FAQ: Can I convert a large stack into .avi, .gif, QuickTime without loading it?
Some stacks are too large to fit in RAM to be loaded and saved in an animation format. How do I overcome this?
Wayne provided this answer in the mailing list:
With ImageJ 1.39k and later, you can frame-by-frame convert a large TIFF by opening stack it using File>Import>TIFF Virtual Stack and saving it using File>Save As>AVI, File>Save As>Gif (animated GIF) or File>Save As>QuickTime Movie. Set the frame rate in the Image>Stacks>Animation Options dialog.