A very simple script to add a name to each annotation in an image in QuPath. Each name is suffixed with an incrementing number.

AnnotationIncrementor.groovy

/*
Probably based on something from here: https://forum.image.sc/tag/qupath 
OR 
something from here: https://gist.github.com/Svidro

Thank You!
*/

hierarchy = getCurrentHierarchy()
def imageName = getProjectEntry().getImageName()
int annotationNumber = 1

for (annotation in getAnnotationObjects()) {
    hierarchy.getSelectionModel().clearSelection();
    selectObjects{p -> p == annotation}
    // name your annotation anything you like
    def annotationName = 'TISSUE-'
    // add the annotation's number as a suffix
    annotation.setName(imageName + ' ' + annotationName + annotationNumber)
    annotationNumber += 1
}