2D histological image registration, human prefrontal brain

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).

Predrag Janjic

Hi Predrag,

Re: atlases

Beyond the 2D Allen Human Reference Atlas, here are some other atlas resources you could take a look at

Hi Predrag,

there are currently multiple options available to register 2D sections onto a 3D atlas. You can find a brief discussion and further links here:

I also suggest checking out the slicereg project which aims at providing a python module to make exactly this problem easier.

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