ImageJ has a feature called "stacks" where a series of images is combined to create a 3D image. Stacks can be created either from multiple image files, or from a multi-image TIFF file. Once you have a stack there are many ways to display it and create projections.
The beauty of ImageJ is that it's both an image processing application and a Java library. That means you can try manually if it can do what you need done, and if it does, you can use its Java API -or its built-in macro language- to automate the task.
I brought this back from the farm where they grow the tiny ads: