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Extract DINO feats

  • download DINO repository
  • store repository path into Environment variable export DINO_REPO=PATH export MIL4WSI_PATH=PATH
  • collect a csv with three columns: slide_name (image), label (0/1), phase (train/test) example:
image label phase
name_1 0 train
name_2 1 test

Launch the feature extraction through submitit!

python run_with_submitit.py --extractedpatchespath HIERARCHICAL_PATH --savepath DESTINATION_PATH --pretrained_weights1 CHECKPOINTDINO20x --pretrained_weights2 CHECKPOINTDINO10x --pretrained_weights3 CHECKPOINTDINO5x --propertiescsv CSV_PATH

EXAMPLE:

python run_with_submitit.py --extractedpatchespath /mnt/beegfs/work/H2020DeciderFicarra/decider/decider_multi --savepath /mnt/beegfs/work/H2020DeciderFicarra/decider/feats/hr --pretrained_weights1 /mnt/beegfs/work/H2020DeciderFicarra/dinodecider20/checkpoint.pth --pretrained_weights2 /mnt/beegfs/work/H2020DeciderFicarra/dinodecider10/checkpoint.pth --pretrained_weights3 /mnt/beegfs/work/H2020DeciderFicarra/dinodecider5/checkpoint.pth --propertiescsv hr.csv