NicoKiaru/DetectCellsABBA.groovy

## DetectCellsABBA.groovy
/**
* ABBA Script : performs a cell detection on the root node annotation
* imported from ABBA and restores the child objects after the detection has been performed
* To use and modify like you need / want
* You need to have imported the regions before running this script. See https://gist.github.com/NicoKiaru/723d8e628a3bb03902bb3f0f2f0fa466 for instance
* See https://biop.github.io/ijp-imagetoatlas/
* Author: Olivier Burri, Nicolas Chiaruttini, BIOP, EPFL
* Date: 2022-01-26
*/

// setImageType('FLUORESCENCE'); // if your image is fluorescent

// If you just want to clear the detections and keep the previously ABBA imported annotations
clearDetections()

// or, if you want to reset and re-import all annotations from ABBA
// clearAllObjects();
// qupath.ext.biop.abba.AtlasTools.loadWarpedAtlasAnnotations(getCurrentImageData(), "acronym", true);

def project = getProject()

// We want to run cell detection only once on the entire brain, which means we need to select the Root node. We can find it by name
def root = getAnnotationObjects().find{ it.getName().equals( 'Root' ) }

// Duplicate root node. It is a bit contrived but this is how you can copy an annotation
def regionMeasured = PathObjectTools.transformObject( root, null, true )

// Temporary name
regionMeasured.setName( "Measured Region" )

// Need to add it to the current hierarchy
addObject( regionMeasured )

// So that we can select it
setSelectedObject( regionMeasured )

// RUN CELL DETECTION
// Modify the line below by inserting your cell detection plugin line
// *********************************************************************
// *********************************************************************
runPlugin( 'qupath.imagej.detect.cells.WatershedCellDetection',
          '{"detectionImage": "FL CY3",  "requestedPixelSizeMicrons": 2.0,  "backgroundRadiusMicrons": 8.0,  "medianRadiusMicrons": 0.0,  "sigmaMicrons": 2.0,  "minAreaMicrons": 20.0,  "maxAreaMicrons": 400.0,  "threshold": 200.0,  "watershedPostProcess": true,  "cellExpansionMicrons": 0.0,  "includeNuclei": true,  "smoothBoundaries": true,  "makeMeasurements": true}')
// *********************************************************************
// *********************************************************************

// We no longer need the object we used for detection. We remove it but keep the child objects, which are the cells
removeObject( regionMeasured, true )

// We can now add the cells to the original root object
def cells = getDetectionObjects()
root.addPathObjects( cells )

// Update the view for the user
fireHierarchyUpdate()

// From here, the rest of the script adds to all cells their coordinates in the reference atlas
// to their measurement list


// Get ABBA transform file located in entry path
def targetEntry = getProjectEntry()
def targetEntryPath = targetEntry.getEntryPath()

def fTransform = new File(targetEntryPath.toFile(), "ABBA-Transform-Adult Mouse Brain - Allen Brain Atlas V3p1.json" )

if ( !fTransform.exists() ) {
    logger.error( "ABBA transformation file not found for entry {}", targetEntry )
    return
}

def pixelToCCFTransform = Warpy.getRealTransform( fTransform ).inverse() // Needs the inverse transform

getDetectionObjects().forEach{ detection ->
    def ccfCoordinates = new RealPoint(3)
    def  ml = detection.getMeasurementList()

    ccfCoordinates.setPosition( [detection.getROI().getCentroidX(),detection.getROI().getCentroidY(), 0] as double[] )
    // The Z=0 pixel coordinate is automatically transformed to the right atlas position in Z thanks to the fact that the slice
    // position is already known by the transform

    // This applies the transform in place to cffCoordinates
    pixelToCCFTransform.apply(ccfCoordinates, ccfCoordinates)

    // Fianlly: Add the coordinates as measurements
    ml.addMeasurement("Allen CCFv3 X mm", ccfCoordinates.getDoublePosition(0) )
    ml.addMeasurement("Allen CCFv3 Y mm", ccfCoordinates.getDoublePosition(1) )
    ml.addMeasurement("Allen CCFv3 Z mm", ccfCoordinates.getDoublePosition(2) )
    ml.addMeasurement("Count: Num Spots", 1 )
}


// imports
import qupath.ext.biop.warpy.*
import net.imglib2.RealPoint
import qupath.lib.measurements.MeasurementList
import qupath.lib.objects.PathObjectTools
import qupath.lib.objects.PathObjects
import qupath.lib.objects.PathCellObject
import qupath.lib.objects.PathObject
import qupath.lib.objects.PathDetectionObject
import qupath.lib.roi.ROIs
import qupath.lib.regions.ImagePlane
	/**
	* ABBA Script : performs a cell detection on the root node annotation
	* imported from ABBA and restores the child objects after the detection has been performed
	* To use and modify like you need / want
	* You need to have imported the regions before running this script. See https://gist.github.com/NicoKiaru/723d8e628a3bb03902bb3f0f2f0fa466 for instance
	* See https://biop.github.io/ijp-imagetoatlas/
	* Author: Olivier Burri, Nicolas Chiaruttini, BIOP, EPFL
	* Date: 2022-01-26
	*/

	// setImageType('FLUORESCENCE'); // if your image is fluorescent

	// If you just want to clear the detections and keep the previously ABBA imported annotations
	clearDetections()

	// or, if you want to reset and re-import all annotations from ABBA
	// clearAllObjects();
	// qupath.ext.biop.abba.AtlasTools.loadWarpedAtlasAnnotations(getCurrentImageData(), "acronym", true);

	def project = getProject()

	// We want to run cell detection only once on the entire brain, which means we need to select the Root node. We can find it by name
	def root = getAnnotationObjects().find{ it.getName().equals( 'Root' ) }

	// Duplicate root node. It is a bit contrived but this is how you can copy an annotation
	def regionMeasured = PathObjectTools.transformObject( root, null, true )

	// Temporary name
	regionMeasured.setName( "Measured Region" )

	// Need to add it to the current hierarchy
	addObject( regionMeasured )

	// So that we can select it
	setSelectedObject( regionMeasured )

	// RUN CELL DETECTION
	// Modify the line below by inserting your cell detection plugin line
	// *********************************************************************
	// *********************************************************************
	runPlugin( 'qupath.imagej.detect.cells.WatershedCellDetection',
	'{"detectionImage": "FL CY3", "requestedPixelSizeMicrons": 2.0, "backgroundRadiusMicrons": 8.0, "medianRadiusMicrons": 0.0, "sigmaMicrons": 2.0, "minAreaMicrons": 20.0, "maxAreaMicrons": 400.0, "threshold": 200.0, "watershedPostProcess": true, "cellExpansionMicrons": 0.0, "includeNuclei": true, "smoothBoundaries": true, "makeMeasurements": true}')
	// *********************************************************************
	// *********************************************************************

	// We no longer need the object we used for detection. We remove it but keep the child objects, which are the cells
	removeObject( regionMeasured, true )

	// We can now add the cells to the original root object
	def cells = getDetectionObjects()
	root.addPathObjects( cells )

	// Update the view for the user
	fireHierarchyUpdate()

	// From here, the rest of the script adds to all cells their coordinates in the reference atlas
	// to their measurement list


	// Get ABBA transform file located in entry path
	def targetEntry = getProjectEntry()
	def targetEntryPath = targetEntry.getEntryPath()

	def fTransform = new File(targetEntryPath.toFile(), "ABBA-Transform-Adult Mouse Brain - Allen Brain Atlas V3p1.json" )

	if ( !fTransform.exists() ) {
	logger.error( "ABBA transformation file not found for entry {}", targetEntry )
	return
	}

	def pixelToCCFTransform = Warpy.getRealTransform( fTransform ).inverse() // Needs the inverse transform

	getDetectionObjects().forEach{ detection ->
	def ccfCoordinates = new RealPoint(3)
	def ml = detection.getMeasurementList()

	ccfCoordinates.setPosition( [detection.getROI().getCentroidX(),detection.getROI().getCentroidY(), 0] as double[] )
	// The Z=0 pixel coordinate is automatically transformed to the right atlas position in Z thanks to the fact that the slice
	// position is already known by the transform

	// This applies the transform in place to cffCoordinates
	pixelToCCFTransform.apply(ccfCoordinates, ccfCoordinates)

	// Fianlly: Add the coordinates as measurements
	ml.addMeasurement("Allen CCFv3 X mm", ccfCoordinates.getDoublePosition(0) )
	ml.addMeasurement("Allen CCFv3 Y mm", ccfCoordinates.getDoublePosition(1) )
	ml.addMeasurement("Allen CCFv3 Z mm", ccfCoordinates.getDoublePosition(2) )
	ml.addMeasurement("Count: Num Spots", 1 )
	}


	// imports
	import qupath.ext.biop.warpy.*
	import net.imglib2.RealPoint
	import qupath.lib.measurements.MeasurementList
	import qupath.lib.objects.PathObjectTools
	import qupath.lib.objects.PathObjects
	import qupath.lib.objects.PathCellObject
	import qupath.lib.objects.PathObject
	import qupath.lib.objects.PathDetectionObject
	import qupath.lib.roi.ROIs
	import qupath.lib.regions.ImagePlane