2022 CCFv3 mouse atlas


Please can you refer me to any documentation/publications regarding the creation of the 2022 adult mouse CCFv3 annotation atlas (only available at 10 um voxel resolution) that includes many new layer annotations: see

It does not appear to be listed on the mouse brain documentation page (Documentation - Allen Mouse Brain Atlas) and I do not recall seeing it mentioned explicitly in any of your recent publications but maybe I missed it.

Do you know if 25, 50, and 100 um resolution versions will also be released soon?

Thank you.


Hi! In general, this post provides a great summary of documentation for the CCF.

As you noted, we added many new annotations last year as part of an early-release to expand annotations to the hippocampus and olfactory bulb. Those are described in this paper.

We do not have any immediate plans to release 25, 50, or 100um versions. However, we’re always interested in feedback from the community. Which version would be most valuable to you? What would these additional versions help with specifically in your work? Is this more a nice to have or absolutely invaluable?

Hi @tylermo

Thank you very much for your helpful reply regarding the ccf_2022 release.

A 25 um resolution ccf_2022 annotation atlas would, I think, be most useful to the community. Could you offer any timeline, even roughly, on when other resolution volumes might be available to download?

Btw, what method does Allen use for down-sampling labelled volumes: is it the Seung Lab tinybrain package or something else?

While the community will appreciate this early data release, inspection of ccf_2022 suggest the task is not yet completed and this will leave the community uncertain about what Allen intends to do about this in future releases. For example, in ccf_2022 while many voxels in hippocampus have now been given leaf region labels, some voxels remain labelled as “hippocampal formation”, which is a the major subdivision not a leaf of the ARA/CCFv3 ontology. So I am sure the community would greatly appreciate more ‘heads-up’ about timing and nature of future data releases to avoid them doing work Allen is already undertaking or has done but not yet released.

Perhaps the community could participate actively in updating the CCFv3 to support its development such as proposing changes to the existing annotations (like a ‘merge request’) that could be expertly reviewed and then, if approved, released as an official update?

Hi @tylermo

Can you share any feedback about the questions posted last month? Given the number views the post has received, I feel sure the community would greatly appreciate hearing about any plans regarding ccf_2022.

Many thanks.

Hi @tylermo

Do you have any news to share with the community regarding mouse ccf_2022 (v3)?
Will a 25 um resolution be released soon?
Will there be any updated annotations for current non-leaf voxels?

Many thanks.

Hi @buddjm,

It sounds like the 25 um version would be especially helpful. Thanks for that feedback, and I really like the idea of “merge requests” to involve the community in CCF v3 refinement.

As mentioned above, currently we don’t have a concrete plan or timeline to release a 25 um version. However, I will make sure we consider this in our next quarterly roadmap planning. If we are able to plan for this, I will share back here with you and the community.


Dear Tyler,

Related to the above but on a different project, we are preparing a manuscript in which we will credit Allen for our use of two datasets but cannot find the specific way to cite you; these items are not included on your Citation Policy page:

  1. This is the data from the Waxholm space for the Allen Institute:

  2. And this is the unpublished data on the Waxholm Space Atlas of the C57BL/6J Mouse Brain from Allen :

Could you kindly advise on the bibliometric citation to use for our upcoming paper?

Thank you in advance for your assistance.

Best regards,
Karin Holm
Science Writer, Research Publications
Blue Brain Project / EPFL
École polytechnique fédérale de Lausanne
Campus Biotech, Geneva, Switzerland
+41 21 695 52 57