It is possible to perform setCellIntensityClassifications in QuPath for a certain class?
Thx
Hi @bp314,
Just to clarify, you want to set cells as positive and negative only for detections belonging to a specific class?
For context, could you explain why you want that? It’s just not immediately clear to me. Is it because you want a different classification for different classes?
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Hello @bp314,
Assuming that @lmurphy is right, maybe something like this could work?
import qupath.lib.objects.PathObject;
import qupath.lib.objects.PathObjects;
import qupath.lib.objects.PathCellObject;
import java.util.stream.Collectors;
// Change measurementName & thresholds variables as you like
def measurementName = "Nucleus: Hematoxylin OD min";
def thresholds = [0.05, 0.2] as double[];
def hierarchy = getCurrentHierarchy();
def cls = PathCellObject.class;
// Define the name of the class to classify
def myClass = "Tumor";
Collection<PathObject> pathObjects = hierarchy.getObjects(null, cls);
// Filter the objects to only retain the ones classified as 'myClass'
pathObjects = pathObjects.stream()
.filter{object -> (object.getPathClass() == null) || (object.getPathClass().toString().substring(0, myClass.size()).equals(myClass))}
.collect(Collectors.toList());
setIntensityClassifications(pathObjects, measurementName, thresholds);
hierarchy.fireObjectClassificationsChangedEvent(cls, pathObjects);
print "Done!"
Though this assumes that you’ve ran the cell detection AND the detection classifier prior. This script will just change the ‘positive/negative’ (or 1+/2+/3+) classifications of the specific class (defined in myClass).
It seems to work for me, hopefully that will help you solve your problem! 
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