Anatomical annotation for each cell

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Hi everyone.

I was wondering to know how can I use metadate tables to endup having a lable as anatomical annotation for each cell in MERFISH data of WMB. I mean for instance, I want to take cells only from CTXsp and split them from original anndata to a new one.

Any help highly appreciated in advance.

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@jeremyinseattle @tylermo Can you please help me with this?

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If you use python, Iā€™d suggest starting here at the ABC Atlas GitHub repo: Allen Brain Cell Atlas - Data Access ā€” Allen Brain Cell Atlas - Data Access. If you use R, or need addition info, please let me know and I can provide more information.

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@jeremyinseattle Hi, Could you guide me how can I map and annotate the different brain regions in my own MERFISH data.

1 Like
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There is another thread about this topic HERE, so please visit that thread for mapping and annotation of MERFISH data.