slideConvert - swvanderlaan/slideToolKit GitHub Wiki

slideConvert facilitates the conversion of digital slide formats into Generic-TIFF using the Bio-Formats tool bfconvert. It includes options to customize the conversion process, handle dependencies, and display version information.

Example usage:

./slideConvert --file AE1234.SR.ndpi

Argument(s):

• -f, --file
  • Specifies the digital slide file to be converted to the default output format (.ome.tiff). Required.

Optional argument(s):

• --bfconvert-args <arguments>
  • Allows the user to provide additional arguments for the bfconvert tool. Optional.
• --ignore-dependencies
  • Ignores missing dependencies, allowing the script to continue execution. Optional.
• -v, --version
  • Outputs version and license information. Optional.
• -h, --help
  • Displays a comprehensive help message with usage details, options, and examples. Optional.