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I am using the StackReg plugin (with FIJI) to align images of a scratch assay. StackReg seems promising, but isn't performing exactly as I would like. I know that once I stack the images, whichever one I have selected when I run StackReg is used as the reference image. However, I would like the entire set of images to be aligned. Is there way to do this such that the entire image set is becomes aligned? Thanks.
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