LiDARPheno – A Low-Cost LiDAR-Based 3D Scanning System for Leaf Morphological Trait Extraction

Abstract

The ever-growing world population brings the challenge for food security in the current world. The gene modification tools have opened a new era for fast-paced research on new crop identification and development. However, the bottleneck in the plant phenotyping technology restricts the alignment in geno-pheno development as phenotyping is the key for the identification of potential crop for improved yield and resistance to the changing environment. Various attempts to making the plant phenotyping a "high-throughput" have been made while utilizing the existing sensors and technology. However, the demand for 'good' phenotypic information for linkage to the genome in understanding the gene-environment interactions is still a bottleneck in the plant phenotyping technologies. Moreover, the available technologies and instruments are inaccessible, expensive, and sometimes bulky. This work attempts to address some of the critical problems, such as exploration and development of a low-cost LiDAR-based platform for phenotyping the plants in-lab and in-field. A low-cost LiDAR-based system design, LiDARPheno, is introduced in this work to assess the feasibility of the inexpensive LiDAR sensor in the leaf trait (length, width, and area) extraction. A detailed design of the LiDARPheno, based on low-cost and off-the-shelf components and modules, is presented. Moreover, the design of the firmware to control the hardware setup of the system and the user-level python-based script for data acquisition is proposed. The software part of the system utilizes the publicly available libraries and Application Programming Interfaces (APIs), making it easy to implement the system by a non-technical user. The LiDAR data analysis methods are presented, and algorithms for processing the data and extracting the leaf traits are developed. The processing includes conversion, cleaning/filtering, segmentation and trait extraction from the LiDAR data. Experiments on indoor plants and canola plants were performed for the development and validation of the methods for estimation of the leaf traits. The results of the LiDARPheno based trait extraction are compared with the SICK LMS400 (a commercial 2D LiDAR) to assess the performance of the developed system.

Plant phenotyping relevance

低コストLiDARを用いた植物表現型取得システムを開発し、葉形質の抽出アルゴリズムを提示、実験と商用LiDAR比較で検証しており、方法が研究の中心である。

Code and data availability

The supplied blocks describe the LiDARPheno hardware and Python-based data acquisition/trait-extraction scripts, but contain no explicit public deposit or availability statement for the authors' code, LiDAR scan data, or phenotype measurements. The footnoted URLs (ROS sick_lms400 wiki, Python, Dropbox, MathWorks) are,

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