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BayraktarLab / cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
https://cell2location.readthedocs.io/en/latest/
Apache License 2.0
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Using MERFISH data as reference dataset. #292

Open jeji0209 opened 1 year ago

jeji0209 commented 1 year ago

Hello, thank you for developing this excellent tool. I want to use the recently published Allen Brain Atlas MERFISH data as my reference, as it is of the single-cell resolution. My data that I want to map is a Visium data. I am aware that MERFISH utilizes a different read count method than 10X chromium or visium. I want to ask your thoughts on using a MERFISH data as a reference dataset to map a Visium data with Cell2location.

Thank you in advance.

vitkl commented 1 year ago

Hi @jeji0209

I would recommend using Allen Brain Atlas 10x or SS4 references because they provide genome-wide reference expression signatures of cell types. You can use MERFISH but the quality of the reference will be lower.