slideLookup - swvanderlaan/slideToolKit GitHub Wiki

slideLookup is designed to perform a whole-slide image (WSI) sample lookup (--samples) in a directory or a set of directories (--dir) containing WSI for a given --study_type (AE or AAA). By default, the script will look for the following directories: CD3, CD34, CD66b, CD68, EVG, FIBRIN, GLYCC, HE, SMA, SR, SR_POLARIZED. These can be changed with the --dir flag. By default a log file is written to the current working directory and is of the form [todays_date.study_type.slideLookup.log.log].

Optionally, the found files can be copied (--copy) to another directory (--copy-dir). By default, the files will be copied to the following directory: ../VirtualSlides/Projects/histo_lookups. The --log flag will change the default output name of the log file, and --copy-dir will change the log-output directory too. It provides extra information (--verbose) if requested.

Example usage:

python slideLookup.py --study_type AE --samples AE4211 AE3422  --dir CD14 CD3 --verbose

Argument(s):

• --samples, -s
  • List of whole-slide image (WSI) samples, e.g. AE4211 AE3422. Required.
• --dir, -d
  • List of directories, e.g. CD14 CD3. Required. Default: CD3, CD34, CD66b, CD68, EVG, FIBRIN, GLYCC, HE, SMA, SR, SR_POLARIZED.
• --study_type, -t
  • Specify the study type prefix, e.g., AE or AAA (no other option is possible). Required.

Optional argument(s):

• --log, -l
  • Specify the log-filename which will be of the form [todays_date.study_type.slideLookup.log.log]. Optional. By default the log file will be written to the current working directory.
• --copy, -c
  • Copy files to copy-dir. Optional.
• --copy_dir, -cd
  • Specify the directory to copy files to. Optional. By default the files will be copied to the following directory: ../VirtualSlides/Projects/histo_lookups.
• --verbose, -v
  • Print extra information. Optional.
• --version, -V
  • Print version. Optional.
• --help, -h
  • Print help message. Optional.