You can get the data here: https://data.broadinstitute.org/bbbc/BBBC010/ (_images.zip and _foreground_eachworm.zip)
The data is provided in tif-files, however our code expects zarr-files
python consolidate_data.py -i ~/data/datasets/data_wormbodies -o ~/data/datasets/data_wormbodies --raw-gfp-min 0 --raw-gfp-max 4095 --raw-bf-min 0 --raw-bf-max 3072 --out-format zarr --parallel 50
python trainTestSplit.py -i ~/data/datasets/data_wormbodies -o ~/data/datasets/data_wormbodies -f zarr
(adapt the input and output paths)
This is the setup used for the results of our ppp model in the paper.
This is the setup used for the results of our ppp+dec model in the paper.