TERRA-REF Documentation
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Primary version
  • Introduction
  • Scientific Objectives
  • Experimental Design
    • The Maricopa Agricultural Center (MAC)
    • Controlled Environment Phenotyping
    • Genomics
  • Data
    • How to Access Data
    • Data Products
      • Environmental conditions
      • Phenotype Data
      • Genomics data
      • Fluorescence intensity imaging
      • Geospatial information
      • Hyperspectral imaging data
      • Infrared heat imaging data
      • Meteorological data
      • Point Cloud Data
      • Controlled Environment phenotype data
    • Data Use Policy
    • Manuscripts and Authorship Guidelines
  • Protocols
    • Field Scanner
    • Sensor Calibration
    • Hyperspectral Data
    • Controlled Environment Protocols
    • Manual Field Data Protocols
    • Phenotractor Protocols
    • UAV Protocols
    • Genomic Protocols
  • Technical Documentation
    • Software
    • Data Standards
      • Existing Data Standards
      • Agronomic and Phenotype Data Standards
      • Genomic Data Standards
      • Sensor Data Standards
      • Data Standards Committee
    • Data Product Levels
    • Directory Structure
    • Data Transfer
    • Data Processing Pipeline
    • Time Series Data in Geostreams
    • Data Backup
    • Systems Configuration
  • Code of Conduct
  • Appendix
    • Glossary
    • Accessing BETYdb with GIS Software
  • References
  • Archived Documentation
    • Developer Manual
      • Submitting data to Clowder
      • Submitting data to BETYdb
      • Submitting Data to CoGe
      • Developing Clowder Extractors
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  • LemnaTec Scanalyzer 3D platform at the Donald Danforth Plant Science Center
  • Computational pipeline
  • Data access
  • Level 1
  • Raw Data
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  1. Data
  2. Data Products

Controlled Environment phenotype data

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Last updated 5 years ago

LemnaTec Scanalyzer 3D platform at the Donald Danforth Plant Science Center

Phenotype data is derived from images generated by the indoor LemnaTec Scanalyzer 3D platform at the Donald Danforth Plant Science Center using . PlantCV is an image analysis package for plant phenotyping. PlantCV is composed of modular functions in order to be applicable to a variety of plant types and imaging systems. PlantCV contains base functions that are required to examine images from an excitation imaging fluorometer (PSII), visible spectrum camera (VIS), and near-infrared camera (NIR). PlantCV is a fully open source project: . For more information, see:

Project website:

Full documentation:

Publications:

To learn more about PlantCV, you can find examples in the repository, which is accessible on GitHub and in the TERRA REF under tutorials/plantcv

  • an ipython notebook demonstration of PlantCV .

For the TERRA-REF project, a PlantCV Clowder extractor was developed to analyze data from the at the Donald Danforth Plant Science Center. Resulting phenotype data is stored in BETYdb.

Computational pipeline

  • Description: Processes VIS/NIR images captured at several angles to generate trait metadata. The trait metadata is associated with the source images in Clowder, and uploaded to the configured BETYdb instance.

  • Output CSV: /sites/danforth/Level_1/<experiment name>

Input

  • Evaluation is triggered whenever a file is added to a dataset

  • Following images must be found

    • 2x NIR side-view = NIR_SV_0, NIR_SV_90

    • 1x NIR top-view = NIR_TV

    • 2x VIS side-view = VIS_SV_0, VIS_SV_90

    • 1x VIS top-view = VIS_TV

  • Per-image metadata in Clowder is required for BETYdb submission; this is how barcode/genotype/treatment/timestamp are determined.

Output

  • Each image will have new metadata appended in Clowder including measures like height, area, perimeter, and longest_axis

  • Average traits for the dataset (3 VIS or 3 NIR images) are inserted into a CSV file and added to the Clowder dataset

  • If configured, the CSV will also be sent to BETYdb

Data access

Level 1

Raw Data

  • Globus and Workbench:

    • /sites/danforth/raw_data/<experiment name>

BETYdb:

For details about accessing BETYdb, please see section and a tutorial on accessing phenotypes from the trait database on the TERRA REF Workbench in .

Clowder:

PlantCV
https://github.com/danforthcenter/plantcv
http://plantcv.danforthcenter.org
http://plantcv.readthedocs.io/en/latest
https://doi.org/10.7717/peerj.4088
https://doi.org/10.1016/j.molp.2015.06.005
terraref/tutorials
workbench
plantcv/plantcv_jupyter_demo.ipynb
Bellwether Foundation Phenotyping Facility
PlantCV extractor
https://terraref.ncsa.illinois.edu/bety
Data Access
traits/04-danforth-indoor-phenotyping-facility.Rmd
Bellwether Phenotyping Facility Space