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danforthcenter / plantcv

Plant phenotyping with image analysis
Mozilla Public License 2.0
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Processing time with poor color correction #1420

Open Stylopidae1793 opened 10 months ago

Stylopidae1793 commented 10 months ago

I am doing some germination studies which were top-watered, and this creates some issues with the detect color card function.

Water pooling on the color cards makes it difficult for color correction to take place, resulting in inconsistent ROIs, which in turn increases processing time.

This increased processing time makes it difficult to obtain a complete dataset which can filter out improper colorspaces.

HaleySchuhl commented 10 months ago

Filter on time point. Suggesting to analyze just one time point per day, and ensuring the time point is not affected by watering. Within the Python workflow be able to parse the filename and only proceed if timepoint is desired timepoint.

HaleySchuhl commented 10 months ago

Also, ok to detect color card (will save chip size for scaling) but SKIP color correction since segmentation is not necessarily/ consistently helped by correcting in this round.