Qupath Multiplex Analysis

The scripts in this project allow to automatically run a multiplex analysis in qupath and add columns for the total numers of each class to the final results table.

Installation

Download the three files CombinationClassCounter.groovy, convert_table.groovy and multiplex_classification.groovy and save them into the folder scripts of your qupath project.

• The script convert_table.groovy will add the total numbers for each class to the results table

  • After having analyzed your images, open the script in the script editor (Automate>Script Editor).
  • Run the script via the command Run from the menu Run of the script editor (do not use Run for project)
  • Select a results file in the tab-separated values (.tsv) format
  • The script will create a new tsv-file in the same folder as the input file

• The script multiplex_classification.groovy, allows to automatically run a multiplex analysis on all images of a project

  • Open the script in the script editor (Automate>Script Editor).
  • Run the script via the command Run for project from the menu Run of the script editor

Step by step protocol

Before getting started, you might want to read the multiplex analysis part of the QuPath-documentation.

1. Create a project and import your images

Run the command File>Project...>Create Project. A dialog will open from which you can create and/or select an empty folder, into which the project files will be saved. Open the folder containing your images in your system's filebrowser and drag them onto the Image list pane of your project in QuPath. On the import dialog, select the image type (for example Fluorescence)) and press the import button.

Depending on the number, type and size of your images, the import might take a while, since a multi-resolution image pyramid has to be created.

2. Setting Channel Names