slideInfo - swvanderlaan/slideToolKit GitHub Wiki

slideInfo retrieves whole-slide image information from a list of given images, allowing for quick inspection. It utilizes ImageMagick (bash-version) or the OpenSlide library (python-version) to extract properties and associated images, providing details such as dimensions, objective power, available levels, and more.

Two versions are available:

• This is a bash implementation.
• This is a python3 implementation which is much faster than the bash version.

This bash implementation uses ImageMagick and is dependent on the following commands, programs:

• identify (ImageMagick)
• tiffinfo (libtiff)
• openslide-show-properties
• perl, awk and file

Example usage:

./slideInfo -f <filename> [--ignore-dependencies] [--help] [--version]

• -f, --file
  • Specifies the virtual slide file to fetch metadata from.
• --ignore-dependencies
  • Ignores missing dependencies and continues with a warning.
• --help
  • Displays the help message.
• --version
  • Displays version and license information.

Example usage:

python slideInfo.py --input AE1234.SR.ndpi --levels m,6

Argument(s):

• -i, --input
  • Specifies the input, which can be either a single image file, a directory containing files, or a wildcard pattern (e.g., *.ndpi). Required.

Optional argument(s):

• -v, --verbose
  • Enables detailed information, displaying all available image properties. Optional.
• -h, --help
  • Show this help message and exit. Optional.