Comparison of Open-Source Three-Dimensional Reconstruction Pipelines for
Maize-Root Phenotyping
Abstract
Understanding three-dimensional (3D) root traits is essential to improve
water uptake, increase nitrogen capture, and raise carbon sequestration
from the atmosphere. However, quantifying 3D root traits by
reconstructing 3D root models for deeper field-grown roots remains a
challenge due to the unknown tradeoff between 3D root-model quality and
3D root-trait accuracy. Therefore, we performed two computational
experiments. We first compared the 3D model quality generated by five
state-of-the-art open-source 3D model reconstruction pipelines on 12
contrasting genotypes of field-grown maize roots. These pipelines
included COLMAP, COLMAP+PMVS (Patch-based Multi-view Stereo), VisualSFM,
Meshroom, and OpenMVG+MVE (Multi-View Environment). The COLMAP pipeline
achieved the best performance regarding 3D model quality versus
computational time and image number needed. Thus, in the second test, we
compared the accuracy of 3D root-trait measurement generated by the
Digital Imaging of Root Traits 3D pipeline (DIRT/3D) using COLMAP-based
3D reconstruction with our current DIRT/3D pipeline that uses a
VisualSFM-based 3D reconstruction (Liu et al., 2021) on the same dataset
of 12 genotypes, with 5~10 replicates per genotype. The
results revealed that, 1) the average number of images needed to build a
denser 3D model was reduced from 3000~3600 (DIRT/3D
[VisualSFM-based 3D reconstruction]) to 300~600
(DIRT/3D [COLMAP-based 3D reconstruction]); 2) denser 3D models
helped improve the accuracy of the 3D root-trait measurement; 3)
reducing the number of images can help resolve data storage capacity
problems. The updated DIRT/3D (COLMAP-based 3D reconstruction) pipeline
enables quicker image collection without compromising the accuracy of 3D
root-trait measurements.