Cost-effective, high-throughput phenotyping system for 3D reconstruction of fruit form

Authors: FELDMANN, MITCHELL - University Of California, Davis; Tabb, Amy

Submitted to: The Plant Phenome Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2021
Publication Date: 2/18/2022
Citation: Feldmann, M.J., Tabb, A. 2022. Cost-effective, high-throughput phenotyping system for 3D reconstruction of fruit form. The Plant Phenome Journal. https://doi.org/10.1002/ppj2.20029.
DOI: https://doi.org/10.1002/ppj2.20029

Interpretive Summary: We designed and implemented hardware and software to generate three-dimensional models of fruits and tubers. To determine the accuracy of our system, we used a three-dimensional printer to print objects of a known shape so that the models from the system were compared with the known shapes. The system described in the paper generates three-dimensional models that are similar to the shapes of the three-dimensional printed objects. This type of system is important for plant phenotyping studies, where it is difficult for fruit three-dimensional shape measurements to be acquired manually.

Technical Abstract: Reliable phenotyping methods that are simple to operate and inexpensive to deploy are critical for studying quantitative traits in plants. Traditional fruit shape phenotyping relies on human raters or 2D analyses to assess form, e.g., size and shape. Systems for 3D imaging using multi-view stereo have been implemented but frequently rely on commercial software and/or specialized hardware, which can lead to limitations in accessibility and scalability. We present a complete system constructed of consumer-grade components for capturing, calibrating, and reconstructing the 3D form of small-to-moderate sized fruits and tubers. Data acquisition and image capture sessions are nine seconds to capture 60 images. The initial prototype cost was $1,600 USD. We measured accuracy by comparing reconstructed models of 3D printed ground truth objects to the original digital files of those same ground truth objects. The R2 between length of the primary, secondary, and tertiary axes, volume, and surface area of the ground-truth object and the reconstructed models was >0.97 and root-mean square error (RMSE) was <3 mm for objects without locally concave regions. Measurements from 1 mm and 2 mm resolution reconstructions were consistent (R2 > 0.99). Qualitative assessments were performed on 48 fruit and tubers, including 18 strawberries, 12 potatoes, five grapes, seven peppers, and four Bosc and two red Anjou pears. Our proposed phenotyping system is fast, relatively low cost, and has demonstrated accuracy for certain shape classes, and could be used for the 3D analysis of fruit form.