Re: Merge Channels Macro

Posted by Lucasphi on Jun 09, 2011; 9:53am
URL: http://imagej.273.s1.nabble.com/Merge-Channels-Macro-tp3684311p3684313.html

Thanks for all of your input everyone! You guys are wonderful <3 Here is the final code if you guys wanted to see it.  What it does is it batch processes and splits multichannel images into separate RGB channels,  pairs RB and GB, sets it to 8bit and inverts it. Cheers!


path = getDirectory("Choose a Directory");
filename = getFileList(path);

newDir = path + "Single_Channel" + File.separator;
File.makeDirectory(newDir);  


for (i=0; i<filename.length; i++) {
        if(endsWith(filename[i], ".tif")) {
                open(path+filename[i]);
                red = filename[i]+" (red)";
                blue = filename[i]+" (blue)";
                green = filename[i]+" (green)";


                run("Split Channels");

                run("Merge Channels...", "red=["+red+"] green=*None* blue=["+blue+"] gray=*None* keep ignore");
                rename(filename[i]+"_external");
                run("8-bit");
                run("Invert");
                saveAs("tiff", newDir+getTitle);
               

                run("Merge Channels...", "red=*None* green=["+green+"] blue=["+blue+"] gray=*None* keep ignore");
                rename(filename[i]+"_internal");
                run("8-bit");
                run("Invert");
                saveAs("tiff", newDir+getTitle);
                close();close();close();close();close();
                setBatchMode(false);
        }
}