: Auto align layers with changing contents but constant shape in Photoshop I have 70+ images of a coloured microsphere taken through a microscope. Between each image, I manually rotated the sphere

@Hamm6457569

Short answer: you'll have to do this mostly by hand.

The reason Auto-Align won't work for you is based on how it works. The algorithm looks for things that match, image to image, such as the background elements in a series of group photographs or the overlapping sections of a panorama. It has no way for you to tell it "this is my point of interest". Your "foreground" and background change from image to image, so there's nothing invariable that the analysis can match.

The most efficient way to proceed with Photoshop is to load the images into layers, drag out guides to the vertical and horizontal center of your frame, then position each layer to place the bead as close to the center as you can. From there, it becomes a matter of blinking the top layer on and off to verify you have it lined up exactly with the one below, then repeating this process all the way down the stack.

Based on your sample images (the 2136 image is slightly smaller than the rest), there are some slight scale differences among your images which you'll also have to tweak by making them about 60% opaque and using Free Transform to scale and position.

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@Reiling762

Note: There's going to have to be some manual labor here not matter how you look at it.


Suggestion

Try to figure out a way to take all of the photos so that the sphere is in the exact same location every time.

Possible Digital Solution

Create an action to crop the images.


Start with a selection like this




I used the magic wand with the Tolerance set to about 160


Now record an action that does the following


Expand Selection by 20 pixels
Image->Crop
Selection->Deslect
Save to a new location
Close

Now you'll have to open all of the images and make a selection and run the action
Then select all of the images in Bridge
Choose Tools->Photoshop->Load Files Into Photoshop Layers
When Photoshop has stacked them all up you'll need to select all of the layers in the layer pallet and center them with each other using the center align buttons ()


That should get them lined up pretty close.

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