DeepSort: Deep convolutional networks for sorting haploid maize seeds

Abstract

Background: Maize is a leading crop in the modern agricultural industry that accounts for more than 40% grain production worldwide. THe double haploid technique that uses fewer breeding generations for generating a maize line has accelerated the pace of development of superior commercial seed varieties and has been transforming the agricultural industry. In this technique the chromosomes of the haploid seeds are doubled and taken forward in the process while the diploids marked for elimination. Traditionally, selective visual expression of a molecular marker within the embryo region of a maize seed has been used to manually discriminate diploids from haploids. Large scale production of inbred maize lines within the agricultural industry would benefit from the development of computer vision methods for this discriminatory task. However the variability in the phenotypic expression of the molecular marker system and the heterogeneity arising out of the maize genotypes and image acquisition have been an enduring challenge towards such efforts. Results: In this work, we propose a novel application of a deep convolutional network (DeepSort) for the sorting of haploid seeds in these realistic settings. Our proposed approach outperforms existing state-of-the-art machine learning classifiers that uses features based on color, texture and morphology. We demonstrate the network derives features that can discriminate the embryo regions using the activations of the neurons in the convolutional layers. Our experiments with different architectures show that the performance decreases with the decrease in the depth of the layers. Conclusion: Our proposed method DeepSort based on the convolutional network is robust to the variation in the phenotypic expression, shape of the corn seeds, and the embryo pose with respect to the camera. In the era of modern digital agriculture, deep learning and convolutional networks will continue to play an important role in advancing research and product development within the agricultural industry.