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?

How To
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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. 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.
  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 on how we have aligned Allen Institute MERFISH data to the Allen common coordinate framework (CCF). This forum post 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