[Save PathObjects instances as label masks] Saves the selected type of PathObject as a label image. Useful for training Deep Models where the ground truth is annotated in QuPath#QuPath

Save objects as masks.groovy

// Save the whole Image

def downsample = 4

// Save the whole Image
def request = RegionRequest.createInstance( getCurrentServer(), downsample )

            
def imageData = getCurrentImageData()

// Get some data to know where to save and how to name the file                
def imageName = GeneralTools.getNameWithoutExtension( getProjectEntry().getImageName() )

def saveDirectory = new File( getProjectBaseDirectory()+"/masks" )
saveDirectory.mkdirs()

// Create a LabeledImageServer
def labelServer = new LabeledImageServer.Builder( imageData )
                            .backgroundLabel(0, ColorTools.BLACK)
                            .multichannelOutput(false)
                            .useInstanceLabels()
                            .useCellNuclei()    // Choose 1
//                            .useDetections()    // Choose 1
//                            .useCells()         // Choose 1
//                            .useAnnotations()   // Choose 1
                            .build()

// Final mask file location
File maskFile = new File(saveDirectory, imageName + "_masks.tif")

// Yay, writing stuff
ImageWriterTools.writeImageRegion(labelServer, request, maskFile.getAbsolutePath())
 
logger.info("Saved image {}", maskFile.getName());

import qupath.lib.objects.PathCellObject;
import qupath.lib.images.servers.LabeledImageServer;