Controlled Environment phenotype data

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. 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: https://github.com/danforthcenter/plantcv. For more information, see:

Project website: http://plantcv.danforthcenter.org

Full documentation: http://plantcv.readthedocs.io/en/latest

Publications:

• https://doi.org/10.7717/peerj.4088

• https://doi.org/10.1016/j.molp.2015.06.005

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

• an ipython notebook demonstration of PlantCV plantcv/plantcv_jupyter_demo.ipynb.

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

Computational pipeline

PlantCV extractor

• 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

• BETYdb: https://terraref.ncsa.illinois.edu/bety

For details about accessing BETYdb, please see Data Access section and a tutorial on accessing phenotypes from the trait database on the TERRA REF Workbench in traits/04-danforth-indoor-phenotyping-facility.Rmd.

Raw Data

• Clowder: Bellwether Phenotyping Facility Space

• Globus and Workbench:

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