0.5.0 Stardist.groovy

import qupath.ext.stardist.StarDist2D
import qupath.lib.gui.dialogs.Dialogs
import qupath.lib.scripting.QP

def modelPath = 'F:/QuPath/Stardist/dsb2018_heavy_augment.pb'

selectAnnotations();

def stardist = StarDist2D
    .builder(modelPath)
    .channels('DAPI')            // Extract channel called 'DAPI'
    .normalizePercentiles(1, 98) // Percentile normalization
    .threshold(0.4)              // Probability (detection) threshold
    .pixelSize(0.5)              // Resolution for detection
    .cellExpansion(5)            // Expand nuclei to approximate cell boundaries
    .measureShape()              // Add shape measurements
    .measureIntensity()          // Add cell measurements (in all compartments)
    .build()
	
def pathObjects = QP.getSelectedObjects()
def imageData = QP.getCurrentImageData()
if (pathObjects.isEmpty()) {
    QP.getLogger().error("No parent objects are selected!")
    return
}
stardist.detectObjects(imageData, pathObjects)
stardist.close() // This can help clean up & regain memory
println('Done!')