Set the classification of a subcellular detection according to whether it is inside or outside the nucleus

QuPath_subcellular_detection_location.groovy

// Note: This sets the class according to spot/cluster location,
// but does not try to set meaningful colors at this point

// Get all spots/clusters
def clusters = getObjects({p -> p.class == qupath.imagej.detect.cells.SubcellularDetection.SubcellularObject.class})

// Loop through all clusters
for (c in clusters) {
    // Find the containing cell
    def cell = c.getParent()
    // Check the current classification - remove the last part if it 
    // was generated by a previous run of this command
    def pathClass = c.getPathClass()
    if (["Nuclear", "Cytoplasmic"].contains(c.getName())) {
        pathClass = pathClass.getParentClass()
    }
    // Check the location of the cluster centroid relative to the nucleus,
    // and classify accordingly
    def nucleus = cell.getNucleusROI()
    if (nucleus != null && nucleus.contains(c.getROI().getCentroidX(), c.getROI().getCentroidY())) {
        c.setPathClass(getDerivedPathClass(c.getPathClass(), "Nuclear"))
    } else
        c.setPathClass(getDerivedPathClass(c.getPathClass(), "Cytoplasmic"))
}
fireHierarchyUpdate()

@ranadeyuq My guess is that in the script editor, the option Run → Include default bindings isn't selected.

In general, these gists are kind of 'throwaway' scripts to answer a specific question. This one would have been written for QuPath v0.1.2 but won't necessarily work in v0.2.0 because some pretty major changes are being made. The really important scripts should become built-in features of the software eventually, so that they can be kept up-to-date with changing versions.