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  • Introduction
  • Data Sources
  • Software
  • Scientific Objectives and Experimental Design
    • Protocols
      • Controlled Environment Protocols
      • Manual Field Data Protocols
      • Phenotractor Protocols
      • Sensor Calibration
      • Template Protocol
      • UAV Protocols
    • Experimental Design
      • Experimental Design Danforth
        • Sorghum Lines Danforth
      • Experimental Design Genomics
        • Sorghum Lines Genomics Year 1
        • Sorghum Lines Genomics Year 1 (continued)
        • Sorghum Lines Genomics Year 2
      • Experimental Design MAC
  • User Manual
    • What Data is Available
    • Data Products
      • Environmental conditions
      • Fluorescence intensity imaging
      • Genomics data
      • Geospatial information
      • Hyperspectral imaging data
      • Infrared heat imaging data
      • Multispectral imaging data
      • Meteorological data
      • Phenotype data
      • Point Cloud Data
    • How to Access Data
      • Using Clowder (Sensor and Genoomics data)
      • Using Globus (Sensor and Genomics data)
      • Using BETYdb (trait data, experimental metadata)
        • Accessing BETYdb via ArcMap and other GIS software
      • Using CoGe (Genomics)
      • Using CyVerse (Genomics)
      • Using Analysis Workbench (all data)
    • Data Use Policy
    • Manuscripts and Authorship Guidelines
    • Release / reprocessing schedule
  • Technical Documentation
    • Data Standards
      • Existing Data Standards
      • Agronomic and Phenotype Data Standards
      • Genomic Data Standards
      • Sensor Data Standards
      • Data Standards Committee
    • Directory Structure
    • Data Storage
    • Data Transfer
    • Data Processing Pipeline
      • Geospatial Time Series Structure
    • Data Backup
    • Data Collection
    • Data Product Creation
      • Genomic Data
      • Hyperspectral Data
    • Quality Assurance and Quality Control
    • Systems Configuration
  • Developer Manual
    • Submitting data to Clowder
    • Submitting data to BETYdb
    • Submitting Data to CoGe
    • Developing Clowder Extractors
  • Tutorials
  • Appendix
    • Code of Conduct
    • Collaboration Tools
    • Glossary
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  • Abstract
  • Materials
  • Methods
  • Tractor
  • Sensors
  • Plant Height with Sonar
  • Thermal Sensor
  • Multispectral Radiometer
  • Georeferencing
  • References
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  1. Scientific Objectives and Experimental Design
  2. Protocols

Phenotractor Protocols

PreviousManual Field Data ProtocolsNextSensor Calibration

Last updated 7 years ago

Authors: Matthew Maimaitiyiming, Wasit Wulamu, and David LeBauer

Center for Sustainability, Saint Louis University, St. Louis, MO 63108

Abstract

This document provides a brief summary of methods, procedures, and workflows to process the tractor data.

Content modified from .

Materials

  • Tractor

  • Sensors

    • Sonar Transducer

    • GreenSeeker Multispectral Radiometer

    • Infrared Thermal Sensor

Methods

Tractor

The Tractor-based plant phenotyping system (Phenotractor) was built on a LeeAgra 3434 DL open rider sprayer. The vehicle has a clearance of 1.93 m. A boom attached to the front end of the tractor frame holds the sensors, data loggers, and other instrumentation components including enclosure boxes and cables. The boom can be moved up and down with sensors remaining on a horizonal plane. An isolated secondary power source supplies 12-V direct current to the electronic components used for phenotyping.

Sensors

The phenotractor was equipped with three types of sensors for measuring plant height, temperature and canopy spectral reflectance. A RTK GPS was installed on top of the tractor, see the figure below.

Plant Height with Sonar

The distance from canopy to sensor position was measured with a sonar proximity sensor ($S\rm{output}$, in mm). Canopy height ($CH$) was determined by combining sonar and GPS elevation data (expressed as meter above sea level). An elevation survey was conducted to determine a baseline reference elevation ($E\rm{ref}$) for the gantry field. CH was computed according to the following equation:

where $E_rm{s}$ is sensor elevation, which was calculated by subtracting the vertical offset between the GPS antenna and sonar sensor from GPS antenna elevation.

Thermal Sensor

Multispectral Radiometer

Canopy spectral reflectance was measured with GreenSeeker sensors and the reflectance data were used to calculate NDVI (Normalized Difference Vegetation Index). GreenSeeker sensors record reflected light energy in near infrared (780 ± 15 nm) and red (660 ± 10 nm ) portion electromagnetic spectrum from top of the canopy by using a self-illuminated light source. NDVI was calculated using following equation:

Where $\rho\rm{NIR}$ and $\rho\rm{red}$ and ρ_red represent fraction of reflected energy in near infrared and red spectral regions, respectively.

Georeferencing

Georefencing was carried out using a specially developed Quantum GIS (GGIS, www.qgis.org ) plug-in by Andrade-Sanchez et al. (2014) during post processing. Latitude and longitude coordinates were converted to UTM coordinate system. Offset from the sensors to the GPS position on the tractor heading were computed and corrected. Next, the tractor data, which uses UTM Zone 12 (MAC coordinates), was transformed to EPSG:4326 (WGS84) USDA coordinates by performing a linear shifting as follows:

  • Latitude: $U_y = M_y – 0.000015258894$

  • Longitude: $U_x = M_x + 0.000020308287$

References

Phenotractor system configuration

An Infrared radiometer (IRT) sensors were used measure canopy temperature and temperature values were recoded as degree Celsius (°C).

where $U_y$ and $U_x$ are latitude and longitude in USDA coordinate system, and $M_y$ and $M_x$ are latitude and longitude in MAC coordinate system (see ). Finally, georeferenced tractor data was overlaid on the gantry field polygon and mean value for each plot/genotype was calculated using the data points that fall inside the plot polygon within ArcGIS Version 10.2 (ESRI. Redlands, CA).

Andrade-Sanchez, Pedro, Michael A. Gore, John T. Heun, Kelly R. Thorp, A. Elizabete Carmo-Silva, Andrew N. French, Michael E. Salvucci, and Jeffrey W. White. "Development and evaluation of a field-based high-throughput phenotyping platform." Functional Plant Biology 41, no. 1 (2014): 68-79.

Apogee SI-121
section on geospatial coordinate systems
doi:10.1071/FP13126
Andrade-Sanchez et al 2014
Picture of Phenotractor Sensors
Diagram of sensor attachments
Diagram of Sensor Offset