2D histological image registration, human prefrontal brain

Hi,
Which tool & atlas combination tested on BICCN human brain atlases would support 2d registration of fluorescent image stacks of 30micron samples from thick prefrontal coronal slices of human brain? The purpose is to obtain comparable XY orientation of the samples from different brains.

As a missing spatial coordinate we have the position of the thick slice/side of the sample along the rostral-caudal axis to eventually select range of slices (if we refer to the Allen’s interactive 2d atlas).

Thanks,
Predrag Janjic