Merge 4 color channels

Posted by woojkim on May 21, 2015; 7:42pm
URL: http://imagej.273.s1.nabble.com/Merge-4-color-channels-tp5012905.html

I'm trying to 4 color image ND2 files into separate color, adjust each color with different parameters, and re-merge them into a single file in a batch mode. The script I wrote is below. At the end of macro, it stops with a dialog box saying " Merge Channels There must be at least one source image or stack [OK]". Could anyone help me to fix it?


dir1 = getDirectory('Choose Directory ');
list = getFileList(dir1);
dir2 = dir1+"JPG"+File.separator;
File.makeDirectory(dir2);

setBatchMode(true);
for (i=0; i<list.length; i++) {
print(dir1 + list[i]);
showProgress(i, list.length);
name = dir1 + list[i];

run("Bio-Formats Importer", "open=name view=Hyperstack stack_order=XYCZT Color mode=Default split_channels");
name1 = list[i];
index = lastIndexOf(name1, ".");
if (index!=-1) name2 = substring(name1, 0, index);
path = dir2 + name2;
print(path);

selectWindow(name1 + ' - C=0');
run("Channels Tool...");
run("Green");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 50);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=1');
run("Channels Tool...");
run("Blue");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 150);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=2');
run("Channels Tool...");
run("Yellow");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 35);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");

selectWindow(name1 + ' - C=3');
run("Channels Tool...");
run("Magenta");
run("RGB Color");
run("Brightness/Contrast...");
setMinAndMax(8, 100);
call("ij.ImagePlus.setDefault16bitRange", 8);
selectWindow("B&C");
run("Close");
selectWindow("Channels");
run("Close");

selectWindow(name1 + ' - C=0');
green = getTitle;
selectWindow(name1 + ' - C=1');
blue = getTitle;
selectWindow(name1 + ' - C=2');
yellow = getTitle;
selectWindow(name1 + ' - C=3');
magenta = getTitle;

print(green);
print(blue);
print(yellow);
print(magenta);

run("Merge Channels...",
"C2=green C3=blue C6=yellow C7=magenta keep");
saveAs("jpeg", path + ".jpg");
run("Close");
}