Choosing a specific atlas ontology and download data


I would like to use the adult mouse brain atlas for my research works, but with an inferior ontology than the one used one the Interactive Atlas Viewer, that includes all small regions for every downloading, whatever the regions you choose to select on the viewer.

In other words, I would like to download the 2D atlas slices with only the main brain regions (typically 5-10 regions covering the whole brain, such as cortex, striatum, thalamus, hippocampus, etc.).

I did not find any answer on this basic question on this FAQ, I apologize in advance if I missed a related topic.

Is it possible to directly download such selected ontology mouse brain atlas slices from your website? Or is it the researcher’s job to post-process raw data from your website?

Many thanks in advance for your help.

Hello Sébastien,

There is no “built-in” functionality to download atlas images annotated with only a subset of structures from the ontology. However, the API is a set of tools that may help you get what you want. See the documentation at this link.

However, even the background images show the delineations of fine structures so I’m not sure if that will help you.

Best regards,

Hello Wayne,

Thanks a lot for your quick answer!

If I understand well, there is no possibility from the API to download the atlas with a chosen level of ontology. Thanks for this precision. I can then do post-processing on images after downloading to merge levels and get my wanted ontology.

So let me adapt my question: is there a possibility to download the atlas slices:
(1) with only regions in colors, including boundaries, without any writing on it?
(2) with only regions in colors without boundaries and any writing on it?

For (1), you gave me a part of the answer on the second link for one of the slices. Now, how to get all the atlas slices from the api as you did for the one on the link?
For (2), I attached in this post an example of an atlas slice I achieved to display on the Interactive Atlas Viewer, without any boundaries and (almost) any writing on it. But when I click on Download Atlas Image, boundaries and writings steel appear on the downloaded image. So is it possible to download such atlas images without any boundaries and writings on it? If yes, how?

Thank you again for your answer,
Best regards,

Can you see if this list of URLs helps get what you need?

Yes, this anwers question (1) in my last post, thank you very much for giving me all the links!
For question (2), I guess I will be able to process the SVG files you gave me in order to remove all boundaries.

Thanks again for your answer, I will come back on this post if I have any further question.
Best regards,

Hi again,

I have just encountered a problem downloading the 73th slice with the corresponding link you gave me for this slice:

Basically, it gives a completely white page.
Maybe there is an error in the link?

Thanks in advance for your answer,

Interesting. Yes, it seems like there are not actually any outlined structures for that image. I can’t say how that may have happened but it was probably an oversight by the original annotator.

I think there is no slice corresponding to this link, because I downloaded all others (excepting that one) and I get 132 slices (the whole brain if I am not mistaken).

Yes, you are correct.