Auto-Align and Auto-Blend Layers in Paint by Zaweba
Line up overlapping shots with Auto-Align, then blend panorama seams or focus stack by sharpness with Auto-Blend Layers in Paint by Zaweba.

Sometimes one photograph isn't enough. A macro shot of an insect has only a sliver in focus. A wide view doesn't fit in one frame. Several shots of the same scene can fix that, but only once they are lined up and combined. Auto-Align Layers and Auto-Blend Layers in Paint by Zaweba do those two steps, and they work on layers you already have in a document, so you stay in control of each stage.
Auto-Align Layers
Auto-Align matches overlapping shots by finding the same details in each and moving, rotating or warping layers so those details sit on top of each other. It offers four methods.
Auto lets the app pick the projection that suits the shots. Perspective treats one layer as the reference and warps the others to fit, which works for flat subjects and modest panoramas. Cylindrical maps the shots as if onto a cylinder, which keeps wide panoramas from bending into a bow-tie shape. Reposition only moves the layers without warping, which is right for shots taken from a tripod that shifted slightly, and for focus stacks where you only need small corrections.
For focus stacks taken handheld, Auto or Reposition only usually gives the best results, since the framing hardly changes between shots.
Auto-Blend Layers
Once the layers are aligned, Auto-Blend combines them in one of two ways.
For panoramas, it makes seams as layer masks. Each layer gets a mask that shows its part of the final picture, with the joins placed where they are least visible. It also evens out tones and colours across the joins, so a slightly brighter frame doesn't stand out as a patch. Because the seams are masks, you can adjust them by painting if a join cuts through something awkward, such as a person's face.
For focus stacks, it compares the layers and keeps, for every area, the sharpest version. Shoot a series from front to back with the focus moving a little each time, align them and blend, and you get a picture that is sharp from the nearest edge to the background. Macro photographers, product photographers and anyone shooting jewellery or small objects use this all the time.
Shooting for good results
For panoramas, overlap each frame by a good amount, keep the exposure the same and turn the camera around its lens rather than around your body if you can. For focus stacks, use a tripod, lock the exposure and the white balance, and take more shots than you think you need, with small focus steps.
Avoid moving subjects. Leaves in the wind and people walking through a panorama are the most common cause of ghosting and odd joins.
When to use the automated panorama instead
Paint by Zaweba also has File > Automate > Panorama, which runs alignment and blending in one go from a set of files, with extra projections, vignette removal, distortion correction and Smart Fill for gaps. That is the quicker path for an ordinary panorama. Auto-Align and Auto-Blend Layers are the better choice when your shots are already layers in a document, when you want to check alignment before blending, or when you are focus stacking.
For combining several shots of a group with different expressions, Photo Blend Layers is designed for the job, and for noise reduction or star photography, Image Stacking under File > Automate combines aligned frames mathematically.
After blending
A focus stack may show halos where sharp edges meet blurry areas from other frames. Paint over them on the masks, or clone carefully from a single frame. A panorama will need cropping to remove the ragged edges, or filling if you want to keep more of the frame.
Both tools turn a series of ordinary photos into one picture that no single exposure could have captured.