slideQuantify v2: 1 ‐ Entropy Segmentation - swvanderlaan/slideToolKit GitHub Wiki

Description: This script automates the generation of masks for images, an essential and first step in the slideQuantify workflow. It operates within a SLURM-based environment and utilizes the EntropyMasker for mask generation.

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

Usage:

./slideQuantify_v2_1_entropy_segmentation.sh [project_dir] [masks_dir] [study_number]

Example Usage:

./slideQuantify_v2_1_entropy_segmentation.sh /path/to/project_dir /path/to/masks_dir 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
• study_number
  • Description: Study number of the processed image.
  • Required: Yes