DeepCount : In-Field Automatic Quantification of Wheat Spikes Using Simple Linear Iterative Clustering and Deep Convolutional Neural Networks.

Abstract

Crop yield is an essential measure for breeders, researchers, and farmers and is composed of and may be calculated by the number of ears per square meter, grains per ear, and thousand grain weight. Manual wheat ear counting, required in breeding programs to evaluate crop yield potential, is labor-intensive and expensive; thus, the development of a real-time wheat head counting system would be a significant advancement. In this paper, we propose a computationally efficient system called DeepCount to automatically identify and count the number of wheat spikes in digital images taken under natural field conditions. The proposed method tackles wheat spike quantification by segmenting an image into superpixels using simple linear iterative clustering (SLIC), deriving canopy relevant features, and then constructing a rational feature model fed into the deep convolutional neural network (CNN) classification for semantic segmentation of wheat spikes. As the method is based on a deep learning model, it replaces hand-engineered features required for traditional machine learning methods with more efficient algorithms. The method is tested on digital images taken directly in the field at different stages of ear emergence/maturity (using visually different wheat varieties), with different canopy complexities (achieved through varying nitrogen inputs) and different heights above the canopy under varying environmental conditions. In addition, the proposed technique is compared with a wheat ear counting method based on a previously developed edge detection technique and morphological analysis. The proposed approach is validated with image-based ear counting and ground-based measurements. The results demonstrate that the DeepCount technique has a high level of robustness regardless of variables, such as growth stage and weather conditions, hence demonstrating the feasibility of the approach in real scenarios. The system is a leap toward a portable and smartphone-assisted wheat ear counting systems, results in reducing the labor involved, and is suitable for high-throughput analysis. It may also be adapted to work on Red; Green; Blue (RGB) images acquired from unmanned aerial vehicle (UAVs).

Plant phenotyping relevance

コムギ穂数という植物形質を圃場画像から自動抽出・計数する手法を開発し、比較検証・地上測定による妥当性確認まで行っており、フェノタイピング手法が研究の中心である。

Code and data availability

The paper provides an authors' public code URL (GitHub profile of the first author) for the DeepCount wheat spike counting model, and a data availability statement directing to the public DFW repository (ckan.grassroots.tools) and supplementary files for the datasets generated in this study.