Batch screening

Hello all,

I have a folder with a handful of slides [about 100] that contains both ER- and ER+. What would be an easy way to know which slides are ER- and which slides are ER+ using Qupath?
Thanks a lot!

Going to need a lot more detail than that :slight_smile:
Whole slide images or fields of view? Brightfield or fluorescence? If IF, do you have a DAPI/nuclear channel? Do you just want mean intensity for the entire image/field of view?

Sorry for the late reply

Field of view (ROI). Fluorescence but we also do brightfield. Basically, the entire image, brightfield, no DAPI but we have hematoxylin. And yes, I want the mean intensity for the entire image. I hope that helps. Thanks a lot!!

I would probably use something like this if your marker is DAB, though you didn’t state that so I’m still not sure. Add hematoxylin of you want a measurement of that.

setColorDeconvolutionStains('{"Name" : "H-DAB default", "Stain 1" : "Hematoxylin", "Values 1" : "0.65111 0.70119 0.29049 ", "Stain 2" : "DAB", "Values 2" : "0.26917 0.56824 0.77759 ", "Background" : " 255 255 255 "}');
runPlugin('qupath.lib.algorithms.IntensityFeaturesPlugin', '{"pixelSizeMicrons": 0.5,  "region": "ROI",  "tileSizeMicrons": 25.0,  "colorOD": true,  "colorStain1": false,  "colorStain2": true,  "colorStain3": false,  "colorRed": false,  "colorGreen": false,  "colorBlue": false,  "colorHue": false,  "colorSaturation": false,  "colorBrightness": false,  "doMean": true,  "doStdDev": true,  "doMinMax": false,  "doMedian": false,  "doHaralick": false,  "haralickDistance": 1,  "haralickBins": 32}');

It is pretty blunt, though. And will probably want to use your own color vectors.

Thanks for getting back to me, and yes it is DAB.
I will go ahead and give it a try.