The best way to work with multichannel color images in ImageJ is in the composite mode. See http://microscopynotes.com/imagej/hyperstackimages01/index.html and http://microscopynotes.com/imagej/getting_started/index.html
However, there is no easy way to make a figure showing each channel individually.
The macro described here is a quick way to solve this problem. If you want other features, please ask.
What the macro does:
How to use:
Install these macros.
Open a composite color image and adjust the color and contrast of each channel.
Make sure the image is in composite mode and all channels turned on before running macro.
Either draw a box over the part of the image you want cropped for the figure or select nothing for the entire image to be made into the figure.
Plugins > Macros > Simple montage figure
The result is automatically copied to the system clipboard so you may switch to PowerPoint or other presentation software and paste directly.
You may also save the result. TIF or PNG, not JPG!!
This macro works on 2, 3, 4, 5 channel images.
Handling composite images with transmitted light as one of the channels may be written based on demand. Ask if you need this or any other changes specific to the types of images you are collecting.
There are other macros too, such as these which process an entire folder of images based on contrast adjustments applied to one of them. http://microscopynotes.com/imagej/macros/composite-colors/user-selected-contrast-colors-names-save8bit.html are useful for single file images with up to six color channels and simple contrast adjustments.
MT, f-actin, DNA/RNA image from circa 1994. Hepatoma cell line prepared by Dr. Phyllis Novikoff & imaged M Cammer on BioRad Radiance 600 laser scanning confocal microscope with 60X N.A. 1.4 lens on fixed tube length Nikon Diaphot in Analytical Imaging Facility at Albert Einstein Coll of Med.