Export Cell Data from an ABBA registered project #BIOP #ABBA #QuPath

ExportCellDataABBA.groovy

// To execute before:
// 0 - https://gist.github.com/NicoKiaru/723d8e628a3bb03902bb3f0f2f0fa466
// 1 - https://gist.github.com/NicoKiaru/f45f56e3ff2d1fb708821c110fbdee62

// save annotations
File directory = new File(buildFilePath(PROJECT_BASE_DIR,'export'));
directory.mkdirs();

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

def filename = imageName//.take(imageName.indexOf('.'))

saveMeasurements(
    imageData,
    PathDetectionObject.class,
    buildFilePath(directory.toString(),filename + '.tsv'),
    "Class",
    "Allen CCFv3 X mm",
    "Allen CCFv3 Y mm",
    "Allen CCFv3 Z mm",
    "Count: Num Spots"
);


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