slideMacro - swvanderlaan/slideToolKit GitHub Wiki

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