export atlas coordinates of manual cell count annotation

[tang37]

Hello,

Thank you for developing such wonderful tools!

I tried to use the groovy script to extract atlas coordinates of my manual cell count annotations in QuPath (replacing getCellObjects() with getAllObjects()), but when I run the script in QuPath, it did not output the measurement .tsv file or the folder. It seemed stopped running immediately after I hit run.

I changed back to getCellObjects() to see what would happen, which suppose to give me "empty objects" warning because I did not use the automatic cell detection, but I also did not get the output file or any message after I hit run.

Any idea how to make it work?

import static qupath.lib.gui.scripting.QPEx. // For intellij editor autocompletion import static ch.epfl.biop.qupath.atlas.allen.api.AtlasTools.

import qupath.lib.objects.PathObjects import qupath.lib.roi.ROIs import qupath.lib.regions.ImagePlane import qupath.lib.measurements.MeasurementList import qupath.lib.objects.PathCellObject

import ch.epfl.biop.qupath.transform.* import net.imglib2.RealPoint

// https://github.com/BIOP/qupath-biop-extensions/blob/master/src/test/resources/abba_scripts/importABBAResults.groovy def targetEntry = getProjectEntry() def targetEntryPath = targetEntry.getEntryPath();

def fTransform = new File (targetEntryPath.toString(),"ABBA-Transform.json")

if (!fTransform.exists()) { System.err.println("ABBA transformation file not found for entry "+targetEntry); return ; }

def pixelToCCFTransform = Warpy.getRealTransform(fTransform).inverse(); // Needs the inverse transform

def imageData = getCurrentImageData(); imageName = ServerTools.getDisplayableImageName(imageData.getServer())

def myObjects = getAllObjects().findAll{it.getName() == 'PathAnnotationObject'}

if (getAllObjects().isEmpty()) { throw new Exception("No cell detections in this file. Please run cell and subcellular spot detection on $imageName.") }

getAllObjects().forEach{detection -> { RealPoint ccfCoordinates = new RealPoint(3); ccfCoordinates.setPosition([ detection.getROI().getCentroidX(), detection.getROI().getCentroidY(), 0 ] as double[]); pixelToCCFTransform.apply(ccfCoordinates, ccfCoordinates); MeasurementList ml = detection.getMeasurementList(); ml.addMeasurement("Allen CCFv3 X mm", ccfCoordinates.getDoublePosition(0) ) ml.addMeasurement("Allen CCFv3 Y mm", ccfCoordinates.getDoublePosition(1) ) ml.addMeasurement("Allen CCFv3 Z mm", ccfCoordinates.getDoublePosition(2) )

if (!ml.containsNamedMeasurement("Subcellular: Channel 5: Num single spots")) {
    throw new Exception("Subcellular spot detection incomplete in this file. Please rerun subcellular spot detection on $imageName.")
}

ml.addMeasurement("Esr1 (Opal 480): Num Spots", ml.getMeasurementValue("Subcellular: Channel 2: Num single spots") )
ml.addMeasurement("Prg (Opal 520): Num Spots", ml.getMeasurementValue("Subcellular: Channel 3: Num single spots") )
ml.addMeasurement("Prlr (Opal 570): Num Spots", ml.getMeasurementValue("Subcellular: Channel 4: Num single spots") )
ml.addMeasurement("Oxt (Opal 620): Num Spots", ml.getMeasurementValue("Subcellular: Channel 5: Num single spots") )

}}

// save annotations //File directory = new File(buildFilePath(PROJECT_BASE_DIR,'export')); File directory = new File(buildFilePath('C:\Users\tangy\Downloads\abba_test2','export')); directory.mkdirs(); def filename = imageName.take(imageName.indexOf('.'))

saveMeasurements( imageData, // PathCellObject.class, PathAnnotationObject.class, buildFilePath(directory.toString(),filename + '.tsv'), "Class", "Allen CCFv3 X mm", "Allen CCFv3 Y mm", "Allen CCFv3 Z mm", "Esr1 (Opal 480): Num Spots", "Prg (Opal 520): Num Spots", "Prlr (Opal 570): Num Spots", "Oxt (Opal 620): Num Spots", );

Appreciate for any help provided! Kelly