Aligning dorsal projection of mouse common coordinate framework with wide-field images of mouse brain

I am trying to register the wide-field GCaMP images to the Allen Brain Atlas.
Exactly how they did is this paper-

Unfortunately, I am unable to get a clue as to how to go about it. I know that I need atleast four marked reference points on my images.
Is there a python example code I can use. I know there are lots of python notebooks on internet but I cannot get my head around them. None of them work with dorsal projection.

thanks a lot

Hi Pankaj,

I don’t have a complete answer to your question, but I can point you to a few resources that might help you get started. I’d definitely suggest reaching out to the authors of the paper you cited. It does sound like they used manual fiducial markers of some type. I’d be curious what those markers were specifically (maybe I missed it, but they didn’t seem to specify), and also how they made the transformation from stereotactic coordinates (assuming that’s the known coordinate system of their fiducial markers) into CCF coordinates.

Here’s a Jupyter notebook that shows some basics for accessing structure masks and other functions in the CCF:

And here are two potentially useful representations of the top down projection:

Hopefully that’s helpful in getting started. Feel free to post back here with follow-up questions as you make progress.


1 Like

Hi Pankaj! Kelly Clancy from that paper here, a few people pointed out you’d posted this question so I’ll try to answer :). Unfortunately I don’t know python, but I can at least walk you through the principle of what we did. So yes, we made marks on the skull itself. We placed very tiny marks with permanent marker using a stereotax, at bregma/lambda and 1 mm lateral of either side of these. We covered these over with cement so they were present throughout recordings. We used the Allen Brain API to determine a dorsal projection of the atlas (you should be able to calculate the dorsal projection yourself, for example could take each pixel of the dorsal plane and find the most superficial brain area for that pixel and assign that pixel to that area). Then we used the bregma/lambda points from the widefield imaging to perform an affine transform of the imaged data into the atlas coordinate system. Hopefully that makes sense, and please let me know if you have any other questions.


Hi Kelly. That all sounds simple enough, the only problem being that the Allen Brain API does not specify where the bregma and lambda are (as per this official explanation). Given this, what did you estimate as the position of bregma and lambda in the CCF coordinates?

I wish I could capture each mouse’s 2P tomography volume and register to the CCF as per this recent work. Unfortunately, we lack the necessary hardware.

EDIT: Based on the Paxinos and Franklin atlas (2012) as well as Allen’s older atlas (2008) which does come with stereotaxic coordinates, I estimated that lambda is at y = 206, bregma is at y = 370, and 1 mm lateral is at z = 195 in the 25 micron volume. Is this close to what you have? This is not a rigorous estimate but combined with a sensory response assay (e.g. visual, somatosensory) may be good enough for delineating large cortical areas.