Hello, I am having trouble aligning LEC stereotactic injection coordinates in the Allen connectivity atlas with coordinates in the Franklin and Paxinos atlas. I have seen in other posts that the Franklin and Paxinos atlas was the reference used for the connectivity injection coordinates, yet many of the indicated connectivity injection sites for LEC are not even within the brain in the Franklin and Paxinos atlas. I am looking at the connectivity atlas with source structure=ENTl and mouse line=wild.
In this example I see the coordinates: Bregma(-4.36, 4.25, 1.4, 0)
Which is outside of the brain:
Other mismatches also come up with these same search parameters…
How can I make sense of these mismatches and what method can I use to best replicate the coordinates in the connectivity atlas?
Thanks!
Hi,
Thank you for your question. Here is an answer from one of our scientific technical expert team members.
Thank you,
Susan
The lateral entorhinal cortex (ENTl, or LEC) is a large brain structure. In the Connectivity Atlas, we made many injections to cover different parts of ENTl (see the attached files of injections in the dorsal and lateral views) based on the Paxinos and Franklin mouse brain atlas. We listed injection coordinates for targeting different locations of ENTl in the Connectivity Atlas. The example you provided is an injection into the anterior part of ENTl. The coordinate in the plate of the Paxinos and Franklin mouse brain atlas you shown is at the posterior part of ENTl. The two coordinates are at very different anterior-posterior level from Bregama -4.36 and -2.8.
If you take a look closely at those ENTl injections in the Connectivity Atlas, you will find some of those injections are in different places when the same coordinates were used. Those results may depend on different injectors. Therefore, the coordinates in the Connectivity Atlas can only be used as a reference. If you want to do the stereotactic injections, we recommend that you get the coordinates from Paxinos and Franklin’s mouse brain atlas directly.
