Methods for alignment spatial of individual ISI session to cortical surface

How To Allen Mouse Brain Connectivity Atlas
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Hi All,

Thank you for this fantastic resource. Its really excellent and will save countless amounts of time, effort and funding.

I recently discovered the ability to overlay the ISI imaging sessions in the “Cortical Map Viewer” (For example by ticking “intrinsic image sign map” at the bottom of the viewer here) thanks to Laurens user guide. This is awesome!

I’m wondering how I can find more details about how the registration was done to produce this overlay. I understand that the injections were normally targeted using the ISI, but I’m not sure how the ISI was aligned to the subsequent injection or CCF. Forgive me if I missed it, I briefly checked the methods of both Jun’s Elife paper and Julies Nature paper as well as the overview whitepaper and didn’t see anything. Some procedure is described in the version 3 2017 whitepaper, but I can’t seem to understand how it was applied to register maps of individual (non-averaged) mice to the cortical surface view.

If you could point me in the right direction or to someone who knows the answer that would be greatly appreciated. The question is important for interpretation of these individual maps and the location of their HVAs relative to the CCF. For example - in some mice does VisP really extend back to the posterior corner/gyrus of the cortical sheet or should we be skeptical that cortical surface posterior to V1 was simply not visible in the ISI session and the alignment procedure has placed it erroneously?

Thanks,
Gregg

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Example here: I could only include 2 links in the post: (example)

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I think there must’ve been some nice alignment procedure because there are examples where likely some cortical surface was obscured and the ISI map is not shown to extend extended to the back of the brain. This is awesome that some alignment was done, but I’m still curious to know more details to understand how to think about the many examples that appear to extend to the posterior edge of the cortical surface!

For example: Experiment ID 503017948 (I cannot post with the link because the system appears to not be permitting links to connectivity(dot)brain-map(dot)org anymore)