export_tiles

Export tiles with annotation from QuPath

Requirements

Inside SLIDE_TILING/{SAMPLE_NAME}/: - {SAMPLE_NAME}.tiff which can be a symbolic link - {SAMPLE_NAME}.geojson with the annotation

Tiling

./launch_tiling.sh /mnt/netapp2/translational_oncology/SLIDE_TILING/COLAB_CHUS_10_20220513_0943_0_5

Filtering

To filter tiles by their percentage of annotated pixels (default: >=50%):

python ./filter_tiles.py /mnt/netapp2/translational_oncology/SLIDE_TILING/COLAB_CHUS_10_20220513_0943_0_5

This will generate a "OK_tiles.txt" file inside the tiles folder listing the names of the tiles that pass the filter

Normalizing

module load miniconda3/4.11.0
conda activate SPAMS_conda4.11.0
./launch_normalize.sh /mnt/netapp2/translational_oncology/SLIDE_TILING/COLAB_CHUS_10_20220513_0943_0_5 vahadane

### Warning You need this in your ~/.bashrc:

channels:
  - conda-forge
  - bioconda
  - defaults
  - r
envs_dirs:
  - /mnt/netapp2/uscmg_aplic/3_environments/python/
pkgs_dirs:
  - /mnt/netapp2/uscmg_aplic/3_environments/python/pkgs