Hi everybody,
I have IHC images (Ki-67 staining) to analyze, and I have hard time counting cells on it.
Probably because of the DAB background staining, ‘Cell detection’ function does not work at all to detect any cells in the image even after changing the parameters.
Could anybody help on how to train Qupath to detect cells in these samples?
I attach my script below and an original image as well. Thanks!
setImageType('BRIGHTFIELD_H_DAB');
setColorDeconvolutionStains('{"Name" : "H-DAB modified", "Stain 1" : "Hematoxylin", "Values 1" : "0.71124 0.61052 0.34843 ", "Stain 2" : "DAB", "Values 2" : "0.10193 0.39945 0.91107 ", "Background" : " 225 175 148 "}');
runPlugin('qupath.imagej.detect.cells.WatershedCellDetection', '{
"detectionImageBrightfield": "Hematoxylin OD",
"requestedPixelSizeMicrons": 0.5,
"backgroundRadiusMicrons": 8.0,
"medianRadiusMicrons": 0.0,
"sigmaMicrons": 1.5,
"minAreaMicrons": 10.0,
"maxAreaMicrons": 400.0,
"threshold": 0.1,
"maxBackground": 2.0,
"watershedPostProcess": true,
"excludeDAB": false,
"cellExpansionMicrons": 5.0,
"includeNuclei": true,
"smoothBoundaries": true,
"makeMeasurements": true
}');