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LemnaTec Indoor extractors

This repository contains extractors that process data originating from the Bellwether Phenotyping Facility LemnaTec Scanalyzer 3D at the Donald Danforth Plant Science Center.

PlantCV extractor

This extractor 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.

Input

  • Evaluation is triggered whenever a file is added to a dataset
  • Following images must be found
    • 4x NIR side-view = NIR_SV_0, NIR_SV_90, NIR_SV_180, NIR_SV_270
    • 1x NIR top-view = NIR_TV
    • 4x VIS side-view = VIS_SV_0, VIS_SV_90, VIS_SV_180, VIS_SV_270
    • 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 (10 images) are inserted into a CSV file and added to the Clowder dataset
  • If configured, the CSV will also be sent to BETYdb