Data Sources

Lemnatec Field Scanner

This section describes the sensors deployed on the Lemnatec Field Scanner in Maricopa, AZ. Device and sensor information, including technical specifications, calibration data, and calibration targets are stored in the TERRA REF Clowder database.

The Maricopa field site is located at the the University of Arizona Maricopa Agricultural Center and USDA Arid Land Research Station in Maricopa, Arizona. At this site, we have deployed the following phenotyping platforms.

The Lemnatec Scanalyzer Field System is the largest field crop analytics robot in the world. This high-throughput phenotyping field-scanning robot has a 30-ton steel gantry that autonomously moves along two 200-meter steel rails while continuously imaging the crops growing below it with a diverse array of cameras and sensors.

Sensor Name

Model and Spec Sheet

Field of View

Technical Specifications

Notes

Imaging Sensors

Stereo RGB Camera

GT3300 (web) (specs)

53°

Laser Scanner

Custom Frauhofer 3D (specs)

0.5m width

Resolution: 0.3-0.9 mm

VNIR Hyperspectral Imager

Inspector VNIR (specs)

21°

380-1000 nm @ 2/3 nm resolution

SWIR Hyperspectral Imager

Inspector SWIR (specs)

44.5°

900-2500 nm @ 2/3 nm resolution

Thermal Infrared

FLIR SC 615 (web) (specs)

25° x 19°

Thermal Sensitivity < 50mK @ 30C

PSII Fluorescence Response

Lemnatec PS II (specs)

25° x 19°

Illumination 635nm x 4000umol/m2/s

Multi-spectral Radiometers

Dedicated NDVI

Skye Multispectral Radiometer (web) (specs)

CH1: 650nm; CH2 800. Bandwidth: 10 nm

1 down, 1 up

Dedicated PRI Sensor

Skye Radiometer (web) (specs)

CH1: 531nm +/- 3nm

PRI = Photochemical Reflectance Index

PAR Sensor

Quantum SQ-300

180°

Spectral Range 410 to 655 nm

VNIR Spectroradioometer

Ocean Optics STS-Vis

Range: 337-824 nm @ 1/2 nm

VNIR+SWIR Spectrometer

Spectral Evolution PSR+

Range 350-2500nm @3-8 nm

Installed 2018

Active Reflectance

Crop Circle ACS430P

Bands: 670, 730, 780 nm

Environmental Sensors

Environmental Sensors

Thies ClimaSensorD (web) (specs)

Wind, Air T, Humidity, Pressure, Light, Precipitation

Open Path CO2 Sensor

GMP 343

Range: 0-1000 ppm

Maricopa Agricultural Center (MAC), Arizona

The Maricopa field site is located at the the University of Arizona Maricopa Agricultural Center and USDA Arid Land Research Station in Maricopa, Arizona. At this site, we have deployed the following phenotyping platforms.

UAV Data

  • weekly flights with RGB and multispectral cameras

Manually Collected Field Data

Data were collected manually using standard field methods. These measurements are used to calibrate and validate phenotypes derived from sensor-collected data.

Controlled-environment phenotyping

Donald Danforth Plant Science Center, Missouri

The Bellwether Foundation Phenotyping Facility is a climate controlled 70 m2 growth house with a conveyor belt system for moving plants to and from fluorescence, color, and near infrared imaging cabinets. This automated, high-throughput platform allows repeated non-destructive time-series image capture and multi-parametric analysis of 1,140 plants in a single experiment.

The Scanalyzer 3D platform at the Bellwether Foundation Phenotyping Facility at the Donald Danforth Plant Science Center consists of multiple digital imaging chambers connected to the Conviron growth house by a conveyor belt system, resulting in a continuous imaging loop. Plants are imaged from the top and/or multiple sides, followed by digital construction of images for analysis.

  • RGB imaging allows visualization and quantification of plant color and structural morphology, such as leaf area, stem diameter and plant height.

  • NIR imaging enables visualization of water distribution in plants in the near infrared spectrum of 900–1700 nm.

  • Fluorescent imaging uses red light excitation to visualize chlorophyll fluorescence between 680 – 900 nm. The system is equipped with a dark adaptation tunnel preceding the fluorescent imaging chamber, allowing the analysis of photosystem II efficiency.

The LemnaTec software suite is used to program and control the Scanalyzer platform, analyze the digital images and mine resulting data. Data and images are saved and stored on a secure server for further review or reanalysis.

Genomics

Genomic data includes whole-genome resequencing data from the HudsonAlpha Institute for Biotechnology, Alabama for 384 samples for accessions from the sorghum Bioenergy Association Panel (BAP) and genotyping-by-sequencing (GBS) data from Kansas State University for 768 samples from a population of sorghum recombinant inbred lines (RIL).