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There used to be a plugin called RGB colour merge or RGB Gray stack merge that would allow you to presubtract the fluorescence image from a brightfield image before doing a color merge.  The pre-subtraction allows greater contrast of the color on the gray background image.  The plugin no longer seems to be in the ImageJ set.  The old versions that I have archived do not do the subtraction as expected.   I can do this by using the Image Calculator but I am wondering what happened to the plugin.  Thanks- Dave