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
informatics-archive/current-release/mouse_ccf/annotation/ccf_2022
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?
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, weâre 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?
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 âhippocampal formationâ, which is a the major subdivision not a leaf of the ARA/CCFv3 ontology. So I am sure the community would greatly appreciate more âheads-upâ 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 âmerge requestâ) that could be expertly reviewed and then, if approved, released as an official update?
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.
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?
It sounds like the 25 um version would be especially helpful. Thanks for that feedback, and I really like the idea of âmerge requestsâ to involve the community in CCF v3 refinement.
As mentioned above, currently we donât 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.
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: