How much RAM does you machine have? It should 24GB or more if you are assigning 20GB to ImageJ. My 5 year old Mac laptop with 8GB of RAM cannot cope with 1GB images.

Thank you for your reply. Yes, it is a 24 GB desktop. I've tried it previously with a 16 Gb desktop as well with designating 14 Gb to ImageJ. Thanks!

Try using Java 8. I just did some testing and found it handles 1GB images much better than Java 6. I run ImageJ with Java 8 on my Mac by changing to the ImageJ directory and using this command:

    java -Xmx7g -jar ij.jar

Or this FAQ describes how to run Fiji using a different version of Java:

http://fiji.sc/Frequently_Asked_Questions#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F

I just tried merging by updating to Java 8 and have the same issue. No noticable changes. Hoping to resolve it!

Created attachment 242
Update on ImageJ merge error

Comment on attachment 242
Update on ImageJ merge error

This was run on a dektop with 18GB of 24 GB RAM allocated to ImageJ. Latest version of JAVA.

Created attachment 243
Screenshot showing merge macro output on OS X

Does the following test macro work as expected on your system? I attached a screenshot that shows what the merged image created by the macro should look like. Before running the macro, you should upgrade to the latest ImageJ daily build (1.49q15). It fixes a bug that caused extremely large images (e.g., 30000x30000) to not be displayed correctly because the minimum magnification was 3.1%. Also, the "Merge Channels" command now deletes the source images only after displaying the composite image. To upgrade, use the Help>Update ImageJ command and select "daily build" from the drop down menu. 

    MB = 850;
    w = sqrt(MB*1024*1024);
    doCommand("Monitor Memory...");
    newImage("c1", "8-bit ramp", w, w, 1);
    newImage("c2", "8-bit ramp", w, w, 1);
    run("Rotate 90 Degrees Right");
    run("Merge Channels...", "c1=c1 c2=c2 create");

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Update on ImageJ merge error-2

Thanks so much for your help on this. I have followed your instructions and run the macro; however, the same error persists (attached screenshot). Not sure if this is a windows error. Please advise.

I am able to duplicate this problem, using images larger than 500 megapixels, on both Mac and Windows machines. It is a problem only with the way images are displayed, so the pixel data is not corrupted. This appears to be a Java bug so it is not something I can fix. You should be able to work around the problem by either scaling your images to 500 megapixels or less or by processing and analyzing the images at full size and then scaling to screen size to view the results. By the way, I observed many JVM crashes, on both Macs and Windows, while working with 500+ megapixel images.

Thanks. Is there way to scale down both channels in imageJ so that they remain the same size? I tried saving each channel as a JPEG but they end up being different sizes and can't be merged.

The following example macro creates two 850 megapixel images, merges them, scales the merged image to 2048x2048, saves it as JPEG and displays it. It does this without displaying any of the 850 megapixel images. The resulting JPEG file is 137K.  

    MB = 850;
    setBatchMode(true);
    w = sqrt(MB*1024*1024);
    doCommand("Monitor Memory...");
    newImage("c1", "8-bit ramp", w, w, 1);
    newImage("c2", "8-bit ramp", w, w, 1);
    run("Rotate 90 Degrees Right");
    run("Merge Channels...", "c1=c1 c2=c2");
    run("Size...", "width=2048 height=2048 constrain interpolation=Bilinear");
    saveAs("Jpeg", "");
    setBatchMode(false);

This version of the macro saves the 850 megapixel merged image as a 15MB (29,854x29,854) JPEG without displaying anything.

    MB = 850;
    setBatchMode(true);
    w = sqrt(MB*1024*1024);
    doCommand("Monitor Memory...");
    newImage("c1", "8-bit ramp", w, w, 1);
    newImage("c2", "8-bit ramp", w, w, 1);
    run("Rotate 90 Degrees Right");
    run("Merge Channels...", "c1=c1 c2=c2");
    saveAs("Jpeg", "");

Thank you very much. I apologize for the unfamiliarity with macros. How do I change the macro you provided so that it uses my two image files (i.e. the two channels) for merging? Also, how do I assig the desired colors using this macro?

You can use the open() function to open images and you can run commands in the Image>Lookup Tables menu to assign colors to the channels. Here is an example:

    open("");
    rename("c1");
    open("");
    rename("c2");
    run("Merge Channels...", "c1=c1 c2=c2 create");
    run("Blue");
    setSlice(2);
    run("Yellow");

The command recorder (Plugins>Macros>Record) is helpful for creating macro code.

Thanks for your support on this!