# Voxel Extraction in Mouse Brain

**URL:** <https://community.brain-map.org/t/voxel-extraction-in-mouse-brain/682>\
**Category:** Technical\
**Tags:** reference-coordinates, anatomy, analysis, how-to, atlas-reference-maps\
**Created:** [August 27, 2020, 2:08am UTC](https://community.brain-map.org/t/voxel-extraction-in-mouse-brain/682 "2020-08-27T02:08:54Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![eobbad](https://avatars.discourse-cdn.com/v4/letter/e/c57346/32.png) [@eobbad](https://community.brain-map.org/u/eobbad)\
**Post date:** [August 27, 2020, 2:08am UTC](https://community.brain-map.org/t/voxel-extraction-in-mouse-brain/682/1 "2020-08-27T02:08:54Z")

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Do you know how to find out which voxels in the 3D adult mouse brain correspond to a specific region (e.g. the dorsal raphe nucleus) and how to then extract expression information for all genes in each one of those specific voxels

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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:** [August 27, 2020, 4:32am UTC](https://community.brain-map.org/t/voxel-extraction-in-mouse-brain/682/2 "2020-08-27T04:32:43Z")

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There are a couple of good posts about [quantification of ISH data](https://community.brain-map.org/t/quantification-of-gene-expression-by-in-situ-hybridization-finding-and-using-the-raw-values/153) and [extracting gene expression values for each gene](https://community.brain-map.org/t/extracting-data-for-all-genes-from-an-roi/507). Instructions for mapping voxels to brain regions in the adult mouse brain atlas is available through [the API, 3D-reference models](http://help.brain-map.org/display/mousebrain/API#API-DownloadAtlas3-DReferenceModels).