Extract cell detection data from segmented areas/annotations in TMA (IF Images) - Qupath

I am trying to extract immune cell detection data from multiplex stained TMA. I am getting all the detection data like it’s in that screenshot, total numbers together. But I also segmented all the cores into tumor and stromal region through manual annotation. How do I get the detection numbers for those annotated regions (tumor/stroma) separately?

Hi @Arif00002,

Aren’t these present in Show annotation measurements? (Right under Show TMA measurements, which I believe is where your screenshot is from)


Hi Melvin,

In the annotation measurement, I get something like this, detection numbers for each separate annotation.

But I want numbers of detection for each type of annotated area (total area). Meaning total tumor or stromal area containing all the respective annotations. And also these data for each core separately. Hope you got what I am trying to get.

So it sounds like you want to cycle through all of the cores, select all annotations per class within a core
(selectObjectsByClass), “Merge selected annotations”?

That will require a script but sounds fairly straightforward. Though, I see a lot of unclassified annotation objects. How do you expect those to be handled?

Also, the resolveHierarchy() at the beginning of @melvingelbard’s next script will fill in the TMA-Core portion of the Annotation measurements.

Adding in a script that does what I mentioned above. It may be fairly slow compared to @melvingelbard’s script below, and WILL result in the change of your objects, merging all annotations of the same class, per TMA Core, into one object. It currently does process all of your null annotations, though I am not sure if that is desired behavior since the existence of the null annotations was not explained.

print "This may take a while depending on how many annotations and cells are present"
Set classes = []
classes = getAnnotationObjects().collect{it?.getPathClass()?.toString()}
getTMACoreList().each{ core ->
        currentObjectSet = getCurrentHierarchy().getObjectsForROI(qupath.lib.objects.PathAnnotationObject, core.getROI())
        //print currentObjectSet.size()
        currentClassObjects = currentObjectSet.findAll{it.getPathClass() == getPathClass(currentClass.toString())}
        //print currentClassObjects.size()
        getCurrentHierarchy().getSelectionModel().setSelectedObjects(currentClassObjects, null)
print "Done"
1 Like

Or if you just want to count the total amount of detections separated by the PathClass of the parent annotation without modifying your objects, I think this is what you want?:

getTMACoreList().forEach { tma ->
    def totalDetections = [:]
    tma.getChildObjects().forEach { child ->
        if (!child.isCell()) {
            if (totalDetections.containsKey(child.getPathClass()))
                totalDetections[child.getPathClass()] += child.getChildObjects().size()
                totalDetections.put(child.getPathClass(), child.getChildObjects().size())
    print "TMA (" + tma.getName() + "): " + totalDetections