QuPath script to apply a global threshold to an image channel, without relying on a saved PixelClassifier

QuPath-Apply global threshold.groovy

/**
 * QuPath script to threshold a single channel of an image.
 * This can also be useful to convert a binary image into QuPath annotations.
 *
 * First written for https://forum.image.sc/t/rendering-wsi-as-overlay-on-top-of-another-wsi/52629/24?u=petebankhead
 *
 * @author Pete Bankhead
 */

int channel = 0                              // 0-based index for the channel to threshold
double threshold = 0.5                       // Threshold value
int level = 2                                // 0-based resolution level for the image pyramid (choosing 0 may be slow)
def belowClass = getPathClass('Ignore*')     // Class for pixels below the threshold
def aboveClass = getPathClass('Thresholded') // Class for pixels above the threshold

// Create a single-resolution server at the desired level, if required
def server = getCurrentServer()
if (level != 0) {
    server = qupath.lib.images.servers.ImageServers.pyramidalize(server, server.getDownsampleForResolution(level))
}

// Create a thresholded image
def thresholdServer = PixelClassifierTools.createThresholdServer(server, channel, threshold, belowClass, aboveClass)

// Create annotations and add to the current object hierarchy
def hierarchy = getCurrentHierarchy()
PixelClassifierTools.createAnnotationsFromPixelClassifier(hierarchy, thresholdServer, -1, -1)