LUTs are typically for 8-bit images, so you can't mix two luts in the same 8-bit image window. Therefore, you should apply the lut to the subregion , then convert to RGB and put everything together in a new RGB image. An example follows.
Leo.
run("2D Gel (38K)");
makeRectangle(265, 61, 196, 139);
run("Duplicate...", "title=2D_Gel.jpg-copy");
run("Spectrum");
run("RGB Color");
run("Select All");
run("Copy");
close();
selectWindow("2D_Gel.jpg");
run("RGB Color");
run("Paste");
run("Select None");
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