slideMacro

slideMacro is designed to extract macro images from whole-slide image (WSI) files (e.g., *.TIF, *.ndpi) in .png-format. It allows users to specify the magnification level and additional options for displaying, saving, and handling the output.

Two versions are available:

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

Supported formats

• TIFF
• Aperio
• Hamamatsu
• iScan
• iScanHT
• Leica

Bash version

The bash version is using ImageMagick.

Examples:

• Setting the file:

  ./slideMacro -f "file.TIF"

• Setting the macro suffix:

  ./slideMacro --file="file.TIF" --macrosuffix=".layer5"

• Forcing a specific layer:

  ./slideMacro --file="file.TIF" -l 3

• Setting additional convert arguments:

  ./slideMacro --file="file.TIF" --convert-args='-resize 300x300 -rotate 90'

• Ignoring dependencies:

  ./slideMacro --file="file.TIF" --ignore-dependencies

• Displaying help:

  ./slideMacro --help

• Displaying version information:

  ./slideMacro --version

Job list examples:

• Print a job list

find "$(pwd)" -iname "*.TIF" -printf 'slideMacro is processing file [ %p ].\n' -exec $(command -v "$SCRIPTNAME") --file "{}" \;

• Print a job list for SLURM

find "$(pwd)" -iname "*.TIF" -type f \
    -exec printf "sbatch $DEFAULT_SLURMARGS --chdir=\"$(pwd)/\" " \; \
    -exec printf "$(command -v "$SCRIPTNAME") " \; \
    -exec echo "--file=\"{}\"" \;

Argument(s):

• -f, --file <filename>
  • Specifies the virtual slide file to create a mask from.

Optional argument(s):

• --macrosuffix <text>
  • Sets the macro suffix. The default is ".macro".
• -l, --layer <integer>
  • Forces a specific layer by layer id.
• --convert-args='<arguments>'
  • Sets convert arguments (use '=' sign and quotes).
• --ignore-dependencies
  • Ignores missing dependencies but gives a warning.
• --help
  • Displays the help message.
• --version
  • Displays version and license information.

Dependencies

• convert

Python version

Example usage:

python slideMacro.py --input AE1234.SR.ndpi

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.
• -l, --levels
  • Magnification level to extract, with '6' as level 6. Try: 6. Required.

Optional argument(s):

• -o, --outdir
  • Output dir, default is present working directory. Optional.
• -s, --suffix
  • Suffix to append to end of file, default is 'm' for thumbnail and '#' for a given level. Optional.
• -t, --type
  • Output file type, default is png (which is slower), other options are tif. Optional.
• -f, --force
  • Force output even if it exists. Optional.
• -v, --verbose
  • While writing images also display image properties. Optional.
• -h, --help
  • Show this help message and exit. Optional.