Hi Andrew.

I´m more familiar with the rat brain. But looking to the first image I can make a guess that you are staining the amygdala. Also, it makes sense to me that your red-IR colocalizes with GAD67, because all the amygdala (Central amygdala, Basolateral amygdala and Medial Amygdala) is very rich in GABA neurons. But according to the images, I would say that you are staining the central amygdala and the basolateral amygdala.

Also, I think that you are staining the globus pallidus too.

Best wishes.

I agree with Juan. I'm also more familiar with the rat brain but based on the shape and size of the hippocampus and the shape of the area overall I'd say you're at the BLA. Not sure if my input helps but just wanted to back Juan up.

Dear Andrew:

Very nice images with labeling of your protein of interest. Congrats! As regards to your question, firstly, it would help if you could specify what you are exactly looking for (in red)? Secondly, the two images you have presented are a bit confusing due to the fact that they depict different anatomical parts and structures of mouse brain labeled in red. E.g., your first image shows coronal section of the mouse brain at the level of thalamus and amigdala and leaves almost completely out the GP, bed nucleus ST and rostral BF, whereas your second image depicts a quite medial sagittal section of the brain, which does not contain for example amigdala. For presentation purpose, try to show slices that are structurally related. Now, to answer your question, in your first image (top), in red are labeled caudal CPu, lateral GP and basal and lateral amigdalar complex (quite extensively) with some labeling of medial GP. In your second image, red labeling is largely in ventral and lateral pallidius but it is also present in some parts of substantial inominata with bed nucleus stria terminalis.

Hope this helps,

Saak 

The second image seems like interfascicular nucleus. But I am comparing with a 3D allen mouse atlas.

Good luck

Thanks for all the input so far. It has been really helpful

For some reason at first I could not get past the thought that the strongest red signal was localized perhaps only a single or two nuclei. But now I realize its much more likely that it overlaps with several regions.

This is especially true given Saak's observation that the coronal and sagital images highlight two different areas. I will need to look at more sections in each plane to get a more complete idea of the distribution. Thanks!

It seems to be too dorsal in the coronal image to be amygdala proper. Will consult Paxinos when back in the lab tomorrow.

In the coronal image, red looks like central amygdala (ventral) and globus pallidus (dorsally), and the sagittal image it looks like ventral pallidum and globus pallidus. 

All these are predominantly GABAergic nuclei, whereas basal-lateral amygdala is glutamatergic.

I am extrapolating from rats, so take with a grain of salt.