PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time

Abstract

Abstract Background High-throughput phenotyping platforms allow the study of the form and function of a large number of genotypes subjected to different growing conditions (GxE). A number of image acquisition and processing pipelines have been developed to automate this process, for micro-plots in the field and for individual plants in controlled conditions. Capturing shoot development requires extracting from images both the evolution of the 3D plant architecture as a whole, and a temporal tracking of the growth of its organs. Results We propose PhenoTrack3D, a new pipeline to extract a 3D+t reconstruction of maize at organ level from plant images. It allows the study of plant architecture and individual organ development over time during the entire growth cycle. PhenoTrack3D improves a former method limited to 3D reconstruction at a single time point [Artzet et al ., 2019] by (i) a novel stem detection method based on deep-learning and (ii) a new and original multiple sequence alignment method to perform the temporal tracking of ligulated leaves. Our method exploits both the consistent geometry of ligulated leaves over time and the unambiguous topology of the stem axis. Growing leaves are tracked afterwards with a distance-based approach. This pipeline is validated on a challenging dataset of 60 maize hybrids imaged daily from emergence to maturity in the PhenoArch platform (ca. 250,000 images). Stem tip was precisely detected over time (RMSE < 2.1cm). 97.7% and 85.3% of ligulated and growing leaves respectively were assigned to the correct rank after tracking, on 30 plants x 43 dates. The pipeline allowed to extract various development and architecture traits at organ level, with good correlation to manual observations overall, on random subsets of 10 to 355 plants. Conclusions We developed a novel phenotyping method based on sequence alignment and deep-learning. It allows to characterise automatically and at a high-throughput the development of maize architecture at organ level. It has been validated for hundreds of plants during the entire development cycle, showing its applicability to the GxE analyses of large maize datasets.

Plant phenotyping relevance

トウモロコシ器官の3D再構成・時系列追跡による表現型抽出パイプラインを開発し、大規模データセットで技術検証しており、方法が研究の中心である。

Code and data availability

The paper explicitly states that the PhenoTrack3D pipeline source code and examples are publicly available on GitHub under an Open Source licence (Cecill-C). This is the authors' analysis code for the paper's maize phenotyping pipeline. No public phenotype dataset or trained model checkpoint URL is stated in the blocks