slideAppend - swvanderlaan/slideToolKit GitHub Wiki

slideAppend is designed to collect results and append them in a CSV file. It processes input CSV files, which are expected to be gzipped. The script creates a log file and organizes data into folders for masks and tile-crossed images. Additionally, it generates a readme file with important information.

Two versions are available:

• slideAppend.sh will concatenate the standard .csv-output.
• slideAppendGCT.sh will concatenate the .GCT-output.

Usage:

bash slideAppend.sh [ARG1] [ARG2] [ARG3] [ARG4]

Example usage:

bash slideAppend.sh FIBRIN AE TIF Image.csv.gz

Argument(s):

• ARG1
  • Name of the stain as it appears in the filenames (e.g., FIBRIN). Required.
• ARG2
  • Study type of the analysis (e.g., AE or AAA). Required.
• ARG3
  • Image file type (e.g., TIF, NDPI). Required.
• ARG4
  • The filename containing results (e.g., Image.csv.gz). Required.