I have 16 images of biological tissue that I ran on the StackReg plugin and I got their alignment to each other. The program also returned an affine transformation matrix for each of those 16. **I was hoping to have further clarification on what the values in the affine transformation matrix represent.**

I believe the first two rows are coefficients a11,a12,a21,a22 and the third row is u and delta u, although I don’t know which is which. This website (http://bigwww.epfl.ch/thevenaz/stackreg/) details the affine transformation equation: x = {{a11, a12}, {a21,a22}} * u + delta u. I was unsure how to apply these values to transform one of the original images into its aligned form.

Thanks!