Create a 'counts' image in QuPath that can be used to compute the local density of specific objects

QuPath-Create counts map.groovy

/**
 * Create a 'counts' image in QuPath that can be used to compute the local density of specific objects.
 *
 * This implementation uses ImageJ to create and display the image, which can then be filtered as required.
 * 
 * Written for QuPath v0.2.0.
 *
 * @author Pete Bankhead
 */

import ij.ImagePlus
import ij.process.FloatProcessor
import qupath.imagej.gui.IJExtension
import qupath.lib.objects.PathObjectTools
import qupath.lib.regions.RegionRequest

import static qupath.lib.gui.scripting.QPEx.*
import qupath.imagej.tools.IJTools

// Define the resolution at which the image should be generated
double requestedPixelSizeMicrons = 20

// Get the current image
def imageData = getCurrentImageData()
def server = imageData.getServer()
// Set the downsample directly (without using the requestedPixelSize) if you want; 1.0 indicates the full resolution
double downsample = requestedPixelSizeMicrons / server.getPixelCalibration().getAveragedPixelSizeMicrons()
def request = RegionRequest.createInstance(server, downsample)
def imp = IJTools.convertToImagePlus(server, request).getImage()

// Get the objects you want to count
// Potentially you can add filters for specific objects, e.g. to get only those with a 'Positive' classification
def detections = getDetectionObjects()
//detections = detections.findAll {it.getPathClass() == getPathClass('Positive')}

// Create a counts image in ImageJ, where each pixel corresponds to the number of centroids at that pixel
int width = imp.getWidth()
int height = imp.getHeight()
def fp = new FloatProcessor(width, height)
for (detection in detections) {
    // Get ROI for a detection; this method gets the nucleus if we have a cell object (and the only ROI for anything else)
    def roi = PathObjectTools.getROI(detection, true)
    int x = (int)(roi.getCentroidX() / downsample)
    int y = (int)(roi.getCentroidY() / downsample)
    fp.setf(x, y, fp.getf(x, y) + 1 as float)
}

// Show the images
IJExtension.getImageJInstance()
imp.show()
new ImagePlus(imp.getTitle() + "-counts", fp).show()

Yes, it is definitely a result of rounding. Thanks for the fix on my non-fix (which you are correct, just shifted the error). We were looking into the densityMaps class but have not had the time to figure out the correct way to script them.