Image J Batch red green channel merge and invert (based of http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.2007.01719.x/full )

batch_rg_channels_merge.bat

.\ImageJ.exe -eval "macfile=File.openAsString('batch_rg_channels_merge.macro'); eval(macfile);"

batch_rg_channels_merge.macro

macro "Batch RG Channels Merge" {
	sourcedir=getDirectory("Select the source images directory");
	resultdir=getDirectory("Select the result images directory");
	flist=getFileList(sourcedir);
	File.makeDirectory(resultdir);
	for (i = 0; i < flist.length; i++){
		open(sourcedir + '/' + flist[i]);
		fname = File.nameWithoutExtension;
		run('RGB Split');
		close();
		selectImage(1);
		run('Rename...', 'title=green');
		selectImage(2);
		run('Rename...', 'title=red');
		run('Image Calculator...', 'image1=[green] operation=AND image2=[red] create');
		run('Invert');
		run('Rename...', 'title=Result');
		selectWindow('red');
		run('Close');
		selectWindow('green');
		run('Close');
		selectWindow('Result');
		save(resultdir + '/' + fname + '_result.tiff');
		run('Close');
	}
}