentation of elaiosomes in milk thistle seed using the Detectron2 deep learning algorithm. One hundred manually labeled images were used to train the initial elaiosome detection model. This model was used to predict elaiosome from new datasets, and the precise predictions were manually selected and used as new labeled images for retraining the model. Such semi-automatic image labeling, i.e., using the prediction results of the previous stage for retraining the model, allowed the production of sufficient labeled data for retraining. Finally, a total of 6,000 labeled images were used to train Detectron2 for elaiosome detection and attained a promising result. The results demonstrate the effectiveness of Detectron2 in detecting milk thistle seed elaiosomes with an accuracy of 99.9%. The proposed method automatically detects and segments elaiosome from the milk thistle seed. The predicted mask images of elaiosome were used to analyze its area as one of the seed phenotypic traits along with other seed morphological traits by image-based high-throughput phenotyping in ImageJ. Enabling high-throughput phenotyping of elaiosome and other seed morphological traits will be useful for breeding milk thistle cultivars with desirable traits.