Open source 3D phenotyping of chickpea plant architecture across plant development

Abstract

In this work, we developed a low-cost 3D scanner and used an open source data processing pipeline to phenotype the 3D structure of individual chickpea plants. Being able to accurately assess the 3D architecture of plant canopies can allow us to better estimate plant productivity and improve our understanding of underlying plant processes. This is especially true if we can monitor these traits across plant development. Photogrammetry techniques, such as structure from motion, have been shown to provide accurate 3D reconstructions of monocot crop species such as wheat and rice, yet there has been little success reconstructing crop species with smaller leaves and more complex branching architectures, such as chickpea. The imaging system we developed consists of a user programmable turntable and three cameras that automatically captures 120 images of each plant and offloads these to a computer for processing. The capture process takes 5-10 minutes for each plant and the majority of the reconstruction process on a Windows PC is automated. Plant height and total plant surface area were validated against “ground truth” measurements, producing R2 > 0.99 and a mean absolute percentage error < 10%. We demonstrate the ability to assess several important architectural traits, including canopy volume and projected area, and estimate relative growth rate in commercial chickpea cultivars and lines from local and international breeding collections. Detailed analysis of individual reconstructions also allowed us to investigate partitioning of plant surface area, and by proxy plant biomass.

Earbox, an open tool for high-throughput measurement of the spatial organization of maize ears and inference of novel traits

“…The system developed and presented in this study is a scalable system providing an accurate, robust, and reliable way to extract precise measurements from maize ear images, including spatial features of grain organization. This work illustrates, like many others [ 50 – 54 ], the possibilities and the efficiency that open-source technologies and low-cost electronics now offer to plant science. They make accurate phenotyping accessible to everyone.…”

Earbox, an open tool for high-throughput measurement of the spatial organization of maize ears and inference of novel traits

“…The system developed and presented in this study is a scalable system providing an accurate, robust, and reliable way to extract precise measurements from maize ear images, including spatial features of grain organization. This work illustrates, like many others (Bagley et al, 2020;Czedik-Eysenberg et al, 2018;Gaggion et al, 2020;Pearce, 2020;Salter et al, 2020), the possibilities and the efficiency that open-source technologies and low-cost electronics now offer to plant science. They make accurate phenotyping accessible to everyone.…”