Basic imageJ macro to separate purple and pink areas from H&E stained IHC images to quantify size of tumor vs necrotic tissues

TumorVsNecroticTissueQuant.ijm

setTool("line");
waitForUser("Image selection", "Please zoom in (+) to where the scale bar is and then draw a line over the scale bar. Click 'OK' when ready.")
run("Original Scale");
run("Set Scale...");
run("Select None");
setTool("polygon");
waitForUser("Image selection", "Please draw to select area you want to keep for analysis\nIf you need to adjust, finish drawing first. Click 'OK' when ready.")
roiManager("Add");
run("Make Inverse");
setBackgroundColor(255, 255, 255);
run("Clear", "slice");
run("Select All");
run("Colour Deconvolution", "vectors=H&E hide");
close();
close();
run("8-bit");
run("Invert");
makeRectangle(528, 581, 50, 50);
waitForUser("MOVE THE SQUARE", "Please move the square to where you think is noise/background. Then Click 'OK'.")
IJ.deleteRows(0, 9999);
run("Set Measurements...", "area mean limit redirect=None decimal=3");
run("Measure");
selectWindow("Results")
run("Select All");
waitForUser("REMEMBER MEAN VALUE", "Remember/Copy the 'mean' value. Paste the value for the next pop up. Click 'OK' when ready.");
run("Subtract...");
//run("Threshold...");
setThreshold(1, 255);
setOption("BlackBackground", false);
run("Convert to Mask");
run("Close-");
run("Analyze Particles...", "size=0.1-Infinity show=Masks display clear");
setTool("Paintbrush Tool");
waitForUser("ERASE NOISE", "Bring up the original image to compare where is true signal. Click and hold to erase noise in the black and white image. Then Click 'OK'.")
run("Invert");
setThreshold(0, 254);
run("Set Measurements...", "area limit redirect=None decimal=3");
IJ.deleteRows(0, 9999);
run("Measure");
roiManager("Select", 0);
run("Subtract...", "value=255");
run("Measure");
run("Close All");
roiManager("Deselect");
roiManager("Delete");