Question about data in AGEA

Hi, I have a question about AGEA.

Does the data in AGEA go through registration?

If I select a gene, like Wfs1, getting into its page which shows its contents like this:

Experiment Detail :: Allen Brain Atlas: Mouse Brain (

at the bottom of this page, there is a xml format that I can click to get its information. Then I can read its energy.mhd from this xml file. So my question is that if I NEED to use the energy.mhd, is it after registration?

thank you

Hi - welcome to the community forum.

So my question is that if I NEED to use the energy.mhd, is it after registration

Yes, all the energy.mhd are registered to the 3D atlas

See this how-to page for more information.
API for Mouse Brain Atlas - How To / Allen Mouse Brain Atlas - Allen Brain Map Community Forum (

Thank you for your reply.
But I still have some questions. If all energy.mhd are registered, then why the images seem to be tilted.
When I display the enery.mhd using my code, the result shows tilted and misalignment with your Reference Models when I merged it to your reference brain. For example the Tac2 gene is shifted to the left when you display its energy.mhd.
So, I asked the former question. But I don’t get your reply because if they are after registration, then why the phenomena would exist?
Thank you for your time again.

The registration is automated and only includes affine transformation as such there can still remaining misalignments in some cases. In general, coronal dataset are better alignment because it contains both hemispheres allowing the algorithm to better localize. Sagittal datasets typically have poorly alignment because it only covers 2/3 of one hemisphere.

So, in the middle-left of every gene’s page, such as Experiment Detail :: Allen Brain Atlas: Mouse Brain (, there is a 3D image of gene in the mouse brain. Is it the perfectly registered image?
And if I need to map the gene in Allen mouse brain, what other steps should I do? or I can just use the original data?