As a last resort, you can use direct screen captures to generate the .gif files for your animation. Usually it is better (and easier) if you can write image files directly from the program that is creating the pictures, but this isn't always possible.

Some screen capture programs let you specify an area of the screen or a specific window to capture. This will usually help a little bit. Otherwise, you may need to use a paint program to clip the full-screen images to the size and area that you want. This is tedious and prone to error, but use it if it's your only choice...