scholarly journals Novel 3D Imaging Systems for High-Throughput Phenotyping of Plants

2021 ◽  
Vol 13 (11) ◽  
pp. 2113
Author(s):  
Tian Gao ◽  
Feiyu Zhu ◽  
Puneet Paul ◽  
Jaspreet Sandhu ◽  
Henry Akrofi Doku ◽  
...  
Keyword(s):  
3D Reconstruction ◽  
High Throughput ◽  
Imaging System ◽  
Point Clouds ◽  
Imaging Systems ◽  
Phenotypic Traits ◽  
Reconstruction Algorithms ◽  
High Quality ◽  
3D Point Clouds ◽  
High Throughput Phenotyping

The use of 3D plant models for high-throughput phenotyping is increasingly becoming a preferred method for many plant science researchers. Numerous camera-based imaging systems and reconstruction algorithms have been developed for the 3D reconstruction of plants. However, it is still challenging to build an imaging system with high-quality results at a low cost. Useful comparative information for existing imaging systems and their improvements is also limited, making it challenging for researchers to make data-based selections. The objective of this study is to explore the possible solutions to address these issues. We introduce two novel systems for plants of various sizes, as well as a pipeline to generate high-quality 3D point clouds and meshes. The higher accuracy and efficiency of the proposed systems make it a potentially valuable tool for enhancing high-throughput phenotyping by integrating 3D traits for increased resolution and measuring traits that are not amenable to 2D imaging approaches. The study shows that the phenotype traits derived from the 3D models are highly correlated with manually measured phenotypic traits (R2 > 0.91). Moreover, we present a systematic analysis of different settings of the imaging systems and a comparison with the traditional system, which provide recommendations for plant scientists to improve the accuracy of 3D construction. In summary, our proposed imaging systems are suggested for 3D reconstruction of plants. Moreover, the analysis results of the different settings in this paper can be used for designing new customized imaging systems and improving their accuracy.

scholarly journals 3D city scale reconstruction using wide area motion imagery

2018 ◽  
Author(s):  
◽  
Raphael Viguier
Keyword(s):  
3D Reconstruction ◽  
Data Compression ◽  
Data Augmentation ◽  
Point Clouds ◽  
Wide Area ◽  
Large Field ◽  
Reconstruction Algorithms ◽  
Detection And Tracking ◽  
3D Point Clouds ◽  
Motion Imagery

3D reconstruction is one of the most challenging but also most necessary part of computer vision. It is generally applied everywhere, from remote sensing to medical imaging and multimedia. Wide Area Motion Imagery is a field that has gained traction over the recent years. It consists in using an airborne large field of view sensor to cover a typically over a square kilometer area for each captured image. This is particularly valuable data for analysis but the amount of information is overwhelming for any human analyst. Algorithms to efficiently and automatically extract information are therefore needed and 3D reconstruction plays a critical part in it, along with detection and tracking. This dissertation work presents novel reconstruction algorithms to compute a 3D probabilistic space, a set of experiments to efficiently extract photo realistic 3D point clouds and a range of transformations for possible applications of the generated 3D data to filtering, data compression and mapping. The algorithms have been successfully tested on our own datasets provided by Transparent Sky and this thesis work also proposes methods to evaluate accuracy, completeness and photo-consistency. The generated data has been successfully used to improve detection and tracking performances, and allows data compression and extrapolation by generating synthetic images from new point of view, and data augmentation with the inferred occlusion areas.

scholarly journals MVS-Pheno: A Portable and Low-Cost Phenotyping Platform for Maize Shoots Using Multiview Stereo 3D Reconstruction

2020 ◽  
Vol 2020 ◽  
pp. 1-17 ◽  
Author(s):  
Sheng Wu ◽  
Weiliang Wen ◽  
Yongjian Wang ◽  
Jiangchuan Fan ◽  
Chuanyu Wang ◽  
...  
Keyword(s):  
Data Management ◽  
High Throughput ◽  
Management System ◽  
Low Cost ◽  
Point Clouds ◽  
Data Management System ◽  
Plant Phenotyping ◽  
Phenotypic Traits ◽  
High Throughput Phenotyping ◽  
Multiview Stereo

Plant phenotyping technologies play important roles in plant research and agriculture. Detailed phenotypes of individual plants can guide the optimization of shoot architecture for plant breeding and are useful to analyze the morphological differences in response to environments for crop cultivation. Accordingly, high-throughput phenotyping technologies for individual plants grown in field conditions are urgently needed, and MVS-Pheno, a portable and low-cost phenotyping platform for individual plants, was developed. The platform is composed of four major components: a semiautomatic multiview stereo (MVS) image acquisition device, a data acquisition console, data processing and phenotype extraction software for maize shoots, and a data management system. The platform’s device is detachable and adjustable according to the size of the target shoot. Image sequences for each maize shoot can be captured within 60-120 seconds, yielding 3D point clouds of shoots are reconstructed using MVS-based commercial software, and the phenotypic traits at the organ and individual plant levels are then extracted by the software. The correlation coefficient (R2) between the extracted and manually measured plant height, leaf width, and leaf area values are 0.99, 0.87, and 0.93, respectively. A data management system has also been developed to store and manage the acquired raw data, reconstructed point clouds, agronomic information, and resulting phenotypic traits. The platform offers an optional solution for high-throughput phenotyping of field-grown plants, which is especially useful for large populations or experiments across many different ecological regions.

scholarly journals High-throughput phenotyping in cotton: a review

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Irish Lorraine B. PABUAYON ◽  
Yazhou SUN ◽  
Wenxuan GUO ◽  
Glen L. RITCHIE
Keyword(s):  
High Throughput ◽  
Cropping Systems ◽  
Three Dimensional ◽  
Growth Yield ◽  
Analytical Techniques ◽  
Phenotypic Traits ◽  
Technological Advances ◽  
Recent Developments ◽  
Potential Applications ◽  
High Throughput Phenotyping

Abstract Recent technological advances in cotton (Gossypium hirsutum L.) phenotyping have offered tools to improve the efficiency of data collection and analysis. High-throughput phenotyping (HTP) is a non-destructive and rapid approach of monitoring and measuring multiple phenotypic traits related to the growth, yield, and adaptation to biotic or abiotic stress. Researchers have conducted extensive experiments on HTP and developed techniques including spectral, fluorescence, thermal, and three-dimensional imaging to measure the morphological, physiological, and pathological resistance traits of cotton. In addition, ground-based and aerial-based platforms were also developed to aid in the implementation of these HTP systems. This review paper highlights the techniques and recent developments for HTP in cotton, reviews the potential applications according to morphological and physiological traits of cotton, and compares the advantages and limitations of these HTP systems when used in cotton cropping systems. Overall, the use of HTP has generated many opportunities to accurately and efficiently measure and analyze diverse traits of cotton. However, because of its relative novelty, HTP has some limitations that constrains the ability to take full advantage of what it can offer. These challenges need to be addressed to increase the accuracy and utility of HTP, which can be done by integrating analytical techniques for big data and continuous advances in imaging.

3D Reconstruction of Plant Leaves for High-Throughput Phenotyping

2018 ◽  
Author(s):  
Feiyu Zhu ◽  
Suresh Thapa ◽  
Tiao Gao ◽  
Yufeng Ge ◽  
Harkamal Walia ◽  
...  
Keyword(s):  
3D Reconstruction ◽  
High Throughput ◽  
Plant Leaves ◽  
High Throughput Phenotyping

CROWD-SOURCED VISUAL DATA COLLECTION FOR MONITORING INDOOR CONSTRUCTION IN 3D

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Fouad Amer ◽  
Mani Golparvar-Fard
Keyword(s):  
Data Collection ◽  
3D Reconstruction ◽  
Structure From Motion ◽  
Reconstruction Algorithm ◽  
Point Clouds ◽  
Reconstruction Method ◽  
Visual Data ◽  
Mapping Algorithm ◽  
3D Point Clouds ◽  
Localization And Mapping

Complete and accurate 3D monitoring of indoor construction progress using visual data is challenging. It requires (a) capturing a large number of overlapping images, which is time-consuming and labor-intensive to collect, and (b) processing using Structure from Motion (SfM) algorithms, which can be computationally expensive. To address these inefficiencies, this paper proposes a hybrid SfM-SLAM 3D reconstruction algorithm along with a decentralized data collection workflow to map indoor construction work locations in 3D and any desired frequency. The hybrid 3D reconstruction method is composed of a pipeline of Structure from Motion (SfM) coupled with Multi-View Stereo (MVS) to generate 3D point clouds and a SLAM (Simultaneous Localization and Mapping) algorithm to register the separately formed models together. Our SfM and SLAM pipelines are built on binary Oriented FAST and Rotated BRIEF (ORB) descriptors to tightly couple these two separate reconstruction workflows and enable fast computation. To elaborate the data capture workflow and validate the proposed method, a case study was conducted on a real-world construction site. Compared to state-of-the-art methods, our preliminary results show a decrease in both registration error and processing time, demonstrating the potential of using daily images captured by different trades coupled with weekly walkthrough videos captured by a field engineer for complete 3D visual monitoring of indoor construction operations.

scholarly journals Evaluation of feature-based methods for automated network orientation

2014 ◽  
Vol XL-5 ◽  
pp. 47-54 ◽  
Author(s):  
F.I. Apollonio ◽  
A. Ballabeni ◽  
M. Gaiani ◽  
F. Remondino
Keyword(s):  
Image Processing ◽  
3D Reconstruction ◽  
Processing Time ◽  
Point Clouds ◽  
Large Networks ◽  
Sift Algorithm ◽  
3D Point Clouds ◽  
Network Orientation ◽  
Feature Based ◽  
Automated Image Processing

Every day new tools and algorithms for automated image processing and 3D reconstruction purposes become available, giving the possibility to process large networks of unoriented and markerless images, delivering sparse 3D point clouds at reasonable processing time. In this paper we evaluate some feature-based methods used to automatically extract the tie points necessary for calibration and orientation procedures, in order to better understand their performances for 3D reconstruction purposes. The performed tests – based on the analysis of the SIFT algorithm and its most used variants – processed some datasets and analysed various interesting parameters and outcomes (e.g. number of oriented cameras, average rays per 3D points, average intersection angles per 3D points, theoretical precision of the computed 3D object coordinates, etc.).

scholarly journals GNSS/INS-Assisted Structure from Motion Strategies for UAV-Based Imagery over Mechanized Agricultural Fields

2020 ◽  
Vol 12 (3) ◽  
pp. 351 ◽  
Author(s):  
Seyyed Meghdad Hasheminasab ◽  
Tian Zhou ◽  
Ayman Habib
Keyword(s):  
3D Reconstruction ◽  
Structure From Motion ◽  
Point Clouds ◽  
Bundle Adjustment ◽  
Agricultural Fields ◽  
System Calibration ◽  
3D Point Clouds ◽  
Digital Agriculture ◽  
Orientation Parameters ◽  
Calibration Parameters

Acquired imagery by unmanned aerial vehicles (UAVs) has been widely used for three-dimensional (3D) reconstruction/modeling in various digital agriculture applications, such as phenotyping, crop monitoring, and yield prediction. 3D reconstruction from well-textured UAV-based images has matured and the user community has access to several commercial and opensource tools that provide accurate products at a high level of automation. However, in some applications, such as digital agriculture, due to repetitive image patterns, these approaches are not always able to produce reliable/complete products. The main limitation of these techniques is their inability to establish a sufficient number of correctly matched features among overlapping images, causing incomplete and/or inaccurate 3D reconstruction. This paper provides two structure from motion (SfM) strategies, which use trajectory information provided by an onboard survey-grade global navigation satellite system/inertial navigation system (GNSS/INS) and system calibration parameters. The main difference between the proposed strategies is that the first one—denoted as partially GNSS/INS-assisted SfM—implements the four stages of an automated triangulation procedure, namely, imaging matching, relative orientation parameters (ROPs) estimation, exterior orientation parameters (EOPs) recovery, and bundle adjustment (BA). The second strategy— denoted as fully GNSS/INS-assisted SfM—removes the EOPs estimation step while introducing a random sample consensus (RANSAC)-based strategy for removing matching outliers before the BA stage. Both strategies modify the image matching by restricting the search space for conjugate points. They also implement a linear procedure for ROPs’ refinement. Finally, they use the GNSS/INS information in modified collinearity equations for a simpler BA procedure that could be used for refining system calibration parameters. Eight datasets over six agricultural fields are used to evaluate the performance of the developed strategies. In comparison with a traditional SfM framework and Pix4D Mapper Pro, the proposed strategies are able to generate denser and more accurate 3D point clouds as well as orthophotos without any gaps.

Development of a Mobile Platform for Wheat Phenotyping

2020 ◽  
Author(s):  
Majid Khak Pour ◽  
Reza Fotouhi ◽  
Pierre Hucl
Keyword(s):  
Data Collection ◽  
High Throughput ◽  
Vegetation Indices ◽  
Field Measurements ◽  
Mobile Platform ◽  
Mechatronic System ◽  
High Quality ◽  
Wheat Field ◽  
Crop Monitoring ◽  
High Throughput Phenotyping

Abstract Designing and implementing an affordable High-Throughput Phenotyping Platform (HTPP) for monitoring crops’ features in different stages of their growth can provide valuable information for crop-breeders to study possible correlation between genotypes and phenotypes. Conducting automatic field measurements can improve crop productions. In this research, we have focused on development of a mechatronic system, hardware and software, for a mobile field-based HTPP for autonomous crop monitoring for wheat field. The system can measure canopy’s height, temperature, vegetation indices and is able to take high quality photos of crops. The system includes developed software for data and image acquisition. The main contribution of this study is autonomous, reliable, and fast data collection for wheat and similar crops.

scholarly journals Leaf Segmentation on Dense Plant Point Clouds with Facet Region Growing

Sensors ◽  
2018 ◽  
Vol 18 (11) ◽  
pp. 3625 ◽  
Author(s):  
Dawei Li ◽  
Yan Cao ◽  
Xue-song Tang ◽  
Siyuan Yan ◽  
Xin Cai
Keyword(s):  
Point Cloud ◽  
Active Material ◽  
Region Growing ◽  
Point Clouds ◽  
Phenotypic Traits ◽  
Individual Leaf ◽  
3D Point Clouds ◽  
Segmentation Approach ◽  
Monstera Deliciosa ◽  
Leaf Segmentation

Leaves account for the largest proportion of all organ areas for most kinds of plants, and are comprise the main part of the photosynthetically active material in a plant. Observation of individual leaves can help to recognize their growth status and measure complex phenotypic traits. Current image-based leaf segmentation methods have problems due to highly restricted species and vulnerability toward canopy occlusion. In this work, we propose an individual leaf segmentation approach for dense plant point clouds using facet over-segmentation and facet region growing. The approach can be divided into three steps: (1) point cloud pre-processing, (2) facet over-segmentation, and (3) facet region growing for individual leaf segmentation. The experimental results show that the proposed method is effective and efficient in segmenting individual leaves from 3D point clouds of greenhouse ornamentals such as Epipremnum aureum, Monstera deliciosa, and Calathea makoyana, and the average precision and recall are both above 90%. The results also reveal the wide applicability of the proposed methodology for point clouds scanned from different kinds of 3D imaging systems, such as stereo vision and Kinect v2. Moreover, our method is potentially applicable in a broad range of applications that aim at segmenting regular surfaces and objects from a point cloud.

scholarly journals Calculation Method for Phenotypic Traits Based on the 3D Reconstruction of Maize Canopies

Sensors ◽  
2019 ◽  
Vol 19 (5) ◽  
pp. 1201 ◽  
Author(s):  
Xiaodan Ma ◽  
Kexin Zhu ◽  
Haiou Guan ◽  
Jiarui Feng ◽  
Song Yu ◽  
...  
Keyword(s):  
3D Reconstruction ◽  
Plant Height ◽  
Calculation Method ◽  
3D Structure ◽  
Calculated Data ◽  
Point Clouds ◽  
Measured Data ◽  
Stem Diameter ◽  
Phenotypic Traits ◽  
Area Index

A reasonable plant type is an essential factor for improving canopy structure, ensuring a reasonable expansion of the leaf area index and obtaining a high-quality spatial distribution of light. It is of great significance in promoting effective selection of the ecological breeding index and production practices for maize. In this study, a method for calculating the phenotypic traits of the maize canopy in three-dimensional (3D) space was proposed, focusing on the problems existing in traditional measurement methods in maize morphological structure research, such as their complex procedures and relatively large error margins. Specifically, the whole maize plant was first scanned with a FastSCAN hand-held scanner to obtain 3D point cloud data for maize. Subsequently, the raw point clouds were simplified by the grid method, and the effect of noise on the quality of the point clouds in maize canopies was further denoised by bilateral filtering. In the last step, the 3D structure of the maize canopy was reconstructed. In accordance with the 3D reconstruction of the maize canopy, the phenotypic traits of the maize canopy, such as plant height, stem diameter and canopy breadth, were calculated by means of a fitting sphere and a fitting cylinder. Thereafter, multiple regression analysis was carried out, focusing on the calculated data and the actual measured data to verify the accuracy of the calculation method proposed in this study. The corresponding results showed that the calculated values of plant height, stem diameter and plant width based on 3D scanning were highly correlated with the actual measured data, and the determinant coefficients R2 were 0.9807, 0.8907 and 0.9562, respectively. In summary, the method proposed in this study can accurately measure the phenotypic traits of maize. Significantly, these research findings provide technical support for further research on the phenotypic traits of other crops and on variety breeding.

Sign in / Sign up

Export Citation Format

Share Document