Fiji has some features that ImageJ does not. Pixels with a value less than the minimum are displayed as black and those with a value greater than the maximum are displayed as white.
The “Difference” option performs a “difference” arithmetic operation rather than a “addition”. uses the LUT that the image currently has (this is often the desired LUT). Select the desired colors from the drop-down options. Run the plugin and select the two images or stacks to be merged.
Click on the new ‘composite’ image to activate it. Select “Create Composite” and click “OK”. Select the fluorescent images in the appropriate R, G and B channels and the DIC or similar image in gray channel. Image/Color/Merge Channels and the Merge Channels box will appear.