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Export Annotated Tiles in QuPath

This script is used to export annotated tiles from a QuPath project. To use this script, you need to open your QuPath project first and then load and run the script.
To load the script, from the menu bar click on Automate -> Script editor and then copy/paste the code into the text box. Then click on Run. You can also put the provided script file into the user or shared scripts folder of your QuPath installation directory.

Script parameters:

  • Export directory:
    def pathOutput = buildFilePath(PROJECT_BASE_DIR, 'tiles', name)
    This parameter defines where the exported tiles will be saved. The default value is set as PROJECT_BASE_DIR/tiles/{image_name}.

  • Downsampling:
    double downsample = 1.0
    This parameter defines how much to scale down the tiles before exporting it. For example, if you want to export a tile at half resolution, set this parameter to 2.

  • Annotation to export:
    .addLabel('vessels.and.small', 1)
    This parameter defines which annotations should be exported. In this case, we are only interested in vessels.and.small annotations and we set the class label to 1 as opposed to 0 for background. If you have other types of annotations that you would like to include, add them here with their corresponding class label ID.

  • Tile size:
    .tileSize(512)
    This parameter defines the size of each tile (in pixels). The default value is 512x512.