# Mouse MERFISH - how to download transcriptomic data?

**URL:** <https://community.brain-map.org/t/mouse-merfish-how-to-download-transcriptomic-data/2594>\
**Category:** Technical\
**Tags:** atlas-cell-types, transcriptomics\
**Created:** [September 22, 2023, 7:11am UTC](https://community.brain-map.org/t/mouse-merfish-how-to-download-transcriptomic-data/2594 "2023-09-22T07:11:36Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![fgmoreno](https://avatars.discourse-cdn.com/v4/letter/f/779978/32.png) [@fgmoreno](https://community.brain-map.org/u/fgmoreno)\
**Post date:** [September 22, 2023, 7:11am UTC](https://community.brain-map.org/t/mouse-merfish-how-to-download-transcriptomic-data/2594/1 "2023-09-22T07:11:36Z")

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Hello,  
I have been exploring the fantastic MERFISH atlas of the mouse brain. Once I have identified the cell cluster which interests us the most, how can we download the related transcriptomic information?  
Of those cell clusters I can only see their brain location at the moment, and their main identity and neurotransmitter class. But I would love to download some transcriptomic information as well. Is it possible??  
Many thanks!  
Fer

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**Author:** ![tmchartrand](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/tmchartrand/32/862_2.png) [@tmchartrand](https://community.brain-map.org/u/tmchartrand)\
**Post date:** [September 26, 2023, 4:23pm UTC](https://community.brain-map.org/t/mouse-merfish-how-to-download-transcriptomic-data/2594/2 "2023-09-26T16:23:35Z")

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Absolutely! See the data access documentation at [Allen Brain Cell Atlas - Data Access — Allen Brain Cell Atlas - Data Access](https://alleninstitute.github.io/abc_atlas_access/intro.html) (or [GitHub - AllenInstitute/abc\_atlas\_access: Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas](https://github.com/AllenInstitute/abc_atlas_access/) if you want to download the tutorial .ipynb notebooks directly).  
The data isn’t organized by cluster, but you can download a single section or the full dataset and then subset to a given cluster.

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**Author:** ![fgmoreno](https://avatars.discourse-cdn.com/v4/letter/f/779978/32.png) [@fgmoreno](https://community.brain-map.org/u/fgmoreno)\
**Post date:** [September 27, 2023, 6:39am UTC](https://community.brain-map.org/t/mouse-merfish-how-to-download-transcriptomic-data/2594/3 "2023-09-27T06:39:15Z")

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Many thanks for your reply! We will definitely give it a try.

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**Author:** ![lane](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lane/32/876_2.png) [@lane](https://community.brain-map.org/u/lane)\
**Post date:** [September 27, 2023, 4:59pm UTC](https://community.brain-map.org/t/mouse-merfish-how-to-download-transcriptomic-data/2594/4 "2023-09-27T16:59:27Z")

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Glad to hear you’re enjoying the atlas tool! We have planed for expanded download capabilities for a future version of the application, but thank you for the early feedback so we can get it prioritized appropriately.