slideQuantify v2: 4 ‐ Cellprofiler - swvanderlaan/slideToolKit GitHub Wiki

Description: script is designed to automate the quantification of stained samples within a given project directory using CellProfiler. It is part of the slideQuantify v2 program, facilitating image analysis workflows.

• Written by: Sander W. van der Laan; Tim Bezemer; Tim van de Kerkhof; Yipei Song; Tim S. Peters;
• E-mail: [email protected]
• Last update: 2021-11-25
• Version: 2.1.0

Usage:

./slideQuantify_v2_4_cellprofiler.sh [DATADIR] [PIPELINE] [STAIN] [SLIDE_NUM] [TILESDIR]

Example Usage:

./slideQuantify_v2_4_cellprofiler.sh /path/to/project /path/to/pipeline/FIBRIN.cppipe FIBRIN AE21 /path/to/tiles

Arguments:

• DATADIR
  • Description: Path to the project directory containing image data.
  • Required: Yes
• PIPELINE
  • Description: Path to the CellProfiler pipeline file (*.cppipe).
  • Required: Yes
• STAIN
  • Description: Name of the stain as it appears in the filenames.
  • Required: Yes
• SLIDE_NUM
  • Description: Slide number being processed (should contain no spaces).
  • Required: Yes
• TILESDIR
  • Description: Path to the directory containing image tiles to be quantified.
  • Required: Yes