To use the Macro Set to align frames and size them more uniformly download it and save it in the CombineZM.exe folder. Load the Set with Macro->Load Macro Set. Load the stack of frames you wish to process and use Macro->Strict Alignment. The start macro calls three nested macros to do the work.
The Projection used to represent the frames will be different, the foreground objects will no longer be larger than the background ones if they lie on different frames.
Measurements of foreground and background objects should be easier to compare.
This set manipulates the Used/Unused state of the Stack, and requires that all frames that are loaded belong to the stack, i.e. you cannot mark frames Unused and hope that they will not be modified.
This Macro Set will fail with some Stacks, especially if frames at the extremes of the stack are not at all similar.