Option to rotate input images for better alignment in compile

[rthiermann]

We usually align the channels to vertical when imaging. For datasets where the channels are askew, we should have the option to rotate them - either by automatically determining the rotation or via user input. Important for background subtraction and tracking.

[rthiermann]

e.g. via https://scikit-image.org/docs/stable/api/skimage.transform.html#skimage.transform.rotate