# Hello everyone, I am trying to map my entire mouse brain MERFISH sections of P4 & P7 to the Allen Brain Atlas and annotate the brain regions. Could anyone clarify the exact input data required for this process?

**URL:** <https://community.brain-map.org/t/hello-everyone-i-am-trying-to-map-my-entire-mouse-brain-merfish-sections-of-p4-p7-to-the-allen-brain-atlas-and-annotate-the-brain-regions-could-anyone-clarify-the-exact-input-data-required-for-this-process/3941>\
**Category:** How To\
**Tags:** reference-coordinates, anatomy, analysis, how-to, atlas-reference-maps\
**Created:** [December 5, 2024, 8:15pm UTC](https://community.brain-map.org/t/hello-everyone-i-am-trying-to-map-my-entire-mouse-brain-merfish-sections-of-p4-p7-to-the-allen-brain-atlas-and-annotate-the-brain-regions-could-anyone-clarify-the-exact-input-data-required-for-this-process/3941 "2024-12-05T20:15:53Z")\
**Posts on this page:** 1\
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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:** [December 6, 2024, 9:36pm UTC](https://community.brain-map.org/t/hello-everyone-i-am-trying-to-map-my-entire-mouse-brain-merfish-sections-of-p4-p7-to-the-allen-brain-atlas-and-annotate-the-brain-regions-could-anyone-clarify-the-exact-input-data-required-for-this-process/3941/3 "2024-12-06T21:36:49Z")

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Hi @kulansam

There are three different topics here that I want to separate.

1. **Data access and exploration of Allen Institute MERFISH data.** If this is what you want to do, then the tutorial above is the correct starting point. I don’t think that is the best approach for your specific use case.
2. **Assigning Allen Institute cell types to user-provided MERFISH data.** This is the exact use case of [MapMyCells](https://portal.brain-map.org/atlases-and-data/bkp/mapmycells). If this is what you want to do, I’d suggest saving your MERFISH data to an h5ad file and mapping to the whole mouse brain taxonomy by following [these steps](https://portal.brain-map.org/atlases-and-data/bkp/mapmycells/step-by-step-guide).
3. **Assigning brain regions to user-provided MERFISH data.** If this is what you want to do, I’d suggest starting with [this newer tutorial](https://alleninstitute.github.io/abc_atlas_access/notebooks/merfish_ccf_registration_tutorial.html) on how we have aligned Allen Institute MERFISH data to the Allen common coordinate framework (CCF). [This forum post](https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359) includes several other related resources.

If you can’t find what you need in the response above, please provide additional details about your use case.

Best,  
Jeremy

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