Image J Auto Alignment for Serial Multi-Channel IF Sections

I am looking for help to align a set of serial images (about 5 images) that each have 2 channels (DAPI and GFP). I have tried a variety of plugins such as Template Matching and the auto align feature on TrakEM. I am looking for any new ideas on how to do this using Image J.

Now that you have made your first post, you should be able to post a sample stack, or if it is too large, host it elsewhere for free and provide a link. That, along with explanations of what went wrong with your other attempts might help people give you some ideas.

Right now there is not a lot to go off of.