slideQuantify v2: 2 ‐ Extract Tiles - swvanderlaan/slideToolKit GitHub Wiki

Description: This script facilitates the extraction of tiles from images, the second process within the slideQuantify workflow. It operates in a SLURM-based environment and utilizes slideExtractTiles.py within slideToolKit for tile extraction.

  • Written by: Tim S. Peters
  • E-mail: [email protected]
  • Last update: 2024-01-09
  • Version: 1.0.0

Usage:

./slideQuantify_v2_2_extract_tiles.sh [project_dir] [masks_dir] [layer] [tile_size] [study_number]

Example Usage:

./slideQuantify_v2_2_extract_tiles.sh /path/to/project_dir /path/to/masks_dir 1 2000 AE21

Arguments:

  • project_dir
    • Description: Path to the project directory containing _ndpi and/or _tif folders with images.
    • Required: Yes
  • masks_dir
    • Description: Path to the directory where masks for the images will be stored.
    • Required: Yes
  • layer
    • Description: Magnification layer of the image from which tiles should be extracted.
    • Required: Yes
  • tile_size
    • Description: Size of the extracted tiles.
    • Required: Yes
  • study_number
    • Description: Study number of the processed image.
    • Required: Yes