This plugin allows you to merge two grayscale stacks into a single RGB stack. It is useful e.g. to merge a brightfield with the corresponding fluorescence image, or two different dye images of the same series.
Adapted from the MBF ImageJ manual:
The Plugins › Color functions › Color Merge function gives the user the option of using the Difference arithmetic processing on the image stacks you select. This is not strictly a merge (when cyan and magenta merge they produce white, not yellow) but facilitates visualization of the separate channels1. You can perform a true merge if you turn off the “Difference” option.
Run the plugin and select the two images or stacks to be merged. It can be 8-bit, 16-bit, RGB… Select the desired colors from the drop-down options.