How can averaged object measurements be sent to annotation measurements?

[Al]

Hi Qupathers!

I'm trying to compare the total mean fluorescent intensity of cells in different annotations. I have annotations with multiple cells and want to make an average "Cell: Channel 1 Mean" measurement for all cells and then send the result to annotation measurements so I have a single figure for each annotation. I've tried a few of the scripts in here https://gist.github.com/Svidro/68dd668af64ad91b2f76022015dd8a45 but none of them do quite what I want to do.

Thanks,

Alan

[micros...@gmail.com]

Note that forum is now here: https://forum.image.sc/tags/qupath

It sounds like you basically want this one within the list you posted. You just need to change the sum created from all cells from "area" to your measurement of interest, and then divide by the number of cells rather than the total area. If you don't want a particular class, remove the findAll that selects only a given class.

[Al]

Hi micros, thank you so much, I have it working! Here is an adapted version of the script for fluorescent channel intensity. Will switch to the new forum. Thanks again!  

import qupath.lib.objects.PathCellObject

hierarchy = getCurrentHierarchy()

for (annotation in getAnnotationObjects()){

    def allCells = hierarchy.getDescendantObjects(annotation,null, PathCellObject)

    double totalintensity = 0

    for (def cell in allCells){

        totalintensity += cell.getMeasurementList().getMeasurementValue("Cell: Channel 1 mean")

    }

    //Comment the following in or out depending on whether you want to see the output

    println("Mean intensity for allCells is: " + totalintensity/allCells.size)

    println("Total intensity is: " + totalintensity)

    

    //Add to annotation measurements

    annotation.getMeasurementList().putMeasurement("Ch1 Mean Intensity", totalintensity/allCells.size)

    annotation.getMeasurementList().putMeasurement("Ch1 Total Intensity", totalintensity)

   }