How does SAW decide to flip the image?

[roanvanscheppingen]

From a previous SAW run we knew the expression of transcripts on the chip. This is displayed on the left of the picture. Therefore, when I started saw count, I made sure that the _ssDNA image had similar orientation (as displayed on the right). I would think, that this would then not require additional rotation or adjustment. However, SAW 8.2 does rotate and flip the picture.

Here is the actual registered picture as from the output HTML.

[Jinghao-Chen]

Hi, due to the principles of chip design, the orientation of the expression matrix is inverted relative to the actual tissue orientation on the chip after the SAW pipeline. Therefore, the SAW will also force a single image flip by default.
After this step, the algorithmically optimal rotation angle will be selected based on the tissue morphology, so adjusting the rotation angle will not alter the algorithm's result.