Automation of Leaf Counting in Maize and Sorghum Using Deep Learning

Abstract

ABSTRACT Leaf number and leaf emergence rate are phenotypes of interest to plant breeders, plant geneticists, and crop modelers. Counting the extant leaves of an individual plant is straightforward even for an untrained individual, but manually tracking changes in leaf numbers for hundreds of individuals across multiple time points is logistically challenging. This study generated a dataset including over 150,000 maize and sorghum images for leaf counting projects. A subset of 17,783 images also includes annotations of the positions of individual leaf tips. With these annotated images, we evaluate two deep learning-based approaches for automated leaf counting: the first based on counting-by-regression from whole image analysis and a second based on counting-by-detection. Both approaches can achieve RMSE (root of mean square error) smaller than one leaf, only moderately inferior to the RMSE between human annotators of between 0.57 and 0.73 leaves. The counting-by-regression approach based on CNNs (convolutional neural networks) exhibited lower accuracy and increased bias for plants with extreme leaf numbers which are underrepresented in this dataset. The counting-by-detection approach based on Faster R-CNN object detection models achieve near human performance for plants where all leaf tips are visible. The annotated image data and model performance metrics generated as part of this study provide large scale resources for the comparison and improvement of algorithms for leaf counting from image data in grain crops.

Plant phenotyping relevance

画像から作物の葉数を自動推定する手法の開発・比較、性能評価、データセット構築が研究の中心であり、植物表現型計測法に該当する。

Code and data availability

The paper describes a large maize/sorghum leaf-counting image dataset with leaf-tip annotations and deep learning models, but the supplied blocks contain no explicit public deposit, availability statement, or authors' URL for the data, code, or trained models. The only URL present is the bioRxiv DOI itself, which is a

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