Controlled Environment phenotype data
Last updated
Last updated
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.
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
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: