Scripts for processing of scanned dishes with 2 rows with 12 seedlings over 10 days, starting with a plate with nongerminated seeds.
A directory with files named apogwas1_set1_day7_20170602_003.tif (bold parts are required). Here 003 identifies dish.
Run
plateproc.py -d input_directory {-o output_directory}
A dish is skipped if the file plant-regions.png exists in its output subdirectory,
For each detected dish a subdirectory named by its identifier (e. g. 003) is created in output directory. Files this directory
- plates-001.png: overview image of the aligned plates (projection in the Z direction)
- seeds-001.tif and seeds-mask-001.tif: masks and inverted masks of seeds drom day 0 image.
- plant-regions.png: overview of defined region
- region data: A tiff file with 11 bands (days 0 -- 10) with a name plant-001-18_2855-3182_3391-5432.tif. The fields: ** -001-: dish identifier, equal to subdirectory name ** -18_: number of plant in the dish, counted from the upper left corner ** _2855-3182_3391-543: UpperLeftX-UpperLeftY_LowerRightX-LowerRightY