# Mouse reference atlas areas volume

**URL:** <https://community.brain-map.org/t/mouse-reference-atlas-areas-volume/3072>\
**Category:** Technical\
**Tags:** atlas-mouse-brain-adult, atlas-reference-maps, anatomy\
**Created:** [February 9, 2024, 4:24pm UTC](https://community.brain-map.org/t/mouse-reference-atlas-areas-volume/3072 "2024-02-09T16:24:31Z")\
**Posts on this page:** 1\
**Showing post:** 3

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**Author:** ![jeremyinseattle](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/jeremyinseattle/32/50_2.png) [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\
**Post date:** [June 5, 2025, 3:35pm UTC](https://community.brain-map.org/t/mouse-reference-atlas-areas-volume/3072/3 "2025-06-05T15:35:19Z")

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You should be able to calculate them by counting the number of voxels per structure from the 3D reference download. [This link](https://community.brain-map.org/t/api-for-allen-developing-mouse-brain-atlas/2855#h-3-d-reference-models-3) should get you started. Even though it is part of the developing mouse brain atlas API, I think it also applies to the main atlas.

[This page](https://download.alleninstitute.org/informatics-archive/october-2014/mouse_expression/Accessing_October_2014_expression_data.pdf) might also help.

Finally, I put this information together many years ago, so it may or may not still be accurate:

**Downloading CCF annotations:**

Download and unzip this: [http://download.alleninstitute.org/informatics-archive/current-release/mouse\_annotation/P56\_Mouse\_gridAnnotation.zip](http://download.alleninstitute.org/informatics-archive/current-release/mouse_annotation/P56_Mouse_gridAnnotation.zip)

To read in these data in R, use the following:

```auto
fn2 = (folder where you unzipped grid annotation data)**
annot = readBin(fn2,what="int",n=159326,size=4)"/energy.raw"), what="double",n=159326,size=4)

```

I think this is the same as the “template” from here: [mouse\_connectivity](http://alleninstitute.github.io/AllenSDK/_static/examples/nb/mouse_connectivity.html#Manipulating-Grid-Data)

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