imagej-scripts/pearson-colocalization at main · VojtechDostal/imagej-scripts · GitHub

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path = getDirectory("Choose input directory");
_RootFolder = getDirectory("Choose output directory");
outputfolder = _RootFolder + "/coloc2_output";
File.makeDirectory(outputfolder);
outputfolderROIs = _RootFolder + "/coloc2_output ROIs";
File.makeDirectory(outputfolderROIs);

filelist = getFileList(path);
for (i=0; i< filelist.length; i++) {
     if (endsWith(filelist[i], ".czi")) {
run("Bio-Formats Importer", "open=[" + path + filelist[i] + "] autoscale color_mode=Default view=Hyperstack stack_order=XYCZT series_1");
title=getTitle();

run("Arrange Channels...", "new=12");
Stack.setChannel(1);
run("Red");
run("Enhance Contrast", "saturated=0.35");

Stack.setChannel(2);
run("Green");
run("Enhance Contrast", "saturated=0.35");

Stack.setDisplayMode("composite");
run("ROI Manager...");

waitForUser("Draw ROI, hit OK");

if (roiManager("Count") == 0){
	waitForUser("Really draw ROI, hit OK");
}


for (j = 0; j < roiManager("count"); j++){
	roiManager("Deselect");
	roiManager("Select", j);
	roiManager("Save selected", _RootFolder + "/coloc2_output ROIs/" + title + "_" + j + ".roi");

	run("Duplicate...", "duplicate");
    run("Clear Outside", "stack");

	run("Split Channels");
	selectImage(2);
	run("8-bit");
	rename("C1");

	selectImage(3);
	rename("C2");
	run("8-bit");

	run("Coloc 2", "channel_1=C1 channel_2=C2 roi_or_mask=<None> threshold_regression=Costes psf=3 costes_randomisations=10");

	selectWindow("Log");
	saveAs("Text", outputfolder + "/" + title + "_" + j + ".txt");
	selectWindow("Log");
	print("\\Clear");
	close("C1");
	close("C2");
}

roiManager("Deselect");
run("Select None");
selectWindow(title);
Stack.setChannel(1);
run("Translate...", "x=75 y=0 interpolation=None slice");

for (j = 0; j < roiManager("count"); j++){
	roiManager("Deselect");
	roiManager("Select", j);

	run("Duplicate...", "duplicate");
    run("Clear Outside", "stack");

	run("Split Channels");
	selectImage(2);
	run("8-bit");
	rename("C1");

	selectImage(3);
	rename("C2");
	run("8-bit");

	run("Coloc 2", "channel_1=C1 channel_2=C2 roi_or_mask=<None> threshold_regression=Costes psf=3 costes_randomisations=10");

	selectWindow("Log");
	saveAs("Text", outputfolder + "/" + title + "_" + j + "_random.txt");
	selectWindow("Log");
	print("\\Clear");

	close("C1");
	close("C2");
}

if (roiManager("Count") > 0){
 roiManager("Delete");
}
run("Close All");

}
	}