High-Throughput Field Plant Phenotyping:A Self-Supervised Sequential CNN Method to Segment Overlapping Plants

High-throughput plant phenotyping—the use of imaging and remote sensing to record plant growth dynamics—is becoming more widely used.The first step in this process is typically plant segmentation,which requires a well-labeled training dataset to enable accurate segmentation of overlapping plants.However,preparing such training data is both time and labor intensive.To solve this problem,we propose a plant image processing pipeline using a self-supervised sequential convolutional neural network method for in-field phenotyping systems.This first step uses plant pixels from greenhouse images to segment nonoverlapping in-field plants in an early growth stage and then applies the segmentation results from those early-stage images as training data for the separation of plants at later growth stages.The proposed pipeline is efficient and self-supervising in the sense that no human-labeled data are needed.We then combine this approach with functional principal components analysis to reveal the relationship between the growth dynamics of plants and genotypes.We show that the proposed pipeline can accurately separate the pixels of foreground plants and estimate their heights when foreground and background plants overlap and can thus be used to efficiently assess the impact of treatments and genotypes on plant growth in a field environment by computer vision techniques.This approach should be useful for answering important scientific questions in the area of high-throughput phenotyping.

KAT4IA:K-Means Assisted Training for Image Analysis of Field-Grown Plant Phenotypes

High-throughput phenotyping enables the efficient collection of plant trait data at scale.One example involves using imaging systems over key phases of a crop growing season.Although the resulting images provide rich data for statistical analyses of plant phenotypes,image processing for trait extraction is required as a prerequisite.Current methods for trait extraction are mainly based on supervised learning with human labeled data or semisupervised learning with a mixture of human labeled data and unsupervised data.Unfortunately,preparing a sufficiently large training data is both time and labor-intensive.We describe a self-supervised pipeline(KAT4IA)that uses K-means clustering on greenhouse images to construct training data for extracting and analyzing plant traits from an image-based field phenotyping system.The KAT4IA pipeline includes these main steps:self-supervised training set construction,plant segmentation from images of field-grown plants,automatic separation of target plants,calculation of plant traits,and functional curve fitting of the extracted traits.To deal with the challenge of separating target plants from noisy backgrounds in field images,we describe a novel approach using row-cuts and column-cuts on images segmented by transform domain neural network learning,which utilizes plant pixels identified from greenhouse images to train a segmentation model for field images.This approach is efficient and does not require human intervention.Our results show that KAT4IA is able to accurately extract plant pixels and estimate plant heights.