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