Try to extract the label from an image in QuPath v0.2 and display it in ImageJ with enhanced contrast

QuPath-Extract_label.groovy

/**
 * Try to extract the label from an image and show this with enhanced contrast using ImageJ as the viewer.
 *
 * This is mostly intended for .czi files, where currently the label seems to be 16-bit
 * and displays as entirely black in QuPath.
 *
 * It assumes that the label exists as an 'associated image' within the server.
 * 
 * This has been tested with QuPath v0.2 - it may not work with other versions.
 *
 * @author Pete Bankhead
 */
 
import qupath.imagej.gui.IJExtension
import javax.swing.SwingUtilities

def server = getCurrentServer()
def labelImageName = server.getAssociatedImageList().find {it.toLowerCase().contains('label')}

if (labelImageName == null) {
    println "Unable to find an associated image with 'label' in the name"
    return
}

def img = server.getAssociatedImage(labelImageName)

// Show using ImageJ, with enhanced contrast
SwingUtilities.invokeLater {
    IJExtension.getImageJInstance()
    def imp = IJTools.convertToUncalibratedImagePlus(labelImageName, img)
    ij.IJ.run(imp, "Enhance Contrast...", " ")
    imp.show()
}