Have you ever spent a considerable amount of time manually aligning and scaling all your images in a focus stack, if so I would highly recommend the Auto align layers tool in Photoshop, no need to align and scale each one individually, let Photoshop do the leg work for you, saving valuable time and effort.
Step 1: Bring all your Images into one Photoshop document
Step 2: Select the layers you would like to focus stack/align
Step 3: Navigate to your top Edit menu and about half way down you will find the Auto Align Layers
Step 4: Click on this option and a dialog box will pop up and should have Auto already pre-selected, this will scale and reposition each image based on the visual content (this is the way photoshop works out how to scale and align)
Step 5: Press OK and let Photoshop do its thing.
Hey presto! You should now have all your images stacked up in the right position, scale and rotation
+ Extra Step if you want to try: Why not try out the Auto blend Layers under the Edit menu just below Auto Align Layers, In my opinion its a little hit and miss but give it a test and judge for yourself
Focus Stacking Alternatives?