Hi,
I’m struggling to resolve the hierarchy after cell detection such that cells are classified with tumour/stroma as Parents and not the initial thresholded “Tissue”. I run cell detection on “tissue” first, which allocates all objects to “tissue” parents. I then run tumour/stroma createAnnotationsFromPixelClassifier
which generates >10,000 annotations. If I perform this first and then run cell detection to correctly allocate detections, the PC crashes as it is trying to do cell detection within those 10,000 annotations. I hoped selecting these tumour/stroma annotations after cell deteciton, then running object classifier would allocate these detections within these parents but they remain allocated to the initial “tissue” parent.
Any suggestions? Many thanks!
setImageType('FLUORESCENCE');
createAnnotationsFromPixelClassifier("Tissue", 0.0, 0.0);
selectObjectsByClassification("Tissue");
runPlugin('qupath.imagej.detect.cells.WatershedCellDetection', '{"detectionImage": "DAPI (DAPI)", "requestedPixelSizeMicrons": 0.4, "backgroundRadiusMicrons": 8.0, "medianRadiusMicrons": 0.0, "sigmaMicrons": 1.4, "minAreaMicrons": 10.0, "maxAreaMicrons": 400.0, "threshold": 5.0, "watershedPostProcess": true, "cellExpansionMicrons": 5.0, "includeNuclei": true, "smoothBoundaries": true, "makeMeasurements": true}');
createAnnotationsFromPixelClassifier("Tumour_Stroma", 0.0, 0.0, "SPLIT")
selectObjectsByClassification("Tumor", "Stroma");
runObjectClassifier("watershed_CD8", "watershed_PDL1", "watershed_CK", "watershed_PD1", "watershed_CD68", "watershed_FOXP3");
detectionToAnnotationDistances(true)