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.
Hi,
Thank you for your help with this and apologies that the stereotactic coordinates I provided in the previous example did not match the atlas link-- I had a lot of examples open.
The connectivity atlas example I had intended to share was this one:
Which gives coordinates that are outside the brain in the Paxinos atlas:
Coords. (AP,ML,DV,∠)
Bregma(-4.36, 3.9, 1.4, 0)
Many of the other injections in the connectivity atlas targeted to anterior entorhinal cortex (all of which are clearly in ENTl based on the images and which I would really like to be able to replicate) have coordinates that are in the auditory cortex in the Paxinos atlas.
Here is one example of this ( I am not allowed to include more than two links so this is the experiment info) : experiment#127397469
ml=4.25 ap=-2.7 dv=2.75
In a different question I posted related to how Bregma was determined for the connectivity atlas, you indicated that the DV coordinates are measured from the surface of the Dura rather than the surface of the skull and also that it is best to inject superficial cortex at an angle perpendicular to the surface (although no angle is indicated in these injections). Perhaps some of this could explain some of these discrepancies with coordinates in the Paxinos atlas? If yes, could you please explain the exact procedure for determining where to drill a hole into the skull and which ML/AP coordinates were used to zero DV on the Dura? The connectivity injections are very precise and clean, so I just want to understand how best to replicate them!
Thank you for all the help,
Paula
Hi Paula,
From the team that handles these activities now and for the Connectivity Atlas:
The ML/AP/DV coordinates for all of the injection targets were initially obtained using a Paxinos atlas referenced to bregma. However, as noted, we used the surface of the brain at those M/L and A/P coordinates, as the zero point for the DV coordinates. Importantly, we did make adjustments to coordinates depending on feedback from our histology team regarding targeting accuracy. Additionally, it’s important to note that all of the injections for the connectivity atlas are then translated into the CCF, which unfortunately does not register back to stereotaxic coordinates. As for superficial cortical injections, the user is correct that it’s best to angle the injector such that it is normal to the laminar structure of the cortex at the M/L and A/P coordinates. As coordinates moved laterally, we went from 0 to 20 to 30 degrees to maintain normality as best we could.
Lastly, here is a link to our technical white paper: Documentation: Mouse Connectivity Atlas
