Welcome! If you haven’t already, take a look at (within CellProfiler) Help > Creating a Project > Loading Image Stacks and Movies. Loading Stacks can be a little daunting at first, but we try to walk you through the procedure in the Help. Please note that you will only see one image of the stack if you double-click on the file within the Images module. But if you have Metadata and NamesAndTypes configured properly, they will all be unpacked once you run the pipeline. After that, the MakeProjection module should be straightforward, and don’t forget a SaveImages module to write the output.
You might also try another tool to create your projection (CellProfiler is great, and can create projections and a lot more, but I’m all for using the tool that is easiest!) – I will often do this in FIJI myself. Then if you like, you can load in the projection to CellProfiler and analyze it there.
If you are still having trouble, upload a sample stack file here (try zipping the file if you have upload issues) and we’ll take a look.