slideQuantify v2: 5 ‐ Wrapup - swvanderlaan/slideToolKit GitHub Wiki

Description: script is designed to wrap up a slideToolKit-CellProfiler analysis for a given slide within the slideQuantify job-session.

• Written by: Sander W. van der Laan; Tim Bezemer; Tim van de Kerkhof; Yipei Song; Tim S. Peters;
• E-mail: [email protected]
• Last update: 2023-02-09
• Version: 2.2.0

Usage:

./slideQuantify_v2_5_wrapup.sh [STUDY_NUM] [STAIN] [OUTPUTFILENAME] [SLIDETOOLKITDIR] [TILESDIR]

Example Usage:

./slideQuantify_v2_5_wrapup.sh AE21 FIBRIN Image.csv /path/to/slideToolkit /path/to/tiles

Arguments:

• STUDY_NUM
  • Description: Study number of the slide being processed (e.g., AE21).
  • Required: Yes
• STAIN
  • Description: Name of the stain as it appears in the filenames (e.g., FIBRIN).
  • Required: Yes
• OUTPUTFILENAME
  • Description: Output filename where the CellProfiler results are stored (e.g., Image.csv).
  • Required: Yes
• SLIDETOOLKITDIR
  • Description: Path to the slideToolkit directory.
  • Required: Yes
• TILESDIR
  • Description: Path to the tiles directory.
  • Required: Yes