[Replace detections as cells via erosion and add measurements] Erodes existing detection objects to create cells and adds all compartment measurements #qupath #groovy #detections

Replace detections as cells via erosion and add measurements.groovy

/**
 * Reduce Detection size to create new cell objects and add measurements
 * @author Olivier Burri
 * @date 20240212
 */
 
// By how much should the existing detections be reduced to create the new "nucleus"
def erosionDistancePx = -5

// Should the intensities be measured on a downsampled image?
def downsample = 1.0


// START OF SCRIPT

// Required objects for adding compartment measurements later
def server = getCurrentServer()

// Choose all intensity measurements inside all compartments
def measurements = ObjectMeasurements.Measurements.values() as List
def compartments = ObjectMeasurements.Compartments.values() as List

// Loop through the annotations and find the detections, shrink them, create a new Cell object and measure
getAnnotationObjects().each{ annotation ->
    
    def oldDetections = annotation.getChildObjects().findAll{ it instanceof qupath.lib.objects.PathDetectionObject }
    
    def newDetections = oldDetections.collect{ d ->
    
        // Previous Detection
        def oldGeom = d.getROI().getGeometry()
        
        // Nucleus created by erosion
        def nuc = oldGeom.buffer( erosionDistancePx )
        
        // Cell outline is the old detection
        def cell = oldGeom
        
        // Create a new cell using the original ROI as "Cell" and the eroded ROI as "Nucleus"
        def smaller = PathObjects.createCellObject( GeometryTools.geometryToROI( cell, d.getROI().getImagePlane() ), 
                                                    GeometryTools.geometryToROI( nuc, d.getROI().getImagePlane()) , 
                                                    d.getPathClass()  // Keep the old PathClass
                                                   )
        
        // Add the measurements
        ObjectMeasurements.addIntensityMeasurements( server, smaller, 1.0, measurements, compartments )
    
        return smaller
    }
    
    // Remove the old objects
    annotation.removeChildObjects( oldDetections )
    
    // Add the new objects
    annotation.addChildObjects( newDetections )
}

fireHierarchyUpdate()

// Necessary import
import qupath.lib.analysis.features.ObjectMeasurements