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ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.
There is a newer version: 1.54p
package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import java.awt.image.*;

/** This plugin implements the Image/Color/Merge Channels command. */
public class RGBStackMerge implements PlugIn {
	private static String none = "*None*";
	private static int maxChannels = 7;
	private static String[] colors = {"red", "green", "blue", "gray", "cyan", "magenta", "yellow"};
	private static boolean staticCreateComposite = true;
	private static boolean staticKeep;
	private static boolean staticIgnoreLuts;
	private ImagePlus imp;
	private byte[] blank;
	private boolean ignoreLuts;
	private boolean autoFillDisabled;
	private String firstChannelName;
	private boolean scaleWhenConverting = true;
 
	public void run(String arg) {
		imp = WindowManager.getCurrentImage();
		mergeStacks();
	}
	
	public static ImagePlus mergeChannels(ImagePlus[] images, boolean keepSourceImages) {
		RGBStackMerge rgbsm = new RGBStackMerge();
		return rgbsm.mergeHyperstacks(images, keepSourceImages);
	}

	/** Combines up to seven grayscale stacks into one RGB or composite stack. */
	public void mergeStacks() {
		int[] wList = WindowManager.getIDList();
		if (wList==null) {
			error("No images are open.");
			return;
		}

		String[] titles = new String[wList.length+1];
		for (int i=0; i1) {
					error("Source hyperstacks cannot have more than 1 channel.");
					return;
				}
				if (img.getNSlices()!=slices || img.getNFrames()!=frames) {
					error("Source hyperstacks must have the same dimensions.");
					return;
				}
				mergeHyperstacks = true;
			} // isHyperStack
			if (img.getWidth()!=width || images[i].getHeight()!=height) {
				error("The source images or stacks must have the same width and height.");
				return;
			}
			if (createComposite && img.getBitDepth()!=bitDepth) {
				error("The source images must have the same bit depth.");
				return;
			}
		}

		ImageStack[] stacks = new ImageStack[maxChannels];
		for (int i=0; i2)
					extraIChannels++;
				if (images[i].getBitDepth()==24)
					isRGB = true;
			}
		}
		if (isRGB && extraIChannels>0) {
			imp2 = mergeUsingRGBProjection(images, createComposite);
		} else if ((createComposite&&!isRGB) || mergeHyperstacks) {
			imp2 = mergeHyperstacks(images, keep);
			if (imp2==null) return;
		} else {
			ImageStack rgb = mergeStacks(width, height, stackSize, stacks[0], stacks[1], stacks[2], keep);
			imp2 = new ImagePlus("RGB", rgb);
			if (createComposite) {
				imp2 = CompositeConverter.makeComposite(imp2);
				imp2.setTitle("Composite");
			}
		}
		for (int i=0; i=0; i--) {
			if (titles!=null && titles[i].startsWith(str) && (firstChannelName==null||titles[i].contains(firstChannelName))) {
				name = titles[i];
	 			if (channel==1) {
	 				if (name==null || name.length()<3)
	 					return none;
	 				firstChannelName = name.substring(3);
	 			}
				break;
			}
		}
	 	if (name==null) {
			for (int i=titles.length-1; i>=0; i--) {
				int index = titles[i].indexOf(colors[channel-1]);
				if (titles!=null && index!=-1 && (firstChannelName==null||titles[i].contains(firstChannelName))) {
					name = titles[i];
	 				if (channel==1 && index>0) 
	 					firstChannelName = name.substring(0, index-1);
					break;
				}
			}
		}
	 	if (channel==1 && name==null)
	 		autoFillDisabled = true;
	 	if (name!=null)
	 		return name;
	 	else
	 		return none;
	 }
	 	
	public ImagePlus mergeHyperstacks(ImagePlus[] images, boolean keep) {
		int n = images.length;
		int channels = 0;
		for (int i=0; i1?"Merged":"Composite";
		ImagePlus imp2 = new ImagePlus(title, stack2);
		imp2.setDimensions(channels, slices, frames);
		imp2 = new CompositeImage(imp2, IJ.COMPOSITE);
		boolean allGrayLuts = true;
		for (int c=0; c